Starting phenix.real_space_refine on Sun Oct 13 03:25:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ves_43173/10_2024/8ves_43173.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ves_43173/10_2024/8ves_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ves_43173/10_2024/8ves_43173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ves_43173/10_2024/8ves_43173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ves_43173/10_2024/8ves_43173.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ves_43173/10_2024/8ves_43173.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-filer2/raid1/xp/phenix/phenix-dev-5477/modules/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: 10.10, per 1000 atoms: 0.71 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: 3.65 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 4.65 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: 4.53 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 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=" 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=" CG LEU A 134 " pdb=" CD1 LEU A 134 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.96e-01 bond pdb=" CG1 ILE E 53 " pdb=" CD1 ILE E 53 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 7.15e-01 bond pdb=" C GLN B 75 " pdb=" N GLY B 76 " ideal model delta sigma weight residual 1.331 1.336 -0.006 6.60e-03 2.30e+04 7.07e-01 bond pdb=" CA MET D 174 " pdb=" C MET D 174 " ideal model delta sigma weight residual 1.520 1.529 -0.009 1.23e-02 6.61e+03 5.33e-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=" 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=" N VAL E 238 " pdb=" CA VAL E 238 " pdb=" CB VAL E 238 " ideal model delta sigma weight residual 112.35 110.03 2.32 1.38e+00 5.25e-01 2.82e+00 angle pdb=" N MET B 174 " pdb=" CA MET B 174 " pdb=" C MET B 174 " ideal model delta sigma weight residual 112.75 115.03 -2.28 1.36e+00 5.41e-01 2.81e+00 angle pdb=" C ILE F 13 " pdb=" CA ILE F 13 " pdb=" CB ILE F 13 " ideal model delta sigma weight residual 110.98 113.15 -2.17 1.37e+00 5.33e-01 2.51e+00 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 3.00e+00 1.11e-01 2.31e+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: 0.470 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: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 37.500 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 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= 0.210 Angle : 0.377 5.263 19651 Z= 0.199 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (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 TRP 0.007 0.001 TRP F 22 HIS 0.002 0.001 HIS D 173 PHE 0.014 0.002 PHE F 249 TYR 0.006 0.001 TYR A 68 ARG 0.007 0.000 ARG F 11 *********************** 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 fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 1.723 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: 0.7778 (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: 0.7925 (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: 0.8640 (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: 0.7693 (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: 0.8137 (tt0) cc_final: 0.7857 (mt-10) REVERT: F 247 GLN cc_start: 0.8099 (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: 0.3696 time to fit residues: 162.7367 Evaluate side-chains 206 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 131 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 150 GLN B 173 HIS E 285 ASN F 173 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 14511 Z= 0.379 Angle : 0.541 5.621 19651 Z= 0.288 Chirality : 0.038 0.147 2250 Planarity : 0.004 0.035 2500 Dihedral : 8.714 90.887 2165 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.87 % Allowed : 6.30 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.20), residues: 1700 helix: 2.50 (0.15), residues: 1121 sheet: 2.13 (0.36), residues: 202 loop : -0.46 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 94 HIS 0.004 0.001 HIS B 224 PHE 0.019 0.002 PHE E 141 TYR 0.008 0.001 TYR A 68 ARG 0.006 0.001 ARG F 37 *********************** 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 214 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 201 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.8912 (ttt-90) cc_final: 0.8597 (ttt-90) REVERT: A 77 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7235 (tp30) REVERT: A 193 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7600 (mp10) REVERT: A 202 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7350 (mp0) REVERT: A 227 GLU cc_start: 0.8468 (tp30) cc_final: 0.7850 (tt0) REVERT: C 40 GLU cc_start: 0.7890 (tp30) cc_final: 0.7675 (tp30) REVERT: C 174 MET cc_start: 0.8432 (tpp) cc_final: 0.8009 (mmm) REVERT: C 184 ARG cc_start: 0.8267 (tpp-160) cc_final: 0.8039 (tpt-90) REVERT: C 246 MET cc_start: 0.8788 (mmp) cc_final: 0.8081 (mmp) REVERT: C 279 MET cc_start: 0.8677 (ttm) cc_final: 0.8415 (mtm) REVERT: B 219 ASP cc_start: 0.8589 (t0) cc_final: 0.8356 (t0) REVERT: B 246 MET cc_start: 0.8658 (mmm) cc_final: 0.8143 (mmp) REVERT: E 202 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7352 (mm-30) REVERT: E 243 ASP cc_start: 0.9157 (t0) cc_final: 0.8790 (t0) REVERT: D 69 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7805 (mt-10) REVERT: D 122 ASP cc_start: 0.7935 (t0) cc_final: 0.7649 (t70) REVERT: F 1 MET cc_start: 0.7732 (ptp) cc_final: 0.7497 (ptt) REVERT: F 40 GLU cc_start: 0.8780 (tp30) cc_final: 0.8352 (tp30) REVERT: F 247 GLN cc_start: 0.8093 (tp40) cc_final: 0.7888 (mt0) REVERT: F 271 GLU cc_start: 0.8575 (tp30) cc_final: 0.8285 (tp30) outliers start: 13 outliers final: 6 residues processed: 209 average time/residue: 0.3383 time to fit residues: 97.0983 Evaluate side-chains 184 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 178 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASN 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 173 HIS 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 84 optimal weight: 4.9990 chunk 47 optimal weight: 20.0000 chunk 126 optimal weight: 0.8980 chunk 103 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14511 Z= 0.298 Angle : 0.492 6.895 19651 Z= 0.259 Chirality : 0.036 0.139 2250 Planarity : 0.003 0.027 2500 Dihedral : 8.708 90.186 2165 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.74 % Allowed : 8.98 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.20), residues: 1700 helix: 2.61 (0.15), residues: 1123 sheet: 2.17 (0.36), residues: 202 loop : -0.51 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 94 HIS 0.008 0.001 HIS B 173 PHE 0.018 0.002 PHE E 141 TYR 0.007 0.001 TYR A 68 ARG 0.006 0.000 ARG F 37 *********************** 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 204 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 193 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.8891 (ttt-90) cc_final: 0.8597 (ttt-90) REVERT: A 67 ARG cc_start: 0.8562 (mtp85) cc_final: 0.8159 (mmm160) REVERT: A 77 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7237 (tp30) REVERT: A 193 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7583 (mp10) REVERT: A 202 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7338 (mp0) REVERT: A 227 GLU cc_start: 0.8430 (tp30) cc_final: 0.7809 (tt0) REVERT: A 261 ILE cc_start: 0.9456 (tp) cc_final: 0.9179 (tp) REVERT: C 111 ARG cc_start: 0.8779 (ttp80) cc_final: 0.8574 (ttp-110) REVERT: C 184 ARG cc_start: 0.8246 (tpp-160) cc_final: 0.8033 (tpt-90) REVERT: C 246 MET cc_start: 0.8887 (mmp) cc_final: 0.8480 (mmp) REVERT: C 279 MET cc_start: 0.8658 (ttm) cc_final: 0.8385 (mtm) REVERT: B 12 GLU cc_start: 0.7389 (tt0) cc_final: 0.7132 (mt-10) REVERT: B 21 THR cc_start: 0.8577 (m) cc_final: 0.8219 (p) REVERT: B 219 ASP cc_start: 0.8563 (t0) cc_final: 0.8351 (t0) REVERT: B 246 MET cc_start: 0.8655 (mmm) cc_final: 0.8047 (mmp) REVERT: E 202 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7354 (mm-30) REVERT: E 243 ASP cc_start: 0.9086 (t0) cc_final: 0.8747 (t0) REVERT: D 122 ASP cc_start: 0.7955 (t0) cc_final: 0.7665 (t70) REVERT: F 1 MET cc_start: 0.7754 (ptp) cc_final: 0.7504 (ptt) REVERT: F 40 GLU cc_start: 0.8763 (tp30) cc_final: 0.8324 (tp30) REVERT: F 271 GLU cc_start: 0.8564 (tp30) cc_final: 0.8285 (tp30) outliers start: 11 outliers final: 7 residues processed: 200 average time/residue: 0.2526 time to fit residues: 69.9919 Evaluate side-chains 177 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 170 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASN 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 D residue 279 MET 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 151 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 145 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS D 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14511 Z= 0.154 Angle : 0.422 6.049 19651 Z= 0.222 Chirality : 0.033 0.127 2250 Planarity : 0.002 0.025 2500 Dihedral : 8.667 91.166 2165 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.14 % Allowed : 10.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.20), residues: 1700 helix: 2.96 (0.14), residues: 1122 sheet: 2.17 (0.36), residues: 200 loop : -0.51 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 180 HIS 0.002 0.000 HIS B 224 PHE 0.016 0.001 PHE E 141 TYR 0.006 0.001 TYR D 68 ARG 0.007 0.000 ARG E 59 *********************** 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 220 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 203 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8474 (mtp85) cc_final: 0.8094 (mmm160) REVERT: A 77 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7220 (tp30) REVERT: A 202 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7229 (mp0) REVERT: A 261 ILE cc_start: 0.9416 (tp) cc_final: 0.9158 (tp) REVERT: B 21 THR cc_start: 0.8569 (m) cc_final: 0.8271 (p) REVERT: B 37 ARG cc_start: 0.8470 (mtt-85) cc_final: 0.8107 (mtp85) REVERT: B 219 ASP cc_start: 0.8300 (t0) cc_final: 0.8082 (t0) REVERT: B 246 MET cc_start: 0.8589 (mmm) cc_final: 0.7806 (mmt) REVERT: E 202 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7405 (mm-30) REVERT: E 203 GLN cc_start: 0.8337 (tt0) cc_final: 0.7902 (tm-30) REVERT: E 205 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7991 (mp) REVERT: D 122 ASP cc_start: 0.7836 (t0) cc_final: 0.7461 (t70) REVERT: D 180 TRP cc_start: 0.7798 (t60) cc_final: 0.7563 (t60) REVERT: F 1 MET cc_start: 0.7751 (ptp) cc_final: 0.7534 (ptt) REVERT: F 21 THR cc_start: 0.9098 (m) cc_final: 0.8848 (p) REVERT: F 40 GLU cc_start: 0.8742 (tp30) cc_final: 0.8324 (tp30) REVERT: F 271 GLU cc_start: 0.8547 (tp30) cc_final: 0.8044 (tp30) outliers start: 17 outliers final: 8 residues processed: 214 average time/residue: 0.3776 time to fit residues: 110.0599 Evaluate side-chains 182 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 173 time to evaluate : 1.770 ------------------------------------------------------------------------------- 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 147 THR Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 279 MET 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 135 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 138 optimal weight: 0.6980 chunk 112 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 145 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14511 Z= 0.331 Angle : 0.508 8.371 19651 Z= 0.263 Chirality : 0.036 0.161 2250 Planarity : 0.003 0.029 2500 Dihedral : 8.768 88.217 2165 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.27 % Allowed : 11.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.20), residues: 1700 helix: 2.82 (0.14), residues: 1120 sheet: 2.11 (0.36), residues: 202 loop : -0.57 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 180 HIS 0.009 0.001 HIS B 173 PHE 0.018 0.002 PHE E 141 TYR 0.008 0.001 TYR C 68 ARG 0.010 0.001 ARG E 59 *********************** 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 196 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 177 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8494 (mtp85) cc_final: 0.8099 (mmm160) REVERT: A 202 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7304 (mp0) REVERT: A 216 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: A 261 ILE cc_start: 0.9449 (tp) cc_final: 0.9171 (tp) REVERT: C 207 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7733 (mp) REVERT: B 21 THR cc_start: 0.8614 (m) cc_final: 0.8351 (p) REVERT: B 37 ARG cc_start: 0.8457 (mtt-85) cc_final: 0.8079 (mtp85) REVERT: B 219 ASP cc_start: 0.8577 (t0) cc_final: 0.8365 (t0) REVERT: B 246 MET cc_start: 0.8661 (mmm) cc_final: 0.8078 (mmp) REVERT: E 203 GLN cc_start: 0.8410 (tt0) cc_final: 0.7949 (tm-30) REVERT: E 205 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7970 (mp) REVERT: D 122 ASP cc_start: 0.7895 (t0) cc_final: 0.7627 (t70) REVERT: D 180 TRP cc_start: 0.7805 (t60) cc_final: 0.7582 (t60) REVERT: F 1 MET cc_start: 0.7766 (ptp) cc_final: 0.7477 (ptt) REVERT: F 40 GLU cc_start: 0.8779 (tp30) cc_final: 0.8433 (tp30) REVERT: F 271 GLU cc_start: 0.8561 (tp30) cc_final: 0.8114 (tp30) outliers start: 19 outliers final: 9 residues processed: 189 average time/residue: 0.3484 time to fit residues: 90.4882 Evaluate side-chains 184 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 172 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 279 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 8.9990 chunk 146 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS D 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2554 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= 0.212 Angle : 0.458 7.486 19651 Z= 0.238 Chirality : 0.034 0.171 2250 Planarity : 0.003 0.024 2500 Dihedral : 8.731 89.042 2165 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.47 % Allowed : 12.20 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.20), residues: 1700 helix: 2.92 (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 TRP 0.013 0.001 TRP E 180 HIS 0.003 0.001 HIS B 224 PHE 0.016 0.002 PHE E 141 TYR 0.006 0.001 TYR C 68 ARG 0.008 0.000 ARG E 59 *********************** 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 205 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 183 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8496 (mtp85) cc_final: 0.8073 (mmm160) REVERT: A 202 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7291 (mp0) REVERT: A 216 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: A 246 MET cc_start: 0.8810 (mmt) cc_final: 0.8053 (mmt) REVERT: A 261 ILE cc_start: 0.9427 (tp) cc_final: 0.9136 (tp) REVERT: C 207 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7717 (mp) REVERT: B 21 THR cc_start: 0.8555 (m) cc_final: 0.8315 (p) REVERT: B 37 ARG cc_start: 0.8524 (mtt-85) cc_final: 0.8052 (mtp85) REVERT: B 219 ASP cc_start: 0.8462 (t0) cc_final: 0.8226 (t0) REVERT: B 246 MET cc_start: 0.8626 (mmm) cc_final: 0.7562 (mmp) REVERT: E 203 GLN cc_start: 0.8491 (tt0) cc_final: 0.7973 (tm-30) REVERT: E 243 ASP cc_start: 0.9022 (t0) cc_final: 0.8642 (t0) REVERT: D 122 ASP cc_start: 0.7914 (t0) cc_final: 0.7648 (t70) REVERT: D 180 TRP cc_start: 0.7795 (t60) cc_final: 0.7588 (t60) REVERT: F 1 MET cc_start: 0.7767 (ptp) cc_final: 0.7488 (ptt) REVERT: F 40 GLU cc_start: 0.8778 (tp30) cc_final: 0.8360 (tp30) REVERT: F 271 GLU cc_start: 0.8556 (tp30) cc_final: 0.8059 (tp30) outliers start: 22 outliers final: 10 residues processed: 196 average time/residue: 0.3242 time to fit residues: 88.6462 Evaluate side-chains 187 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 175 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 246 MET 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 123 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 272 LEU 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 156 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 161 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14511 Z= 0.257 Angle : 0.481 7.133 19651 Z= 0.248 Chirality : 0.035 0.166 2250 Planarity : 0.003 0.026 2500 Dihedral : 8.758 88.121 2165 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.14 % Allowed : 13.00 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.12 (0.20), residues: 1700 helix: 2.87 (0.14), residues: 1122 sheet: 1.94 (0.35), residues: 210 loop : -0.58 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 180 HIS 0.004 0.001 HIS B 173 PHE 0.017 0.002 PHE E 141 TYR 0.007 0.001 TYR C 68 ARG 0.008 0.000 ARG E 59 *********************** 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 192 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 175 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8503 (mtp85) cc_final: 0.8078 (mmm160) REVERT: A 179 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7869 (tm-30) REVERT: A 202 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7286 (mp0) REVERT: A 216 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8111 (tt0) REVERT: A 246 MET cc_start: 0.8850 (mmt) cc_final: 0.8032 (mmt) REVERT: A 261 ILE cc_start: 0.9435 (tp) cc_final: 0.9134 (tp) REVERT: C 207 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7736 (mp) REVERT: B 21 THR cc_start: 0.8584 (m) cc_final: 0.8355 (p) REVERT: B 37 ARG cc_start: 0.8523 (mtt-85) cc_final: 0.8057 (mtp85) REVERT: B 219 ASP cc_start: 0.8495 (t0) cc_final: 0.8277 (t0) REVERT: B 246 MET cc_start: 0.8907 (mmm) cc_final: 0.8521 (mmm) REVERT: E 243 ASP cc_start: 0.9038 (t0) cc_final: 0.8679 (t0) REVERT: D 122 ASP cc_start: 0.7923 (t0) cc_final: 0.7670 (t70) REVERT: D 180 TRP cc_start: 0.7790 (t60) cc_final: 0.7587 (t60) REVERT: F 1 MET cc_start: 0.7766 (ptp) cc_final: 0.7487 (ptt) REVERT: F 40 GLU cc_start: 0.8812 (tp30) cc_final: 0.8440 (tp30) REVERT: F 271 GLU cc_start: 0.8560 (tp30) cc_final: 0.8061 (tp30) outliers start: 17 outliers final: 12 residues processed: 187 average time/residue: 0.3216 time to fit residues: 84.0049 Evaluate side-chains 178 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 163 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 207 LEU 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 E residue 123 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 79 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14511 Z= 0.239 Angle : 0.477 6.672 19651 Z= 0.245 Chirality : 0.035 0.159 2250 Planarity : 0.003 0.032 2500 Dihedral : 8.751 87.901 2165 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.68 % Allowed : 12.67 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.20), residues: 1700 helix: 2.87 (0.14), residues: 1122 sheet: 1.88 (0.35), residues: 210 loop : -0.56 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 180 HIS 0.004 0.001 HIS B 224 PHE 0.016 0.002 PHE E 141 TYR 0.008 0.001 TYR C 68 ARG 0.008 0.000 ARG F 37 *********************** 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 192 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8505 (mtp85) cc_final: 0.8078 (mmm160) REVERT: A 179 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: A 202 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7252 (mp0) REVERT: A 216 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: A 246 MET cc_start: 0.8831 (mmt) cc_final: 0.8031 (mmt) REVERT: A 261 ILE cc_start: 0.9427 (tp) cc_final: 0.9129 (tp) REVERT: C 207 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7732 (mp) REVERT: B 21 THR cc_start: 0.8601 (m) cc_final: 0.8390 (p) REVERT: B 37 ARG cc_start: 0.8505 (mtt-85) cc_final: 0.8074 (mtp85) REVERT: B 219 ASP cc_start: 0.8511 (t0) cc_final: 0.8273 (t0) REVERT: E 203 GLN cc_start: 0.8250 (tt0) cc_final: 0.7968 (tt0) REVERT: D 122 ASP cc_start: 0.7984 (t0) cc_final: 0.7711 (t70) REVERT: D 180 TRP cc_start: 0.7796 (t60) cc_final: 0.7596 (t60) REVERT: F 1 MET cc_start: 0.7783 (ptp) cc_final: 0.7508 (ptt) REVERT: F 40 GLU cc_start: 0.8809 (tp30) cc_final: 0.8438 (tp30) REVERT: F 271 GLU cc_start: 0.8560 (tp30) cc_final: 0.8064 (tp30) outliers start: 25 outliers final: 15 residues processed: 184 average time/residue: 0.3456 time to fit residues: 89.0357 Evaluate side-chains 191 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 173 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 246 MET 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 E residue 123 LEU Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain D residue 126 ILE 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 12 GLU Chi-restraints excluded: chain F residue 79 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14511 Z= 0.203 Angle : 0.470 8.111 19651 Z= 0.240 Chirality : 0.034 0.155 2250 Planarity : 0.003 0.031 2500 Dihedral : 8.716 87.985 2165 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.21 % Allowed : 13.20 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.18 (0.20), residues: 1700 helix: 2.94 (0.14), residues: 1122 sheet: 1.88 (0.35), residues: 210 loop : -0.56 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 180 HIS 0.003 0.001 HIS B 224 PHE 0.016 0.002 PHE E 141 TYR 0.014 0.001 TYR C 68 ARG 0.008 0.000 ARG C 111 *********************** 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 199 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 181 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8498 (mtp85) cc_final: 0.8065 (mmm160) REVERT: A 179 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7924 (tm-30) REVERT: A 202 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7246 (mp0) REVERT: A 246 MET cc_start: 0.8766 (mmt) cc_final: 0.8000 (mmt) REVERT: A 261 ILE cc_start: 0.9416 (tp) cc_final: 0.9127 (tp) REVERT: C 204 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8225 (mt-10) REVERT: C 207 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7720 (mp) REVERT: B 21 THR cc_start: 0.8596 (m) cc_final: 0.8393 (p) REVERT: B 37 ARG cc_start: 0.8495 (mtt-85) cc_final: 0.8056 (mtp85) REVERT: B 219 ASP cc_start: 0.8479 (t0) cc_final: 0.8269 (t0) REVERT: E 203 GLN cc_start: 0.8241 (tt0) cc_final: 0.7896 (tt0) REVERT: E 243 ASP cc_start: 0.9026 (t0) cc_final: 0.8646 (t0) REVERT: D 122 ASP cc_start: 0.8004 (t0) cc_final: 0.7742 (t70) REVERT: D 180 TRP cc_start: 0.7824 (t60) cc_final: 0.7613 (t60) REVERT: F 1 MET cc_start: 0.7800 (ptp) cc_final: 0.7534 (ptt) REVERT: F 40 GLU cc_start: 0.8794 (tp30) cc_final: 0.8430 (tp30) REVERT: F 271 GLU cc_start: 0.8553 (tp30) cc_final: 0.8064 (tp30) outliers start: 18 outliers final: 14 residues processed: 192 average time/residue: 0.3224 time to fit residues: 86.2455 Evaluate side-chains 182 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 166 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain F residue 79 ILE 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 97 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 110 optimal weight: 0.0870 chunk 167 optimal weight: 8.9990 chunk 154 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN B 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14511 Z= 0.282 Angle : 0.506 7.515 19651 Z= 0.258 Chirality : 0.036 0.156 2250 Planarity : 0.003 0.037 2500 Dihedral : 8.781 86.615 2165 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.27 % Allowed : 13.00 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.20), residues: 1700 helix: 2.83 (0.14), residues: 1122 sheet: 1.83 (0.35), residues: 210 loop : -0.58 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 180 HIS 0.005 0.001 HIS B 224 PHE 0.017 0.002 PHE E 141 TYR 0.007 0.001 TYR A 8 ARG 0.009 0.000 ARG C 111 ********************** 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 184 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7929 (tm-30) REVERT: A 193 GLN cc_start: 0.7936 (tp-100) cc_final: 0.6733 (mp10) REVERT: A 216 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8097 (tt0) REVERT: A 246 MET cc_start: 0.8868 (mmt) cc_final: 0.8197 (mmt) REVERT: A 261 ILE cc_start: 0.9435 (tp) cc_final: 0.9147 (tp) REVERT: C 1 MET cc_start: 0.7876 (tpp) cc_final: 0.7594 (tpp) REVERT: C 207 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7740 (mp) REVERT: B 21 THR cc_start: 0.8619 (m) cc_final: 0.8410 (p) REVERT: B 37 ARG cc_start: 0.8476 (mtt-85) cc_final: 0.8008 (mtp85) REVERT: B 219 ASP cc_start: 0.8540 (t0) cc_final: 0.8297 (t0) REVERT: E 203 GLN cc_start: 0.8267 (tt0) cc_final: 0.7962 (tt0) REVERT: D 122 ASP cc_start: 0.8046 (t0) cc_final: 0.7571 (t70) REVERT: F 1 MET cc_start: 0.7806 (ptp) cc_final: 0.7535 (ptt) REVERT: F 40 GLU cc_start: 0.8803 (tp30) cc_final: 0.8417 (tp30) REVERT: F 271 GLU cc_start: 0.8567 (tp30) cc_final: 0.8129 (tp30) outliers start: 19 outliers final: 14 residues processed: 176 average time/residue: 0.3396 time to fit residues: 82.1681 Evaluate side-chains 180 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 163 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 246 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 E residue 123 LEU Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain F residue 79 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.144925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.109285 restraints weight = 17563.584| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.28 r_work: 0.3141 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2759 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= 0.181 Angle : 0.472 8.356 19651 Z= 0.241 Chirality : 0.034 0.152 2250 Planarity : 0.003 0.032 2500 Dihedral : 8.694 87.697 2165 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.07 % Allowed : 13.47 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.20), residues: 1700 helix: 2.96 (0.14), residues: 1123 sheet: 1.91 (0.35), residues: 209 loop : -0.63 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 180 HIS 0.004 0.001 HIS B 224 PHE 0.015 0.001 PHE E 141 TYR 0.014 0.001 TYR C 68 ARG 0.009 0.000 ARG C 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2990.26 seconds wall clock time: 72 minutes 29.71 seconds (4349.71 seconds total)