Starting phenix.real_space_refine on Thu Aug 6 07:27:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s10_54429/08_2026/9s10_54429_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s10_54429/08_2026/9s10_54429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9s10_54429/08_2026/9s10_54429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s10_54429/08_2026/9s10_54429.map" model { file = "/net/cci-nas-00/data/ceres_data/9s10_54429/08_2026/9s10_54429_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s10_54429/08_2026/9s10_54429_neut.cif" } resolution = 3.07 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= 0.001 sd= 0.027 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: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 2 5.21 5 S 61 5.16 5 C 8639 2.51 5 N 2346 2.21 5 O 2633 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13711 Number of models: 1 Model: "" Number of chains: 10 Chain: "H" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 451 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain breaks: 1 Chain: "a" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2214 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 10, 'TRANS': 267} Chain: "b" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2214 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 10, 'TRANS': 267} Chain: "c" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2214 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 10, 'TRANS': 267} Chain: "d" Number of atoms: 2181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2181 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 10, 'TRANS': 262} Chain breaks: 1 Chain: "e" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2173 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain breaks: 1 Chain: "f" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2173 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 261} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.32, per 1000 atoms: 0.24 Number of scatterers: 13711 At special positions: 0 Unit cell: (82.5, 129.525, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 61 16.00 P 30 15.00 Mg 2 11.99 O 2633 8.00 N 2346 7.00 C 8639 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: 1.45 Conformation dependent library (CDL) restraints added in 732.9 milliseconds 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3118 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 14 sheets defined 51.5% alpha, 8.4% beta 6 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'a' and resid 18 through 35 Processing helix chain 'a' and resid 38 through 46 Processing helix chain 'a' and resid 46 through 55 Processing helix chain 'a' and resid 56 through 78 removed outlier: 3.866A pdb=" N SER a 61 " --> pdb=" O SER a 57 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN a 62 " --> pdb=" O ASN a 58 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS a 64 " --> pdb=" O ARG a 60 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU a 76 " --> pdb=" O LYS a 72 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR a 77 " --> pdb=" O ILE a 73 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS a 78 " --> pdb=" O MET a 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 79 through 85 removed outlier: 3.854A pdb=" N TYR a 83 " --> pdb=" O THR a 79 " (cutoff:3.500A) Processing helix chain 'a' and resid 92 through 95 removed outlier: 4.003A pdb=" N SER a 95 " --> pdb=" O ASP a 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 92 through 95' Processing helix chain 'a' and resid 96 through 106 Processing helix chain 'a' and resid 108 through 121 Processing helix chain 'a' and resid 139 through 151 removed outlier: 3.726A pdb=" N ALA a 146 " --> pdb=" O ASN a 142 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL a 151 " --> pdb=" O ILE a 147 " (cutoff:3.500A) Processing helix chain 'a' and resid 183 through 194 removed outlier: 4.351A pdb=" N GLU a 188 " --> pdb=" O ALA a 184 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER a 189 " --> pdb=" O LYS a 185 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ALA a 192 " --> pdb=" O GLU a 188 " (cutoff:3.500A) Processing helix chain 'a' and resid 237 through 243 Processing helix chain 'a' and resid 255 through 259 removed outlier: 4.216A pdb=" N GLY a 259 " --> pdb=" O HIS a 256 " (cutoff:3.500A) Processing helix chain 'a' and resid 262 through 276 Processing helix chain 'b' and resid 18 through 35 removed outlier: 3.620A pdb=" N ARG b 23 " --> pdb=" O LYS b 19 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 46 Processing helix chain 'b' and resid 46 through 55 removed outlier: 3.616A pdb=" N ALA b 55 " --> pdb=" O ILE b 51 " (cutoff:3.500A) Processing helix chain 'b' and resid 56 through 78 removed outlier: 3.632A pdb=" N LYS b 64 " --> pdb=" O ARG b 60 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR b 77 " --> pdb=" O ILE b 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 80 through 85 Processing helix chain 'b' and resid 96 through 105 removed outlier: 3.562A pdb=" N ASN b 105 " --> pdb=" O ILE b 101 " (cutoff:3.500A) Processing helix chain 'b' and resid 108 through 121 Processing helix chain 'b' and resid 139 through 151 removed outlier: 3.596A pdb=" N VAL b 151 " --> pdb=" O ILE b 147 " (cutoff:3.500A) Processing helix chain 'b' and resid 166 through 170 removed outlier: 4.010A pdb=" N VAL b 170 " --> pdb=" O ASN b 167 " (cutoff:3.500A) Processing helix chain 'b' and resid 186 through 194 removed outlier: 3.647A pdb=" N ALA b 192 " --> pdb=" O GLU b 188 " (cutoff:3.500A) Processing helix chain 'b' and resid 237 through 243 Processing helix chain 'b' and resid 262 through 276 Processing helix chain 'c' and resid 18 through 35 Processing helix chain 'c' and resid 38 through 46 Processing helix chain 'c' and resid 46 through 53 removed outlier: 3.566A pdb=" N SER c 52 " --> pdb=" O ALA c 48 " (cutoff:3.500A) Processing helix chain 'c' and resid 57 through 78 removed outlier: 3.810A pdb=" N SER c 61 " --> pdb=" O SER c 57 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN c 62 " --> pdb=" O ASN c 58 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS c 64 " --> pdb=" O ARG c 60 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 85 removed outlier: 3.729A pdb=" N TYR c 83 " --> pdb=" O THR c 79 " (cutoff:3.500A) Processing helix chain 'c' and resid 96 through 105 removed outlier: 3.553A pdb=" N ASN c 105 " --> pdb=" O ILE c 101 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 121 Processing helix chain 'c' and resid 139 through 151 removed outlier: 3.604A pdb=" N VAL c 151 " --> pdb=" O ILE c 147 " (cutoff:3.500A) Processing helix chain 'c' and resid 166 through 170 removed outlier: 4.220A pdb=" N VAL c 170 " --> pdb=" O ASN c 167 " (cutoff:3.500A) Processing helix chain 'c' and resid 186 through 195 Processing helix chain 'c' and resid 237 through 243 Processing helix chain 'c' and resid 262 through 276 Processing helix chain 'd' and resid 18 through 34 Processing helix chain 'd' and resid 41 through 46 Processing helix chain 'd' and resid 46 through 54 removed outlier: 3.718A pdb=" N TYR d 50 " --> pdb=" O ASP d 46 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER d 52 " --> pdb=" O ALA d 48 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 78 removed outlier: 3.638A pdb=" N SER d 61 " --> pdb=" O SER d 57 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS d 64 " --> pdb=" O ARG d 60 " (cutoff:3.500A) Processing helix chain 'd' and resid 79 through 85 removed outlier: 3.709A pdb=" N TYR d 83 " --> pdb=" O THR d 79 " (cutoff:3.500A) Processing helix chain 'd' and resid 96 through 106 Processing helix chain 'd' and resid 108 through 121 Processing helix chain 'd' and resid 139 through 150 removed outlier: 3.794A pdb=" N ILE d 143 " --> pdb=" O GLY d 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 195 removed outlier: 3.730A pdb=" N ALA d 192 " --> pdb=" O GLU d 188 " (cutoff:3.500A) Processing helix chain 'd' and resid 237 through 243 Processing helix chain 'd' and resid 262 through 276 Processing helix chain 'e' and resid 19 through 28 removed outlier: 3.742A pdb=" N ARG e 23 " --> pdb=" O LYS e 19 " (cutoff:3.500A) Processing helix chain 'e' and resid 29 through 35 removed outlier: 3.706A pdb=" N ASP e 33 " --> pdb=" O GLY e 29 " (cutoff:3.500A) Processing helix chain 'e' and resid 38 through 46 Processing helix chain 'e' and resid 46 through 55 removed outlier: 3.776A pdb=" N TYR e 50 " --> pdb=" O ASP e 46 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 61 Processing helix chain 'e' and resid 62 through 70 Processing helix chain 'e' and resid 71 through 77 Processing helix chain 'e' and resid 80 through 85 Processing helix chain 'e' and resid 96 through 105 removed outlier: 3.549A pdb=" N ASN e 105 " --> pdb=" O ILE e 101 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 121 Processing helix chain 'e' and resid 124 through 127 Processing helix chain 'e' and resid 139 through 151 removed outlier: 3.747A pdb=" N VAL e 151 " --> pdb=" O ILE e 147 " (cutoff:3.500A) Processing helix chain 'e' and resid 164 through 170 removed outlier: 4.014A pdb=" N ASP e 168 " --> pdb=" O PRO e 165 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL e 170 " --> pdb=" O ASN e 167 " (cutoff:3.500A) Processing helix chain 'e' and resid 186 through 194 removed outlier: 3.615A pdb=" N ALA e 192 " --> pdb=" O GLU e 188 " (cutoff:3.500A) Processing helix chain 'e' and resid 237 through 243 Processing helix chain 'e' and resid 262 through 276 Processing helix chain 'f' and resid 18 through 35 removed outlier: 3.587A pdb=" N ARG f 23 " --> pdb=" O LYS f 19 " (cutoff:3.500A) Processing helix chain 'f' and resid 38 through 46 Processing helix chain 'f' and resid 46 through 54 Processing helix chain 'f' and resid 56 through 78 removed outlier: 3.866A pdb=" N LYS f 64 " --> pdb=" O ARG f 60 " (cutoff:3.500A) Processing helix chain 'f' and resid 79 through 85 removed outlier: 3.922A pdb=" N TYR f 83 " --> pdb=" O THR f 79 " (cutoff:3.500A) Processing helix chain 'f' and resid 92 through 95 Processing helix chain 'f' and resid 96 through 105 Processing helix chain 'f' and resid 108 through 121 Processing helix chain 'f' and resid 124 through 127 Processing helix chain 'f' and resid 142 through 151 removed outlier: 3.593A pdb=" N VAL f 151 " --> pdb=" O ILE f 147 " (cutoff:3.500A) Processing helix chain 'f' and resid 166 through 170 removed outlier: 3.568A pdb=" N CYS f 169 " --> pdb=" O PHE f 166 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL f 170 " --> pdb=" O ASN f 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 166 through 170' Processing helix chain 'f' and resid 187 through 194 Processing helix chain 'f' and resid 234 through 236 No H-bonds generated for 'chain 'f' and resid 234 through 236' Processing helix chain 'f' and resid 237 through 245 Processing helix chain 'f' and resid 255 through 259 Processing helix chain 'f' and resid 262 through 275 Processing sheet with id=AA1, first strand: chain 'a' and resid 154 through 156 removed outlier: 5.982A pdb=" N GLY a 155 " --> pdb=" O TRP a 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 199 through 203 removed outlier: 4.253A pdb=" N VAL a 199 " --> pdb=" O ILE a 211 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN a 203 " --> pdb=" O SER a 207 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N SER a 207 " --> pdb=" O GLN a 203 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 227 through 229 Processing sheet with id=AA4, first strand: chain 'b' and resid 154 through 156 removed outlier: 6.169A pdb=" N GLY b 155 " --> pdb=" O TRP b 176 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLU b 178 " --> pdb=" O GLY b 155 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE b 175 " --> pdb=" O ILE b 217 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N THR b 219 " --> pdb=" O ILE b 175 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N TRP b 177 " --> pdb=" O THR b 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 199 through 203 removed outlier: 3.623A pdb=" N VAL b 199 " --> pdb=" O ILE b 211 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLN b 203 " --> pdb=" O SER b 207 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N SER b 207 " --> pdb=" O GLN b 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 154 through 156 removed outlier: 6.079A pdb=" N GLY c 155 " --> pdb=" O TRP c 176 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE c 175 " --> pdb=" O ILE c 217 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N THR c 219 " --> pdb=" O ILE c 175 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP c 177 " --> pdb=" O THR c 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 199 through 201 removed outlier: 3.643A pdb=" N VAL c 199 " --> pdb=" O ILE c 211 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'c' and resid 227 through 229 Processing sheet with id=AA9, first strand: chain 'd' and resid 154 through 156 removed outlier: 5.936A pdb=" N GLY d 155 " --> pdb=" O TRP d 176 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE d 175 " --> pdb=" O ILE d 217 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N THR d 219 " --> pdb=" O ILE d 175 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TRP d 177 " --> pdb=" O THR d 219 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE d 130 " --> pdb=" O VAL d 218 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N SER d 220 " --> pdb=" O ILE d 130 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU d 132 " --> pdb=" O SER d 220 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'd' and resid 199 through 201 Processing sheet with id=AB2, first strand: chain 'e' and resid 154 through 156 removed outlier: 6.511A pdb=" N GLY e 155 " --> pdb=" O TRP e 176 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE e 175 " --> pdb=" O ILE e 217 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N THR e 219 " --> pdb=" O ILE e 175 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N TRP e 177 " --> pdb=" O THR e 219 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE e 130 " --> pdb=" O VAL e 218 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N SER e 220 " --> pdb=" O ILE e 130 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU e 132 " --> pdb=" O SER e 220 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'e' and resid 199 through 203 removed outlier: 3.705A pdb=" N VAL e 199 " --> pdb=" O ILE e 211 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLN e 203 " --> pdb=" O SER e 207 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N SER e 207 " --> pdb=" O GLN e 203 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'f' and resid 155 through 157 removed outlier: 6.332A pdb=" N GLY f 155 " --> pdb=" O TRP f 176 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE f 175 " --> pdb=" O ILE f 217 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR f 129 " --> pdb=" O PHE f 246 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N PHE f 248 " --> pdb=" O THR f 129 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP f 131 " --> pdb=" O PHE f 248 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'f' and resid 200 through 201 555 hydrogen bonds defined for protein. 1608 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 4437 1.36 - 1.51: 4167 1.51 - 1.66: 5375 1.66 - 1.80: 52 1.80 - 1.95: 45 Bond restraints: 14076 Sorted by residual: bond pdb=" O3A AGS b1000 " pdb=" PA AGS b1000 " ideal model delta sigma weight residual 1.664 1.565 0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C3' DC H 23 " pdb=" C2' DC H 23 " ideal model delta sigma weight residual 1.516 1.555 -0.039 8.00e-03 1.56e+04 2.43e+01 bond pdb=" O3B AGS b1000 " pdb=" PB AGS b1000 " ideal model delta sigma weight residual 1.673 1.576 0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" O3B AGS a1000 " pdb=" PB AGS a1000 " ideal model delta sigma weight residual 1.673 1.581 0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" O3A AGS a1000 " pdb=" PA AGS a1000 " ideal model delta sigma weight residual 1.664 1.581 0.083 2.00e-02 2.50e+03 1.72e+01 ... (remaining 14071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 18580 2.32 - 4.65: 477 4.65 - 6.97: 63 6.97 - 9.30: 19 9.30 - 11.62: 26 Bond angle restraints: 19165 Sorted by residual: angle pdb=" O4' DT H 28 " pdb=" C1' DT H 28 " pdb=" N1 DT H 28 " ideal model delta sigma weight residual 108.00 103.52 4.48 7.00e-01 2.04e+00 4.09e+01 angle pdb=" O4' DC H 23 " pdb=" C1' DC H 23 " pdb=" N1 DC H 23 " ideal model delta sigma weight residual 108.00 103.87 4.13 7.00e-01 2.04e+00 3.48e+01 angle pdb=" O4' DC H 100 " pdb=" C1' DC H 100 " pdb=" N1 DC H 100 " ideal model delta sigma weight residual 108.00 103.89 4.11 7.00e-01 2.04e+00 3.45e+01 angle pdb=" O4' DC H 25 " pdb=" C1' DC H 25 " pdb=" N1 DC H 25 " ideal model delta sigma weight residual 108.00 103.95 4.05 7.00e-01 2.04e+00 3.35e+01 angle pdb=" O4' DG H 30 " pdb=" C1' DG H 30 " pdb=" N9 DG H 30 " ideal model delta sigma weight residual 108.00 112.00 -4.00 7.00e-01 2.04e+00 3.27e+01 ... (remaining 19160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.42: 8023 33.42 - 66.85: 260 66.85 - 100.27: 52 100.27 - 133.70: 3 133.70 - 167.12: 2 Dihedral angle restraints: 8340 sinusoidal: 3533 harmonic: 4807 Sorted by residual: dihedral pdb=" CA GLN e 62 " pdb=" C GLN e 62 " pdb=" N ILE e 63 " pdb=" CA ILE e 63 " ideal model delta harmonic sigma weight residual 180.00 147.69 32.31 0 5.00e+00 4.00e-02 4.18e+01 dihedral pdb=" CA SER d 38 " pdb=" C SER d 38 " pdb=" N GLU d 39 " pdb=" CA GLU d 39 " ideal model delta harmonic sigma weight residual 180.00 149.84 30.16 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA THR d 37 " pdb=" C THR d 37 " pdb=" N SER d 38 " pdb=" CA SER d 38 " ideal model delta harmonic sigma weight residual -180.00 -150.85 -29.15 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 8337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1809 0.086 - 0.172: 243 0.172 - 0.258: 13 0.258 - 0.344: 4 0.344 - 0.429: 19 Chirality restraints: 2088 Sorted by residual: chirality pdb=" P DA H 94 " pdb=" OP1 DA H 94 " pdb=" OP2 DA H 94 " pdb=" O5' DA H 94 " both_signs ideal model delta sigma weight residual True 2.34 -2.76 -0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" P DT H 32 " pdb=" OP1 DT H 32 " pdb=" OP2 DT H 32 " pdb=" O5' DT H 32 " both_signs ideal model delta sigma weight residual True 2.34 -2.76 -0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" P DC H 31 " pdb=" OP1 DC H 31 " pdb=" OP2 DC H 31 " pdb=" O5' DC H 31 " both_signs ideal model delta sigma weight residual True 2.34 -2.76 -0.43 2.00e-01 2.50e+01 4.53e+00 ... (remaining 2085 not shown) Planarity restraints: 2351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC H 29 " 0.019 2.00e-02 2.50e+03 3.17e-02 2.26e+01 pdb=" N1 DC H 29 " -0.076 2.00e-02 2.50e+03 pdb=" C2 DC H 29 " 0.048 2.00e-02 2.50e+03 pdb=" O2 DC H 29 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DC H 29 " -0.017 2.00e-02 2.50e+03 pdb=" C4 DC H 29 " 0.000 2.00e-02 2.50e+03 pdb=" N4 DC H 29 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DC H 29 " 0.013 2.00e-02 2.50e+03 pdb=" C6 DC H 29 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET e 25 " 0.022 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C MET e 25 " -0.077 2.00e-02 2.50e+03 pdb=" O MET e 25 " 0.029 2.00e-02 2.50e+03 pdb=" N GLU e 26 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC H 23 " 0.053 2.00e-02 2.50e+03 2.88e-02 1.86e+01 pdb=" N1 DC H 23 " -0.066 2.00e-02 2.50e+03 pdb=" C2 DC H 23 " 0.000 2.00e-02 2.50e+03 pdb=" O2 DC H 23 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DC H 23 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DC H 23 " 0.007 2.00e-02 2.50e+03 pdb=" N4 DC H 23 " 0.015 2.00e-02 2.50e+03 pdb=" C5 DC H 23 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DC H 23 " -0.002 2.00e-02 2.50e+03 ... (remaining 2348 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 16 2.44 - 3.06: 9191 3.06 - 3.67: 20362 3.67 - 4.29: 31382 4.29 - 4.90: 50532 Nonbonded interactions: 111483 Sorted by model distance: nonbonded pdb=" O3G AGS a1000 " pdb="MG MG a1001 " model vdw 1.826 2.170 nonbonded pdb=" O2B AGS b1000 " pdb="MG MG b1001 " model vdw 1.850 2.170 nonbonded pdb=" O3G AGS b1000 " pdb="MG MG b1001 " model vdw 1.864 2.170 nonbonded pdb=" O2B AGS a1000 " pdb="MG MG a1001 " model vdw 1.950 2.170 nonbonded pdb=" OG1 THR a 141 " pdb="MG MG a1001 " model vdw 1.958 2.170 ... (remaining 111478 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 12 through 203 or resid 207 through 227 or resid 234 throu \ gh 288)) selection = (chain 'b' and (resid 12 through 203 or resid 207 through 227 or resid 234 throu \ gh 288)) selection = (chain 'c' and (resid 12 through 203 or resid 207 through 227 or resid 234 throu \ gh 288)) selection = (chain 'd' and (resid 12 through 203 or resid 207 through 227 or resid 234 throu \ gh 288)) selection = (chain 'e' and (resid 12 through 203 or resid 207 through 288)) selection = (chain 'f' and (resid 12 through 227 or resid 234 through 288)) } 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: 4.100 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.710 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 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 : 0.005 0.099 14076 Z= 0.270 Angle : 0.986 11.622 19165 Z= 0.552 Chirality : 0.066 0.429 2088 Planarity : 0.009 0.123 2351 Dihedral : 17.345 167.122 5222 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.60 % Favored : 95.16 % Rotamer: Outliers : 1.05 % Allowed : 9.68 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.24 (0.19), residues: 1631 helix: -1.15 (0.16), residues: 727 sheet: 0.20 (0.36), residues: 216 loop : -0.57 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.002 ARG d 60 TYR 0.021 0.005 TYR d 111 PHE 0.028 0.003 PHE e 248 TRP 0.031 0.005 TRP b 176 HIS 0.010 0.002 HIS a 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.27 (14076) covalent geometry : angle 0.98614 / 0.55 (19165) hydrogen bonds : bond 0.15516 / 16.09 ( 572) hydrogen bonds : angle 6.35857 / 6.45 ( 1642) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 392 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.8060 (m) cc_final: 0.7649 (p) REVERT: a 32 VAL cc_start: 0.8166 (t) cc_final: 0.7706 (m) REVERT: a 50 TYR cc_start: 0.7689 (t80) cc_final: 0.7300 (t80) REVERT: a 99 TYR cc_start: 0.8176 (t80) cc_final: 0.7839 (t80) REVERT: a 130 ILE cc_start: 0.6650 (mt) cc_final: 0.6126 (mt) REVERT: a 153 PHE cc_start: 0.7979 (m-80) cc_final: 0.7314 (m-80) REVERT: a 160 THR cc_start: 0.7643 (p) cc_final: 0.7124 (t) REVERT: a 170 VAL cc_start: 0.7317 (t) cc_final: 0.6062 (m) REVERT: a 172 LYS cc_start: 0.6684 (mmtm) cc_final: 0.5988 (mmtm) REVERT: a 194 LEU cc_start: 0.8084 (mt) cc_final: 0.7781 (mt) REVERT: a 200 ARG cc_start: 0.6066 (ttt90) cc_final: 0.5572 (ttm-80) REVERT: a 206 LYS cc_start: 0.7085 (mmtm) cc_final: 0.6850 (mmtm) REVERT: a 211 ILE cc_start: 0.5441 (mt) cc_final: 0.5234 (mt) REVERT: a 216 VAL cc_start: 0.6268 (t) cc_final: 0.6002 (p) REVERT: a 224 MET cc_start: 0.7266 (mmm) cc_final: 0.7013 (mmm) REVERT: a 245 MET cc_start: 0.7090 (mtt) cc_final: 0.6610 (mtm) REVERT: a 275 ASP cc_start: 0.7757 (m-30) cc_final: 0.7497 (m-30) REVERT: b 74 MET cc_start: 0.7710 (mtt) cc_final: 0.7281 (mtt) REVERT: b 78 LYS cc_start: 0.7555 (mttt) cc_final: 0.7106 (mtpp) REVERT: b 87 GLN cc_start: 0.7635 (mt0) cc_final: 0.7157 (mt0) REVERT: b 171 ASP cc_start: 0.7146 (t0) cc_final: 0.6900 (t0) REVERT: b 175 ILE cc_start: 0.7311 (mt) cc_final: 0.7034 (mt) REVERT: b 179 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7363 (mm-30) REVERT: b 224 MET cc_start: 0.7582 (mmm) cc_final: 0.6564 (mmm) REVERT: c 33 ASP cc_start: 0.7259 (m-30) cc_final: 0.6846 (m-30) REVERT: c 50 TYR cc_start: 0.8018 (t80) cc_final: 0.6739 (t80) REVERT: c 61 SER cc_start: 0.7406 (OUTLIER) cc_final: 0.7127 (p) REVERT: c 74 MET cc_start: 0.7885 (mtp) cc_final: 0.7528 (mtm) REVERT: c 99 TYR cc_start: 0.7521 (t80) cc_final: 0.7195 (t80) REVERT: c 103 GLU cc_start: 0.7463 (tt0) cc_final: 0.6995 (pp20) REVERT: c 131 TRP cc_start: 0.6487 (t60) cc_final: 0.6243 (t60) REVERT: c 175 ILE cc_start: 0.6745 (mt) cc_final: 0.6488 (mt) REVERT: c 251 THR cc_start: 0.6501 (m) cc_final: 0.6261 (t) REVERT: c 264 GLN cc_start: 0.7317 (tp40) cc_final: 0.6978 (tp-100) REVERT: c 271 ARG cc_start: 0.7437 (tpt-90) cc_final: 0.7126 (tpp80) REVERT: c 279 GLU cc_start: 0.6176 (mm-30) cc_final: 0.5962 (mm-30) REVERT: d 34 LYS cc_start: 0.8188 (mmtm) cc_final: 0.7716 (mmmm) REVERT: d 46 ASP cc_start: 0.5746 (t0) cc_final: 0.5271 (p0) REVERT: d 263 LYS cc_start: 0.7860 (mtpt) cc_final: 0.7581 (mtpt) REVERT: f 28 VAL cc_start: 0.8770 (t) cc_final: 0.8539 (p) REVERT: f 33 ASP cc_start: 0.7617 (m-30) cc_final: 0.7180 (m-30) REVERT: f 41 GLN cc_start: 0.7976 (mt0) cc_final: 0.7574 (mt0) REVERT: f 47 GLN cc_start: 0.7848 (mt0) cc_final: 0.7543 (tt0) REVERT: f 49 SER cc_start: 0.7858 (t) cc_final: 0.7562 (p) REVERT: f 59 SER cc_start: 0.8181 (m) cc_final: 0.7519 (p) REVERT: f 69 ASN cc_start: 0.8286 (m-40) cc_final: 0.7899 (m-40) REVERT: f 78 LYS cc_start: 0.8108 (mmtt) cc_final: 0.7581 (mmmm) REVERT: f 93 ILE cc_start: 0.7990 (tp) cc_final: 0.7650 (tp) REVERT: f 100 LYS cc_start: 0.8780 (ttmm) cc_final: 0.8506 (mtpp) REVERT: f 110 GLN cc_start: 0.7010 (tt0) cc_final: 0.6537 (tp-100) REVERT: f 164 PHE cc_start: 0.4825 (OUTLIER) cc_final: 0.4356 (t80) REVERT: f 167 ASN cc_start: 0.7366 (p0) cc_final: 0.6977 (m-40) REVERT: f 173 MET cc_start: 0.7792 (mmp) cc_final: 0.7196 (mmm) REVERT: f 271 ARG cc_start: 0.6644 (tpt170) cc_final: 0.6365 (tpt-90) REVERT: f 281 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7133 (mt-10) REVERT: f 282 HIS cc_start: 0.7247 (m90) cc_final: 0.7002 (m90) outliers start: 15 outliers final: 7 residues processed: 405 average time/residue: 0.1193 time to fit residues: 69.9312 Evaluate side-chains 358 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 349 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 17 ARG Chi-restraints excluded: chain b residue 61 SER Chi-restraints excluded: chain c residue 19 LYS Chi-restraints excluded: chain c residue 61 SER Chi-restraints excluded: chain c residue 256 HIS Chi-restraints excluded: chain e residue 158 ASN Chi-restraints excluded: chain e residue 186 VAL Chi-restraints excluded: chain f residue 164 PHE Chi-restraints excluded: chain f residue 233 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.0670 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 44 GLN ** a 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 237 HIS a 242 GLN a 256 HIS b 47 GLN b 54 ASN b 221 ASN b 282 HIS c 167 ASN d 54 ASN e 96 ASN e 221 ASN f 44 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.202637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.163309 restraints weight = 23848.965| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 3.13 r_work: 0.3950 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14076 Z= 0.195 Angle : 0.723 9.707 19165 Z= 0.394 Chirality : 0.052 0.357 2088 Planarity : 0.004 0.032 2351 Dihedral : 15.854 165.958 2080 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.86 % Allowed : 15.15 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.08 (0.20), residues: 1631 helix: 0.40 (0.19), residues: 725 sheet: 0.42 (0.34), residues: 234 loop : -0.32 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 244 TYR 0.019 0.002 TYR c 99 PHE 0.034 0.002 PHE f 246 TRP 0.030 0.002 TRP f 176 HIS 0.006 0.001 HIS b 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (14076) covalent geometry : angle 0.72302 / 0.39 (19165) hydrogen bonds : bond 0.04898 / 5.28 ( 572) hydrogen bonds : angle 4.78683 / 4.92 ( 1642) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 393 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 20 THR cc_start: 0.8947 (m) cc_final: 0.8675 (t) REVERT: a 21 SER cc_start: 0.8613 (m) cc_final: 0.8319 (p) REVERT: a 153 PHE cc_start: 0.8515 (m-80) cc_final: 0.8156 (m-80) REVERT: a 170 VAL cc_start: 0.8045 (t) cc_final: 0.7670 (m) REVERT: a 267 LYS cc_start: 0.8823 (mttt) cc_final: 0.8586 (mmmm) REVERT: a 275 ASP cc_start: 0.8127 (m-30) cc_final: 0.7771 (m-30) REVERT: a 283 GLU cc_start: 0.5982 (mm-30) cc_final: 0.5568 (mm-30) REVERT: b 59 SER cc_start: 0.7545 (m) cc_final: 0.7256 (p) REVERT: b 74 MET cc_start: 0.7589 (mtt) cc_final: 0.7318 (mtp) REVERT: b 171 ASP cc_start: 0.7213 (t0) cc_final: 0.6873 (t0) REVERT: b 224 MET cc_start: 0.7916 (mmm) cc_final: 0.7564 (mmm) REVERT: c 33 ASP cc_start: 0.7213 (m-30) cc_final: 0.6837 (m-30) REVERT: c 74 MET cc_start: 0.8079 (mtp) cc_final: 0.7855 (mtm) REVERT: c 153 PHE cc_start: 0.7360 (m-80) cc_final: 0.7091 (m-80) REVERT: c 224 MET cc_start: 0.7923 (mmm) cc_final: 0.7619 (mmm) REVERT: c 253 ARG cc_start: 0.7055 (mtp180) cc_final: 0.6811 (mtp-110) REVERT: c 271 ARG cc_start: 0.7967 (tpt-90) cc_final: 0.7759 (tpp80) REVERT: d 21 SER cc_start: 0.7739 (m) cc_final: 0.7256 (p) REVERT: d 25 MET cc_start: 0.7528 (mmm) cc_final: 0.7313 (mmt) REVERT: d 34 LYS cc_start: 0.8399 (mmtm) cc_final: 0.8140 (mmmm) REVERT: d 263 LYS cc_start: 0.8335 (mtpt) cc_final: 0.7779 (mtpt) REVERT: e 25 MET cc_start: 0.5709 (mtm) cc_final: 0.5502 (mtm) REVERT: e 182 MET cc_start: -0.0016 (mmm) cc_final: -0.0241 (mmt) REVERT: f 27 LEU cc_start: 0.8795 (tp) cc_final: 0.8519 (tp) REVERT: f 33 ASP cc_start: 0.7285 (m-30) cc_final: 0.7034 (m-30) REVERT: f 47 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: f 59 SER cc_start: 0.7961 (m) cc_final: 0.7656 (p) REVERT: f 69 ASN cc_start: 0.8410 (m-40) cc_final: 0.7994 (m-40) REVERT: f 173 MET cc_start: 0.8489 (mmp) cc_final: 0.8261 (mmm) REVERT: f 218 VAL cc_start: 0.8155 (p) cc_final: 0.7816 (m) outliers start: 55 outliers final: 34 residues processed: 415 average time/residue: 0.1246 time to fit residues: 74.5400 Evaluate side-chains 398 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 363 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 137 THR Chi-restraints excluded: chain a residue 197 SER Chi-restraints excluded: chain a residue 199 VAL Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 54 ASN Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 90 VAL Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain b residue 198 LYS Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 21 SER Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 40 LYS Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 197 SER Chi-restraints excluded: chain c residue 256 HIS Chi-restraints excluded: chain c residue 288 LYS Chi-restraints excluded: chain d residue 20 THR Chi-restraints excluded: chain d residue 54 ASN Chi-restraints excluded: chain d residue 68 ASP Chi-restraints excluded: chain d residue 141 THR Chi-restraints excluded: chain d residue 199 VAL Chi-restraints excluded: chain d residue 277 VAL Chi-restraints excluded: chain f residue 23 ARG Chi-restraints excluded: chain f residue 34 LYS Chi-restraints excluded: chain f residue 40 LYS Chi-restraints excluded: chain f residue 47 GLN Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 79 THR Chi-restraints excluded: chain f residue 105 ASN Chi-restraints excluded: chain f residue 183 THR Chi-restraints excluded: chain f residue 219 THR Chi-restraints excluded: chain f residue 277 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 153 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 43 optimal weight: 0.0020 chunk 31 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 101 optimal weight: 0.4980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 44 GLN a 105 ASN ** a 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 242 GLN b 282 HIS c 88 GLN c 105 ASN ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 238 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.201979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.162235 restraints weight = 24060.573| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 3.19 r_work: 0.3931 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14076 Z= 0.154 Angle : 0.633 8.858 19165 Z= 0.341 Chirality : 0.048 0.265 2088 Planarity : 0.003 0.034 2351 Dihedral : 15.319 167.487 2064 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.30 % Allowed : 19.50 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.22 (0.21), residues: 1631 helix: 0.72 (0.19), residues: 736 sheet: 0.55 (0.37), residues: 211 loop : -0.52 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG b 200 TYR 0.026 0.002 TYR a 99 PHE 0.019 0.002 PHE a 246 TRP 0.030 0.001 TRP a 119 HIS 0.006 0.001 HIS b 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (14076) covalent geometry : angle 0.63261 / 0.34 (19165) hydrogen bonds : bond 0.04364 / 4.64 ( 572) hydrogen bonds : angle 4.51470 / 4.59 ( 1642) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 379 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 26 GLU cc_start: 0.8274 (tt0) cc_final: 0.8023 (tm-30) REVERT: a 58 ASN cc_start: 0.8042 (t0) cc_final: 0.7837 (t0) REVERT: a 62 GLN cc_start: 0.8444 (tt0) cc_final: 0.8242 (tt0) REVERT: a 88 GLN cc_start: 0.6583 (mm-40) cc_final: 0.6243 (mm-40) REVERT: a 107 TYR cc_start: 0.8066 (m-80) cc_final: 0.7685 (m-80) REVERT: a 267 LYS cc_start: 0.8800 (mttt) cc_final: 0.8560 (mmmm) REVERT: a 275 ASP cc_start: 0.8088 (m-30) cc_final: 0.7760 (m-30) REVERT: a 283 GLU cc_start: 0.6150 (mm-30) cc_final: 0.5744 (mm-30) REVERT: b 36 ILE cc_start: 0.8580 (mt) cc_final: 0.8363 (mt) REVERT: b 59 SER cc_start: 0.7602 (m) cc_final: 0.7303 (p) REVERT: b 74 MET cc_start: 0.7760 (mtt) cc_final: 0.7452 (mtp) REVERT: b 171 ASP cc_start: 0.7308 (t0) cc_final: 0.6990 (t0) REVERT: c 21 SER cc_start: 0.8016 (m) cc_final: 0.7116 (p) REVERT: c 74 MET cc_start: 0.8181 (mtp) cc_final: 0.7974 (mtp) REVERT: c 198 LYS cc_start: 0.8030 (mttt) cc_final: 0.7746 (mttt) REVERT: c 253 ARG cc_start: 0.7251 (mtp180) cc_final: 0.7028 (mtt-85) REVERT: c 271 ARG cc_start: 0.8064 (tpt-90) cc_final: 0.7815 (tpp80) REVERT: d 21 SER cc_start: 0.7770 (m) cc_final: 0.7308 (p) REVERT: d 34 LYS cc_start: 0.8379 (mmtm) cc_final: 0.8096 (mmmm) REVERT: d 45 GLU cc_start: 0.7223 (tp30) cc_final: 0.7015 (tp30) REVERT: d 263 LYS cc_start: 0.8266 (mtpt) cc_final: 0.7767 (mtpt) REVERT: d 267 LYS cc_start: 0.7028 (mttm) cc_final: 0.6736 (mttm) REVERT: e 25 MET cc_start: 0.5695 (mtm) cc_final: 0.5405 (mtm) REVERT: e 224 MET cc_start: -0.3318 (mmt) cc_final: -0.5202 (tmm) REVERT: f 27 LEU cc_start: 0.8853 (tp) cc_final: 0.8457 (tt) REVERT: f 33 ASP cc_start: 0.7303 (m-30) cc_final: 0.7045 (m-30) REVERT: f 47 GLN cc_start: 0.8282 (mt0) cc_final: 0.8035 (tt0) REVERT: f 59 SER cc_start: 0.7976 (m) cc_final: 0.7721 (p) REVERT: f 69 ASN cc_start: 0.8334 (m-40) cc_final: 0.7937 (m-40) REVERT: f 173 MET cc_start: 0.8483 (mmp) cc_final: 0.8259 (mmm) REVERT: f 218 VAL cc_start: 0.8236 (p) cc_final: 0.7954 (m) outliers start: 47 outliers final: 35 residues processed: 395 average time/residue: 0.1074 time to fit residues: 61.4622 Evaluate side-chains 409 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 374 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 186 VAL Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 90 VAL Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain b residue 198 LYS Chi-restraints excluded: chain b residue 211 ILE Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 64 LYS Chi-restraints excluded: chain c residue 88 GLN Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 167 ASN Chi-restraints excluded: chain c residue 175 ILE Chi-restraints excluded: chain c residue 182 MET Chi-restraints excluded: chain c residue 197 SER Chi-restraints excluded: chain c residue 218 VAL Chi-restraints excluded: chain c residue 256 HIS Chi-restraints excluded: chain c residue 281 GLU Chi-restraints excluded: chain d residue 20 THR Chi-restraints excluded: chain d residue 44 GLN Chi-restraints excluded: chain d residue 141 THR Chi-restraints excluded: chain d residue 277 VAL Chi-restraints excluded: chain f residue 23 ARG Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 93 ILE Chi-restraints excluded: chain f residue 105 ASN Chi-restraints excluded: chain f residue 219 THR Chi-restraints excluded: chain f residue 234 THR Chi-restraints excluded: chain f residue 281 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 159 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 89 optimal weight: 0.4980 chunk 102 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 44 GLN ** a 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 242 GLN d 54 ASN ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 110 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.198195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.158682 restraints weight = 23581.480| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 3.10 r_work: 0.3888 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 14076 Z= 0.176 Angle : 0.625 9.296 19165 Z= 0.334 Chirality : 0.048 0.239 2088 Planarity : 0.003 0.034 2351 Dihedral : 15.022 170.939 2064 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.75 % Rotamer: Outliers : 4.00 % Allowed : 20.34 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.17 (0.21), residues: 1631 helix: 0.76 (0.19), residues: 737 sheet: 0.38 (0.35), residues: 221 loop : -0.61 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 17 TYR 0.015 0.002 TYR c 99 PHE 0.018 0.002 PHE e 246 TRP 0.015 0.002 TRP f 176 HIS 0.004 0.001 HIS b 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (14076) covalent geometry : angle 0.62504 / 0.33 (19165) hydrogen bonds : bond 0.04282 / 4.58 ( 572) hydrogen bonds : angle 4.40467 / 4.47 ( 1642) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 395 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 26 GLU cc_start: 0.8236 (tt0) cc_final: 0.8009 (tm-30) REVERT: a 50 TYR cc_start: 0.8370 (t80) cc_final: 0.8123 (t80) REVERT: a 52 SER cc_start: 0.8275 (p) cc_final: 0.7922 (t) REVERT: a 83 TYR cc_start: 0.7847 (m-80) cc_final: 0.7614 (m-80) REVERT: a 88 GLN cc_start: 0.6655 (mm-40) cc_final: 0.6252 (mm-40) REVERT: a 107 TYR cc_start: 0.8290 (m-80) cc_final: 0.7857 (m-80) REVERT: a 159 TRP cc_start: 0.8550 (OUTLIER) cc_final: 0.8084 (m-90) REVERT: a 263 LYS cc_start: 0.8455 (ttpt) cc_final: 0.8200 (mtpp) REVERT: a 267 LYS cc_start: 0.8802 (mttt) cc_final: 0.8532 (mmmm) REVERT: a 275 ASP cc_start: 0.8149 (m-30) cc_final: 0.7828 (m-30) REVERT: a 283 GLU cc_start: 0.6260 (mm-30) cc_final: 0.5880 (mm-30) REVERT: b 59 SER cc_start: 0.7647 (m) cc_final: 0.7348 (p) REVERT: b 74 MET cc_start: 0.7860 (mtt) cc_final: 0.7545 (mtp) REVERT: b 145 GLU cc_start: 0.7330 (tt0) cc_final: 0.6989 (tt0) REVERT: b 171 ASP cc_start: 0.7391 (t0) cc_final: 0.7056 (t0) REVERT: b 200 ARG cc_start: 0.8035 (mtp85) cc_final: 0.7687 (mtp85) REVERT: b 264 GLN cc_start: 0.7886 (tp40) cc_final: 0.7526 (tp40) REVERT: c 21 SER cc_start: 0.8319 (OUTLIER) cc_final: 0.7325 (p) REVERT: c 33 ASP cc_start: 0.7474 (m-30) cc_final: 0.7134 (m-30) REVERT: c 171 ASP cc_start: 0.7654 (t70) cc_final: 0.7411 (t0) REVERT: c 198 LYS cc_start: 0.8206 (mttt) cc_final: 0.7681 (mttt) REVERT: c 242 GLN cc_start: 0.8397 (mt0) cc_final: 0.8102 (mt0) REVERT: c 253 ARG cc_start: 0.7533 (mtp180) cc_final: 0.7302 (mtt-85) REVERT: d 21 SER cc_start: 0.8086 (m) cc_final: 0.7733 (p) REVERT: d 34 LYS cc_start: 0.8432 (mmtm) cc_final: 0.8110 (mmmm) REVERT: d 45 GLU cc_start: 0.7287 (tp30) cc_final: 0.6973 (tp30) REVERT: d 263 LYS cc_start: 0.8311 (mtpt) cc_final: 0.7832 (mtpt) REVERT: d 267 LYS cc_start: 0.7143 (mttm) cc_final: 0.6857 (mttm) REVERT: e 25 MET cc_start: 0.5681 (mtm) cc_final: 0.5408 (mtm) REVERT: e 182 MET cc_start: 0.3859 (mmt) cc_final: 0.3634 (mmt) REVERT: f 27 LEU cc_start: 0.8831 (tp) cc_final: 0.8597 (tt) REVERT: f 33 ASP cc_start: 0.7299 (m-30) cc_final: 0.7035 (m-30) REVERT: f 59 SER cc_start: 0.8079 (m) cc_final: 0.7785 (p) REVERT: f 173 MET cc_start: 0.8516 (mmp) cc_final: 0.8301 (mmm) REVERT: f 218 VAL cc_start: 0.8221 (p) cc_final: 0.7884 (m) outliers start: 57 outliers final: 39 residues processed: 420 average time/residue: 0.1008 time to fit residues: 61.2163 Evaluate side-chains 430 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 389 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 84 LEU Chi-restraints excluded: chain a residue 159 TRP Chi-restraints excluded: chain a residue 189 SER Chi-restraints excluded: chain a residue 197 SER Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 90 VAL Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain b residue 198 LYS Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain b residue 220 SER Chi-restraints excluded: chain c residue 21 SER Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 37 THR Chi-restraints excluded: chain c residue 40 LYS Chi-restraints excluded: chain c residue 64 LYS Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 167 ASN Chi-restraints excluded: chain c residue 175 ILE Chi-restraints excluded: chain c residue 182 MET Chi-restraints excluded: chain c residue 197 SER Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 266 VAL Chi-restraints excluded: chain c residue 288 LYS Chi-restraints excluded: chain d residue 20 THR Chi-restraints excluded: chain d residue 52 SER Chi-restraints excluded: chain d residue 54 ASN Chi-restraints excluded: chain d residue 141 THR Chi-restraints excluded: chain d residue 277 VAL Chi-restraints excluded: chain f residue 23 ARG Chi-restraints excluded: chain f residue 40 LYS Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 79 THR Chi-restraints excluded: chain f residue 93 ILE Chi-restraints excluded: chain f residue 105 ASN Chi-restraints excluded: chain f residue 183 THR Chi-restraints excluded: chain f residue 234 THR Chi-restraints excluded: chain f residue 241 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 71 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 58 ASN ** a 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 47 GLN b 54 ASN b 62 GLN b 110 GLN b 238 GLN b 242 GLN ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 41 GLN f 47 GLN ** f 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 110 GLN f 238 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.196250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.155672 restraints weight = 23451.963| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 3.18 r_work: 0.3849 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14076 Z= 0.179 Angle : 0.615 9.578 19165 Z= 0.327 Chirality : 0.048 0.246 2088 Planarity : 0.004 0.054 2351 Dihedral : 14.817 170.480 2062 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Rotamer: Outliers : 4.84 % Allowed : 21.04 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.10 (0.20), residues: 1631 helix: 0.69 (0.19), residues: 740 sheet: 0.28 (0.35), residues: 222 loop : -0.61 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG c 271 TYR 0.015 0.002 TYR c 99 PHE 0.018 0.002 PHE e 246 TRP 0.018 0.001 TRP a 119 HIS 0.003 0.001 HIS a 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (14076) covalent geometry : angle 0.61539 / 0.33 (19165) hydrogen bonds : bond 0.04240 / 4.49 ( 572) hydrogen bonds : angle 4.34925 / 4.52 ( 1642) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 405 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 26 GLU cc_start: 0.8173 (tt0) cc_final: 0.7937 (tm-30) REVERT: a 40 LYS cc_start: 0.8036 (ttmm) cc_final: 0.7663 (ttmt) REVERT: a 50 TYR cc_start: 0.8423 (t80) cc_final: 0.8067 (t80) REVERT: a 52 SER cc_start: 0.8369 (p) cc_final: 0.8046 (t) REVERT: a 88 GLN cc_start: 0.6649 (mm-40) cc_final: 0.6322 (mm-40) REVERT: a 107 TYR cc_start: 0.8325 (m-80) cc_final: 0.7872 (m-80) REVERT: a 159 TRP cc_start: 0.8626 (OUTLIER) cc_final: 0.8384 (m-90) REVERT: a 204 LYS cc_start: 0.7620 (mttm) cc_final: 0.7265 (mttm) REVERT: a 258 PHE cc_start: 0.8335 (t80) cc_final: 0.8106 (t80) REVERT: a 267 LYS cc_start: 0.8792 (mttt) cc_final: 0.8507 (mmmm) REVERT: a 275 ASP cc_start: 0.8196 (m-30) cc_final: 0.7869 (m-30) REVERT: a 283 GLU cc_start: 0.6397 (mm-30) cc_final: 0.6013 (mm-30) REVERT: b 59 SER cc_start: 0.7712 (m) cc_final: 0.7403 (p) REVERT: b 61 SER cc_start: 0.8787 (m) cc_final: 0.8210 (t) REVERT: b 74 MET cc_start: 0.8011 (mtt) cc_final: 0.7698 (mtp) REVERT: b 145 GLU cc_start: 0.7403 (tt0) cc_final: 0.7033 (tt0) REVERT: b 171 ASP cc_start: 0.7430 (t0) cc_final: 0.7119 (t0) REVERT: b 264 GLN cc_start: 0.7965 (tp40) cc_final: 0.7755 (tp40) REVERT: c 21 SER cc_start: 0.8597 (OUTLIER) cc_final: 0.7734 (p) REVERT: c 32 VAL cc_start: 0.8550 (t) cc_final: 0.8342 (m) REVERT: c 33 ASP cc_start: 0.7626 (m-30) cc_final: 0.7253 (m-30) REVERT: c 74 MET cc_start: 0.8346 (mtp) cc_final: 0.8134 (mtm) REVERT: c 143 ILE cc_start: 0.7936 (mt) cc_final: 0.7081 (mm) REVERT: c 171 ASP cc_start: 0.7793 (t70) cc_final: 0.7523 (t0) REVERT: c 253 ARG cc_start: 0.7793 (mtp180) cc_final: 0.7484 (mtp-110) REVERT: d 27 LEU cc_start: 0.8615 (tp) cc_final: 0.8370 (tp) REVERT: d 34 LYS cc_start: 0.8453 (mmtm) cc_final: 0.8110 (mmmm) REVERT: d 263 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7791 (mtpt) REVERT: d 267 LYS cc_start: 0.7261 (mttm) cc_final: 0.6961 (mttm) REVERT: e 25 MET cc_start: 0.5886 (mtm) cc_final: 0.5569 (mtm) REVERT: e 224 MET cc_start: -0.3009 (mmt) cc_final: -0.5356 (tmm) REVERT: f 27 LEU cc_start: 0.8789 (tp) cc_final: 0.8328 (tt) REVERT: f 31 LEU cc_start: 0.8395 (mt) cc_final: 0.8169 (mp) REVERT: f 33 ASP cc_start: 0.7400 (m-30) cc_final: 0.7053 (m-30) REVERT: f 41 GLN cc_start: 0.8354 (mt0) cc_final: 0.8077 (mt0) REVERT: f 59 SER cc_start: 0.8114 (m) cc_final: 0.7801 (p) REVERT: f 173 MET cc_start: 0.8543 (mmp) cc_final: 0.8278 (mmm) REVERT: f 218 VAL cc_start: 0.8231 (p) cc_final: 0.7925 (m) outliers start: 69 outliers final: 45 residues processed: 437 average time/residue: 0.1058 time to fit residues: 67.5487 Evaluate side-chains 441 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 394 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 25 MET Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 84 LEU Chi-restraints excluded: chain a residue 159 TRP Chi-restraints excluded: chain a residue 189 SER Chi-restraints excluded: chain a residue 197 SER Chi-restraints excluded: chain a residue 206 LYS Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 54 ASN Chi-restraints excluded: chain b residue 87 GLN Chi-restraints excluded: chain b residue 90 VAL Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain b residue 151 VAL Chi-restraints excluded: chain b residue 198 LYS Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 21 SER Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 37 THR Chi-restraints excluded: chain c residue 167 ASN Chi-restraints excluded: chain c residue 175 ILE Chi-restraints excluded: chain c residue 182 MET Chi-restraints excluded: chain c residue 197 SER Chi-restraints excluded: chain c residue 235 PHE Chi-restraints excluded: chain c residue 288 LYS Chi-restraints excluded: chain d residue 20 THR Chi-restraints excluded: chain d residue 44 GLN Chi-restraints excluded: chain d residue 59 SER Chi-restraints excluded: chain d residue 141 THR Chi-restraints excluded: chain d residue 199 VAL Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain d residue 277 VAL Chi-restraints excluded: chain e residue 28 VAL Chi-restraints excluded: chain f residue 20 THR Chi-restraints excluded: chain f residue 23 ARG Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 79 THR Chi-restraints excluded: chain f residue 93 ILE Chi-restraints excluded: chain f residue 105 ASN Chi-restraints excluded: chain f residue 147 ILE Chi-restraints excluded: chain f residue 183 THR Chi-restraints excluded: chain f residue 234 THR Chi-restraints excluded: chain f residue 241 LEU Chi-restraints excluded: chain f residue 266 VAL Chi-restraints excluded: chain f residue 277 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 116 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 109 optimal weight: 0.1980 chunk 73 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 129 optimal weight: 0.0170 chunk 90 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 62 GLN a 238 GLN b 238 GLN b 242 GLN c 44 GLN c 105 ASN d 54 ASN d 167 ASN ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.194600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.154693 restraints weight = 23418.081| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 3.03 r_work: 0.3838 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14076 Z= 0.169 Angle : 0.606 10.020 19165 Z= 0.322 Chirality : 0.047 0.254 2088 Planarity : 0.004 0.036 2351 Dihedral : 14.673 171.282 2062 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.75 % Rotamer: Outliers : 3.65 % Allowed : 23.07 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.15 (0.20), residues: 1631 helix: 0.80 (0.19), residues: 738 sheet: 0.21 (0.35), residues: 222 loop : -0.65 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 200 TYR 0.019 0.002 TYR c 83 PHE 0.024 0.002 PHE b 53 TRP 0.020 0.001 TRP a 119 HIS 0.002 0.001 HIS b 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (14076) covalent geometry : angle 0.60638 / 0.32 (19165) hydrogen bonds : bond 0.04147 / 4.39 ( 572) hydrogen bonds : angle 4.33633 / 4.52 ( 1642) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 401 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 20 THR cc_start: 0.8998 (m) cc_final: 0.8753 (t) REVERT: a 26 GLU cc_start: 0.8143 (tt0) cc_final: 0.7898 (tm-30) REVERT: a 40 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7743 (ttmt) REVERT: a 50 TYR cc_start: 0.8461 (t80) cc_final: 0.8045 (t80) REVERT: a 52 SER cc_start: 0.8469 (p) cc_final: 0.8160 (t) REVERT: a 88 GLN cc_start: 0.6685 (mm-40) cc_final: 0.6372 (mm-40) REVERT: a 107 TYR cc_start: 0.8311 (m-80) cc_final: 0.7888 (m-80) REVERT: a 204 LYS cc_start: 0.7641 (mttm) cc_final: 0.7274 (mttm) REVERT: a 258 PHE cc_start: 0.8371 (t80) cc_final: 0.8148 (t80) REVERT: a 267 LYS cc_start: 0.8767 (mttt) cc_final: 0.8456 (mmmm) REVERT: a 283 GLU cc_start: 0.6489 (mm-30) cc_final: 0.6101 (mm-30) REVERT: a 287 LYS cc_start: 0.8381 (ptmm) cc_final: 0.8111 (pttm) REVERT: b 59 SER cc_start: 0.7878 (m) cc_final: 0.7476 (p) REVERT: b 61 SER cc_start: 0.8853 (m) cc_final: 0.8394 (p) REVERT: b 62 GLN cc_start: 0.8073 (tt0) cc_final: 0.7868 (mt0) REVERT: b 74 MET cc_start: 0.8163 (mtt) cc_final: 0.7871 (mtp) REVERT: b 145 GLU cc_start: 0.7470 (tt0) cc_final: 0.7167 (tt0) REVERT: b 171 ASP cc_start: 0.7531 (t0) cc_final: 0.7231 (t0) REVERT: b 200 ARG cc_start: 0.8383 (mtp85) cc_final: 0.7984 (mtp85) REVERT: b 260 LYS cc_start: 0.8299 (mtmt) cc_final: 0.7970 (mtpp) REVERT: b 264 GLN cc_start: 0.7964 (tp40) cc_final: 0.7724 (tp40) REVERT: c 32 VAL cc_start: 0.8602 (t) cc_final: 0.8382 (m) REVERT: c 33 ASP cc_start: 0.7660 (m-30) cc_final: 0.7268 (m-30) REVERT: c 68 ASP cc_start: 0.7774 (t0) cc_final: 0.7315 (t0) REVERT: c 72 LYS cc_start: 0.8587 (mttp) cc_final: 0.8330 (mttp) REVERT: c 143 ILE cc_start: 0.8068 (mt) cc_final: 0.7324 (mm) REVERT: c 171 ASP cc_start: 0.7832 (t70) cc_final: 0.7553 (t0) REVERT: c 172 LYS cc_start: 0.8393 (mmtm) cc_final: 0.8099 (mmtm) REVERT: c 197 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8388 (p) REVERT: c 224 MET cc_start: 0.8399 (mmm) cc_final: 0.8069 (mmm) REVERT: c 253 ARG cc_start: 0.7890 (mtp180) cc_final: 0.7325 (mtt-85) REVERT: c 268 ASP cc_start: 0.7596 (m-30) cc_final: 0.7316 (m-30) REVERT: d 27 LEU cc_start: 0.8683 (tp) cc_final: 0.8461 (tp) REVERT: d 34 LYS cc_start: 0.8441 (mmtm) cc_final: 0.8080 (mmmm) REVERT: d 263 LYS cc_start: 0.8273 (mtpt) cc_final: 0.7777 (mtpt) REVERT: d 267 LYS cc_start: 0.7294 (mttm) cc_final: 0.6991 (mttm) REVERT: e 25 MET cc_start: 0.5894 (mtm) cc_final: 0.5618 (mtm) REVERT: e 224 MET cc_start: -0.3134 (mmt) cc_final: -0.5516 (tmm) REVERT: e 245 MET cc_start: 0.0850 (mtm) cc_final: -0.0175 (mtm) REVERT: f 27 LEU cc_start: 0.8774 (tp) cc_final: 0.8535 (tt) REVERT: f 33 ASP cc_start: 0.7396 (m-30) cc_final: 0.7051 (m-30) REVERT: f 59 SER cc_start: 0.8158 (m) cc_final: 0.7812 (p) REVERT: f 173 MET cc_start: 0.8584 (mmp) cc_final: 0.8298 (mmm) REVERT: f 218 VAL cc_start: 0.8215 (p) cc_final: 0.7896 (m) REVERT: f 284 PHE cc_start: 0.7789 (t80) cc_final: 0.7062 (t80) outliers start: 52 outliers final: 36 residues processed: 428 average time/residue: 0.1171 time to fit residues: 72.3545 Evaluate side-chains 435 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 398 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 189 SER Chi-restraints excluded: chain a residue 197 SER Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 39 GLU Chi-restraints excluded: chain b residue 54 ASN Chi-restraints excluded: chain b residue 87 GLN Chi-restraints excluded: chain b residue 90 VAL Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain b residue 198 LYS Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 167 ASN Chi-restraints excluded: chain c residue 175 ILE Chi-restraints excluded: chain c residue 182 MET Chi-restraints excluded: chain c residue 197 SER Chi-restraints excluded: chain c residue 235 PHE Chi-restraints excluded: chain c residue 288 LYS Chi-restraints excluded: chain d residue 20 THR Chi-restraints excluded: chain d residue 44 GLN Chi-restraints excluded: chain d residue 141 THR Chi-restraints excluded: chain d residue 199 VAL Chi-restraints excluded: chain d residue 277 VAL Chi-restraints excluded: chain e residue 28 VAL Chi-restraints excluded: chain f residue 23 ARG Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 79 THR Chi-restraints excluded: chain f residue 93 ILE Chi-restraints excluded: chain f residue 105 ASN Chi-restraints excluded: chain f residue 183 THR Chi-restraints excluded: chain f residue 234 THR Chi-restraints excluded: chain f residue 241 LEU Chi-restraints excluded: chain f residue 266 VAL Chi-restraints excluded: chain f residue 281 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 47 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 135 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 83 optimal weight: 0.4980 chunk 155 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 140 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 238 GLN b 242 GLN c 44 GLN d 54 ASN ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.194155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.154283 restraints weight = 23250.480| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 3.03 r_work: 0.3832 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14076 Z= 0.152 Angle : 0.594 9.083 19165 Z= 0.316 Chirality : 0.046 0.256 2088 Planarity : 0.004 0.052 2351 Dihedral : 14.541 172.286 2062 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.37 % Favored : 96.57 % Rotamer: Outliers : 3.72 % Allowed : 23.21 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.16 (0.21), residues: 1631 helix: 0.83 (0.19), residues: 739 sheet: 0.13 (0.35), residues: 225 loop : -0.64 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 60 TYR 0.021 0.001 TYR c 83 PHE 0.016 0.001 PHE f 153 TRP 0.029 0.001 TRP a 119 HIS 0.002 0.001 HIS c 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (14076) covalent geometry : angle 0.59389 / 0.32 (19165) hydrogen bonds : bond 0.03950 / 4.17 ( 572) hydrogen bonds : angle 4.30911 / 4.49 ( 1642) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 401 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 20 THR cc_start: 0.9000 (m) cc_final: 0.8773 (t) REVERT: a 26 GLU cc_start: 0.8116 (tt0) cc_final: 0.7865 (tm-30) REVERT: a 40 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7834 (ttmt) REVERT: a 50 TYR cc_start: 0.8446 (t80) cc_final: 0.8055 (t80) REVERT: a 54 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7637 (m-40) REVERT: a 88 GLN cc_start: 0.6765 (mm-40) cc_final: 0.6457 (mm-40) REVERT: a 107 TYR cc_start: 0.8323 (m-80) cc_final: 0.7855 (m-80) REVERT: a 172 LYS cc_start: 0.7933 (mmtm) cc_final: 0.7683 (mmtm) REVERT: a 204 LYS cc_start: 0.7645 (mttm) cc_final: 0.7262 (mttm) REVERT: a 279 GLU cc_start: 0.7732 (pp20) cc_final: 0.7350 (pp20) REVERT: a 283 GLU cc_start: 0.6506 (mm-30) cc_final: 0.6092 (mm-30) REVERT: b 59 SER cc_start: 0.7945 (m) cc_final: 0.7606 (p) REVERT: b 61 SER cc_start: 0.8845 (m) cc_final: 0.8449 (p) REVERT: b 74 MET cc_start: 0.8211 (mtt) cc_final: 0.7952 (mtp) REVERT: b 145 GLU cc_start: 0.7474 (tt0) cc_final: 0.7180 (tt0) REVERT: b 171 ASP cc_start: 0.7549 (t0) cc_final: 0.7258 (t0) REVERT: b 260 LYS cc_start: 0.8312 (mtmt) cc_final: 0.7971 (mtpp) REVERT: b 264 GLN cc_start: 0.7948 (tp40) cc_final: 0.7688 (tp40) REVERT: c 21 SER cc_start: 0.8747 (OUTLIER) cc_final: 0.7917 (p) REVERT: c 32 VAL cc_start: 0.8682 (t) cc_final: 0.8471 (m) REVERT: c 33 ASP cc_start: 0.7707 (m-30) cc_final: 0.7314 (m-30) REVERT: c 68 ASP cc_start: 0.7827 (t0) cc_final: 0.7388 (t0) REVERT: c 72 LYS cc_start: 0.8656 (mttp) cc_final: 0.8389 (mttp) REVERT: c 171 ASP cc_start: 0.7822 (t70) cc_final: 0.7566 (t0) REVERT: c 172 LYS cc_start: 0.8500 (mmtm) cc_final: 0.8166 (mmtm) REVERT: c 183 THR cc_start: 0.8199 (m) cc_final: 0.7587 (p) REVERT: c 197 SER cc_start: 0.8814 (OUTLIER) cc_final: 0.8452 (p) REVERT: c 253 ARG cc_start: 0.7875 (mtp180) cc_final: 0.7288 (mtt180) REVERT: d 27 LEU cc_start: 0.8736 (tp) cc_final: 0.8506 (tp) REVERT: d 34 LYS cc_start: 0.8438 (mmtm) cc_final: 0.8074 (mmmm) REVERT: d 62 GLN cc_start: 0.8316 (mt0) cc_final: 0.8090 (mt0) REVERT: d 68 ASP cc_start: 0.8209 (t0) cc_final: 0.7948 (t0) REVERT: d 263 LYS cc_start: 0.8263 (mtpt) cc_final: 0.7687 (mtpt) REVERT: e 25 MET cc_start: 0.5969 (mtm) cc_final: 0.5730 (mtm) REVERT: e 28 VAL cc_start: 0.6857 (OUTLIER) cc_final: 0.6451 (t) REVERT: e 224 MET cc_start: -0.2994 (mmt) cc_final: -0.5446 (tmm) REVERT: e 245 MET cc_start: 0.0858 (mtm) cc_final: -0.0122 (mtm) REVERT: f 33 ASP cc_start: 0.7376 (m-30) cc_final: 0.7030 (m-30) REVERT: f 59 SER cc_start: 0.8124 (m) cc_final: 0.7750 (p) REVERT: f 79 THR cc_start: 0.7123 (OUTLIER) cc_final: 0.6899 (p) REVERT: f 173 MET cc_start: 0.8577 (mmp) cc_final: 0.8308 (mmm) REVERT: f 218 VAL cc_start: 0.8254 (p) cc_final: 0.7944 (m) outliers start: 53 outliers final: 37 residues processed: 427 average time/residue: 0.1066 time to fit residues: 66.0117 Evaluate side-chains 434 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 392 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 54 ASN Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain b residue 151 VAL Chi-restraints excluded: chain b residue 198 LYS Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain c residue 19 LYS Chi-restraints excluded: chain c residue 21 SER Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 167 ASN Chi-restraints excluded: chain c residue 175 ILE Chi-restraints excluded: chain c residue 182 MET Chi-restraints excluded: chain c residue 197 SER Chi-restraints excluded: chain c residue 216 VAL Chi-restraints excluded: chain c residue 235 PHE Chi-restraints excluded: chain c residue 288 LYS Chi-restraints excluded: chain d residue 20 THR Chi-restraints excluded: chain d residue 44 GLN Chi-restraints excluded: chain d residue 54 ASN Chi-restraints excluded: chain d residue 141 THR Chi-restraints excluded: chain d residue 199 VAL Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain d residue 277 VAL Chi-restraints excluded: chain e residue 28 VAL Chi-restraints excluded: chain f residue 23 ARG Chi-restraints excluded: chain f residue 40 LYS Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 79 THR Chi-restraints excluded: chain f residue 93 ILE Chi-restraints excluded: chain f residue 105 ASN Chi-restraints excluded: chain f residue 147 ILE Chi-restraints excluded: chain f residue 183 THR Chi-restraints excluded: chain f residue 241 LEU Chi-restraints excluded: chain f residue 262 THR Chi-restraints excluded: chain f residue 266 VAL Chi-restraints excluded: chain f residue 281 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 9 optimal weight: 0.0570 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 88 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 110 optimal weight: 0.0070 chunk 141 optimal weight: 1.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 105 ASN b 105 ASN b 238 GLN b 242 GLN ** c 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 47 GLN c 237 HIS d 41 GLN ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.194609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.154595 restraints weight = 23227.864| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 3.04 r_work: 0.3838 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14076 Z= 0.125 Angle : 0.580 9.764 19165 Z= 0.307 Chirality : 0.045 0.260 2088 Planarity : 0.004 0.045 2351 Dihedral : 14.456 173.233 2062 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.68 % Favored : 96.26 % Rotamer: Outliers : 3.44 % Allowed : 23.35 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.24 (0.21), residues: 1631 helix: 0.90 (0.19), residues: 742 sheet: 0.18 (0.35), residues: 218 loop : -0.60 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG b 252 TYR 0.014 0.001 TYR c 99 PHE 0.016 0.001 PHE b 164 TRP 0.025 0.001 TRP a 119 HIS 0.003 0.000 HIS f 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (14076) covalent geometry : angle 0.58033 / 0.31 (19165) hydrogen bonds : bond 0.03648 / 3.85 ( 572) hydrogen bonds : angle 4.23315 / 4.37 ( 1642) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 398 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 20 THR cc_start: 0.8994 (m) cc_final: 0.8755 (t) REVERT: a 26 GLU cc_start: 0.8138 (tt0) cc_final: 0.7888 (tm-30) REVERT: a 40 LYS cc_start: 0.8164 (ttmm) cc_final: 0.7821 (ttmt) REVERT: a 50 TYR cc_start: 0.8432 (t80) cc_final: 0.8049 (t80) REVERT: a 88 GLN cc_start: 0.6815 (mm-40) cc_final: 0.6551 (mm-40) REVERT: a 107 TYR cc_start: 0.8251 (m-80) cc_final: 0.7812 (m-80) REVERT: a 119 TRP cc_start: 0.7889 (t60) cc_final: 0.7676 (t60) REVERT: a 172 LYS cc_start: 0.7929 (mmtm) cc_final: 0.7659 (mmtm) REVERT: a 204 LYS cc_start: 0.7659 (mttm) cc_final: 0.7266 (mttm) REVERT: a 267 LYS cc_start: 0.8767 (mttt) cc_final: 0.8525 (mmmt) REVERT: a 279 GLU cc_start: 0.7725 (pp20) cc_final: 0.7348 (pp20) REVERT: a 283 GLU cc_start: 0.6552 (mm-30) cc_final: 0.6132 (mm-30) REVERT: b 59 SER cc_start: 0.7920 (m) cc_final: 0.7627 (p) REVERT: b 61 SER cc_start: 0.8807 (m) cc_final: 0.8454 (p) REVERT: b 74 MET cc_start: 0.8183 (mtt) cc_final: 0.7942 (mtp) REVERT: b 104 LEU cc_start: 0.8678 (tt) cc_final: 0.7997 (tt) REVERT: b 171 ASP cc_start: 0.7544 (t0) cc_final: 0.7271 (t0) REVERT: b 200 ARG cc_start: 0.8476 (mtp85) cc_final: 0.8104 (mtp85) REVERT: b 260 LYS cc_start: 0.8299 (mtmt) cc_final: 0.7966 (mtpp) REVERT: b 264 GLN cc_start: 0.7902 (tp40) cc_final: 0.7644 (tp40) REVERT: c 21 SER cc_start: 0.8731 (m) cc_final: 0.7893 (p) REVERT: c 33 ASP cc_start: 0.7700 (m-30) cc_final: 0.7338 (m-30) REVERT: c 59 SER cc_start: 0.7221 (m) cc_final: 0.6935 (p) REVERT: c 68 ASP cc_start: 0.7862 (t0) cc_final: 0.7449 (t0) REVERT: c 72 LYS cc_start: 0.8665 (mttp) cc_final: 0.8416 (mttp) REVERT: c 143 ILE cc_start: 0.8092 (mt) cc_final: 0.7383 (mm) REVERT: c 171 ASP cc_start: 0.7771 (t70) cc_final: 0.7519 (t0) REVERT: c 172 LYS cc_start: 0.8547 (mmtm) cc_final: 0.8194 (mmtm) REVERT: c 183 THR cc_start: 0.8182 (m) cc_final: 0.7604 (p) REVERT: c 197 SER cc_start: 0.8808 (OUTLIER) cc_final: 0.8474 (p) REVERT: c 224 MET cc_start: 0.8402 (mmm) cc_final: 0.8153 (mmm) REVERT: c 236 GLU cc_start: 0.7741 (tp30) cc_final: 0.7505 (tp30) REVERT: c 251 THR cc_start: 0.7642 (OUTLIER) cc_final: 0.7285 (p) REVERT: c 253 ARG cc_start: 0.7851 (mtp180) cc_final: 0.7182 (mtp180) REVERT: d 27 LEU cc_start: 0.8735 (tp) cc_final: 0.8504 (tp) REVERT: d 34 LYS cc_start: 0.8433 (mmtm) cc_final: 0.8051 (mmmm) REVERT: d 62 GLN cc_start: 0.8328 (mt0) cc_final: 0.8100 (mt0) REVERT: d 68 ASP cc_start: 0.8251 (t0) cc_final: 0.7992 (t0) REVERT: d 224 MET cc_start: 0.1398 (mmp) cc_final: 0.1053 (mmp) REVERT: d 263 LYS cc_start: 0.8241 (mtpt) cc_final: 0.7679 (mtpt) REVERT: e 25 MET cc_start: 0.6017 (mtm) cc_final: 0.5778 (mtm) REVERT: e 245 MET cc_start: 0.0788 (mtm) cc_final: 0.0100 (mtm) REVERT: f 33 ASP cc_start: 0.7328 (m-30) cc_final: 0.6981 (m-30) REVERT: f 59 SER cc_start: 0.8097 (m) cc_final: 0.7729 (p) REVERT: f 79 THR cc_start: 0.7078 (OUTLIER) cc_final: 0.6839 (p) REVERT: f 126 LYS cc_start: 0.8066 (mmpt) cc_final: 0.7788 (mmmm) REVERT: f 173 MET cc_start: 0.8493 (mmp) cc_final: 0.8233 (mmm) REVERT: f 218 VAL cc_start: 0.8217 (p) cc_final: 0.7938 (m) outliers start: 49 outliers final: 37 residues processed: 423 average time/residue: 0.1139 time to fit residues: 69.2486 Evaluate side-chains 431 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 391 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 54 ASN Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 39 GLU Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 151 VAL Chi-restraints excluded: chain b residue 198 LYS Chi-restraints excluded: chain b residue 211 ILE Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain c residue 19 LYS Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 167 ASN Chi-restraints excluded: chain c residue 175 ILE Chi-restraints excluded: chain c residue 182 MET Chi-restraints excluded: chain c residue 197 SER Chi-restraints excluded: chain c residue 216 VAL Chi-restraints excluded: chain c residue 235 PHE Chi-restraints excluded: chain c residue 251 THR Chi-restraints excluded: chain c residue 288 LYS Chi-restraints excluded: chain d residue 20 THR Chi-restraints excluded: chain d residue 44 GLN Chi-restraints excluded: chain d residue 59 SER Chi-restraints excluded: chain d residue 64 LYS Chi-restraints excluded: chain d residue 141 THR Chi-restraints excluded: chain d residue 182 MET Chi-restraints excluded: chain e residue 28 VAL Chi-restraints excluded: chain f residue 23 ARG Chi-restraints excluded: chain f residue 40 LYS Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 79 THR Chi-restraints excluded: chain f residue 93 ILE Chi-restraints excluded: chain f residue 105 ASN Chi-restraints excluded: chain f residue 183 THR Chi-restraints excluded: chain f residue 234 THR Chi-restraints excluded: chain f residue 241 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 112 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 0.0270 chunk 144 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 overall best weight: 0.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 105 ASN b 110 GLN b 158 ASN b 242 GLN c 44 GLN c 237 HIS d 54 ASN ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 221 ASN ** f 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.192951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.152912 restraints weight = 23206.186| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 3.07 r_work: 0.3812 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14076 Z= 0.158 Angle : 0.596 8.524 19165 Z= 0.316 Chirality : 0.046 0.269 2088 Planarity : 0.004 0.060 2351 Dihedral : 14.447 173.171 2062 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.56 % Favored : 96.38 % Rotamer: Outliers : 3.58 % Allowed : 24.05 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.22 (0.21), residues: 1631 helix: 0.88 (0.19), residues: 751 sheet: 0.10 (0.35), residues: 218 loop : -0.58 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG b 252 TYR 0.013 0.001 TYR c 99 PHE 0.027 0.002 PHE a 124 TRP 0.036 0.002 TRP d 131 HIS 0.003 0.001 HIS f 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (14076) covalent geometry : angle 0.59620 / 0.32 (19165) hydrogen bonds : bond 0.03848 / 4.05 ( 572) hydrogen bonds : angle 4.26758 / 4.44 ( 1642) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 396 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 20 THR cc_start: 0.9017 (m) cc_final: 0.8757 (t) REVERT: a 26 GLU cc_start: 0.8083 (tt0) cc_final: 0.7832 (tm-30) REVERT: a 40 LYS cc_start: 0.8326 (ttmm) cc_final: 0.7931 (ttmt) REVERT: a 50 TYR cc_start: 0.8444 (t80) cc_final: 0.8033 (t80) REVERT: a 88 GLN cc_start: 0.6814 (mm-40) cc_final: 0.6584 (mm-40) REVERT: a 107 TYR cc_start: 0.8250 (m-80) cc_final: 0.7801 (m-80) REVERT: a 119 TRP cc_start: 0.7816 (t60) cc_final: 0.7492 (t60) REVERT: a 163 ASN cc_start: 0.8131 (t0) cc_final: 0.7870 (m-40) REVERT: a 172 LYS cc_start: 0.7982 (mmtm) cc_final: 0.7706 (mmtm) REVERT: a 204 LYS cc_start: 0.7701 (mttm) cc_final: 0.7319 (mttm) REVERT: a 258 PHE cc_start: 0.8437 (t80) cc_final: 0.8114 (t80) REVERT: a 267 LYS cc_start: 0.8773 (mttt) cc_final: 0.8538 (mmmt) REVERT: a 279 GLU cc_start: 0.7774 (pp20) cc_final: 0.7383 (pp20) REVERT: a 283 GLU cc_start: 0.6596 (mm-30) cc_final: 0.6156 (mm-30) REVERT: a 287 LYS cc_start: 0.8499 (ptmm) cc_final: 0.8144 (ptmm) REVERT: b 53 PHE cc_start: 0.8068 (m-80) cc_final: 0.7751 (m-80) REVERT: b 59 SER cc_start: 0.8016 (m) cc_final: 0.7714 (p) REVERT: b 61 SER cc_start: 0.8771 (m) cc_final: 0.8429 (p) REVERT: b 74 MET cc_start: 0.8229 (mtt) cc_final: 0.7984 (mtp) REVERT: b 171 ASP cc_start: 0.7616 (t0) cc_final: 0.7370 (t0) REVERT: b 200 ARG cc_start: 0.8528 (mtp85) cc_final: 0.8182 (mtp85) REVERT: b 243 ASP cc_start: 0.7987 (m-30) cc_final: 0.7723 (m-30) REVERT: b 260 LYS cc_start: 0.8352 (mtmt) cc_final: 0.8042 (mtpp) REVERT: c 21 SER cc_start: 0.8817 (m) cc_final: 0.8001 (p) REVERT: c 33 ASP cc_start: 0.7816 (m-30) cc_final: 0.7447 (m-30) REVERT: c 59 SER cc_start: 0.7354 (m) cc_final: 0.7065 (p) REVERT: c 68 ASP cc_start: 0.7914 (t0) cc_final: 0.7519 (t0) REVERT: c 72 LYS cc_start: 0.8675 (mttp) cc_final: 0.8409 (mttp) REVERT: c 171 ASP cc_start: 0.7809 (t70) cc_final: 0.7595 (t0) REVERT: c 183 THR cc_start: 0.8381 (m) cc_final: 0.7901 (p) REVERT: c 197 SER cc_start: 0.8803 (OUTLIER) cc_final: 0.8485 (p) REVERT: c 224 MET cc_start: 0.8502 (mmm) cc_final: 0.8161 (mmm) REVERT: c 236 GLU cc_start: 0.7783 (tp30) cc_final: 0.7569 (tp30) REVERT: c 251 THR cc_start: 0.7640 (OUTLIER) cc_final: 0.7321 (p) REVERT: c 253 ARG cc_start: 0.7907 (mtp180) cc_final: 0.7228 (mtp-110) REVERT: d 27 LEU cc_start: 0.8777 (tp) cc_final: 0.8549 (tp) REVERT: d 30 TRP cc_start: 0.8600 (t60) cc_final: 0.8190 (t60) REVERT: d 34 LYS cc_start: 0.8444 (mmtm) cc_final: 0.7973 (mmmm) REVERT: d 62 GLN cc_start: 0.8346 (mt0) cc_final: 0.8131 (mt0) REVERT: d 68 ASP cc_start: 0.8272 (t0) cc_final: 0.8028 (t0) REVERT: d 224 MET cc_start: 0.1918 (mmp) cc_final: 0.1651 (mmp) REVERT: d 263 LYS cc_start: 0.8260 (mtpt) cc_final: 0.7693 (mtpt) REVERT: e 25 MET cc_start: 0.6058 (mtm) cc_final: 0.5805 (mtm) REVERT: e 182 MET cc_start: 0.3544 (mmt) cc_final: 0.3251 (mmt) REVERT: e 224 MET cc_start: -0.2537 (mmt) cc_final: -0.6781 (tmm) REVERT: e 245 MET cc_start: 0.0900 (mtm) cc_final: 0.0064 (mtm) REVERT: f 33 ASP cc_start: 0.7394 (m-30) cc_final: 0.7033 (m-30) REVERT: f 59 SER cc_start: 0.8129 (m) cc_final: 0.7726 (p) REVERT: f 79 THR cc_start: 0.7155 (OUTLIER) cc_final: 0.6933 (p) REVERT: f 126 LYS cc_start: 0.8097 (mmpt) cc_final: 0.7810 (mmmm) REVERT: f 173 MET cc_start: 0.8492 (mmp) cc_final: 0.8217 (mmm) REVERT: f 218 VAL cc_start: 0.8166 (p) cc_final: 0.7895 (m) REVERT: f 260 LYS cc_start: 0.8066 (mptt) cc_final: 0.7846 (tptt) outliers start: 51 outliers final: 37 residues processed: 419 average time/residue: 0.1169 time to fit residues: 69.7222 Evaluate side-chains 432 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 392 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 241 LEU Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 87 GLN Chi-restraints excluded: chain b residue 151 VAL Chi-restraints excluded: chain b residue 198 LYS Chi-restraints excluded: chain b residue 211 ILE Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 62 GLN Chi-restraints excluded: chain c residue 64 LYS Chi-restraints excluded: chain c residue 167 ASN Chi-restraints excluded: chain c residue 175 ILE Chi-restraints excluded: chain c residue 182 MET Chi-restraints excluded: chain c residue 197 SER Chi-restraints excluded: chain c residue 216 VAL Chi-restraints excluded: chain c residue 235 PHE Chi-restraints excluded: chain c residue 251 THR Chi-restraints excluded: chain c residue 288 LYS Chi-restraints excluded: chain d residue 20 THR Chi-restraints excluded: chain d residue 54 ASN Chi-restraints excluded: chain d residue 64 LYS Chi-restraints excluded: chain d residue 141 THR Chi-restraints excluded: chain d residue 199 VAL Chi-restraints excluded: chain e residue 28 VAL Chi-restraints excluded: chain f residue 23 ARG Chi-restraints excluded: chain f residue 44 GLN Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 79 THR Chi-restraints excluded: chain f residue 93 ILE Chi-restraints excluded: chain f residue 105 ASN Chi-restraints excluded: chain f residue 183 THR Chi-restraints excluded: chain f residue 234 THR Chi-restraints excluded: chain f residue 241 LEU Chi-restraints excluded: chain f residue 266 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 86 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 110 optimal weight: 0.0370 chunk 163 optimal weight: 5.9990 chunk 14 optimal weight: 0.4980 chunk 118 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 105 ASN b 158 ASN b 242 GLN c 237 HIS d 54 ASN e 41 GLN ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 41 GLN ** f 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 276 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.193312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.153082 restraints weight = 23159.376| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 3.04 r_work: 0.3818 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.5750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14076 Z= 0.139 Angle : 0.594 10.966 19165 Z= 0.311 Chirality : 0.045 0.268 2088 Planarity : 0.004 0.044 2351 Dihedral : 14.410 174.083 2062 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.86 % Favored : 96.08 % Rotamer: Outliers : 2.88 % Allowed : 25.25 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.25 (0.21), residues: 1631 helix: 0.89 (0.19), residues: 752 sheet: 0.06 (0.34), residues: 230 loop : -0.55 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG b 252 TYR 0.020 0.001 TYR c 154 PHE 0.023 0.001 PHE a 124 TRP 0.033 0.001 TRP d 131 HIS 0.010 0.001 HIS f 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (14076) covalent geometry : angle 0.59374 / 0.31 (19165) hydrogen bonds : bond 0.03731 / 3.93 ( 572) hydrogen bonds : angle 4.21980 / 4.34 ( 1642) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 393 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 26 GLU cc_start: 0.8067 (tt0) cc_final: 0.7808 (tm-30) REVERT: a 40 LYS cc_start: 0.8286 (ttmm) cc_final: 0.7926 (ttmt) REVERT: a 50 TYR cc_start: 0.8390 (t80) cc_final: 0.8003 (t80) REVERT: a 88 GLN cc_start: 0.6820 (mm-40) cc_final: 0.6574 (mm-40) REVERT: a 119 TRP cc_start: 0.7728 (t60) cc_final: 0.7293 (t60) REVERT: a 163 ASN cc_start: 0.8123 (t0) cc_final: 0.7869 (m-40) REVERT: a 172 LYS cc_start: 0.7965 (mmtm) cc_final: 0.7676 (mmtm) REVERT: a 204 LYS cc_start: 0.7620 (mttm) cc_final: 0.7240 (mttm) REVERT: a 258 PHE cc_start: 0.8453 (t80) cc_final: 0.8167 (t80) REVERT: a 267 LYS cc_start: 0.8753 (mttt) cc_final: 0.8519 (mmmt) REVERT: a 279 GLU cc_start: 0.7762 (pp20) cc_final: 0.7394 (pp20) REVERT: a 287 LYS cc_start: 0.8490 (ptmm) cc_final: 0.8132 (ptmm) REVERT: b 53 PHE cc_start: 0.8141 (m-80) cc_final: 0.7836 (m-80) REVERT: b 59 SER cc_start: 0.8013 (m) cc_final: 0.7766 (p) REVERT: b 61 SER cc_start: 0.8729 (m) cc_final: 0.8435 (p) REVERT: b 74 MET cc_start: 0.8274 (mtt) cc_final: 0.8020 (mtp) REVERT: b 171 ASP cc_start: 0.7609 (t0) cc_final: 0.7319 (t0) REVERT: b 200 ARG cc_start: 0.8530 (mtp85) cc_final: 0.8195 (mtp85) REVERT: b 260 LYS cc_start: 0.8345 (mtmt) cc_final: 0.8038 (mtpp) REVERT: c 21 SER cc_start: 0.8776 (m) cc_final: 0.8058 (p) REVERT: c 33 ASP cc_start: 0.7715 (m-30) cc_final: 0.7395 (m-30) REVERT: c 59 SER cc_start: 0.7360 (m) cc_final: 0.7079 (p) REVERT: c 68 ASP cc_start: 0.7909 (t0) cc_final: 0.7537 (t0) REVERT: c 72 LYS cc_start: 0.8611 (mttp) cc_final: 0.8349 (mttp) REVERT: c 171 ASP cc_start: 0.7753 (t70) cc_final: 0.7542 (t0) REVERT: c 183 THR cc_start: 0.8440 (m) cc_final: 0.7951 (p) REVERT: c 197 SER cc_start: 0.8763 (OUTLIER) cc_final: 0.8448 (p) REVERT: c 224 MET cc_start: 0.8486 (mmm) cc_final: 0.8189 (mmm) REVERT: c 253 ARG cc_start: 0.7867 (mtp180) cc_final: 0.7189 (mtp180) REVERT: d 27 LEU cc_start: 0.8808 (tp) cc_final: 0.8572 (tp) REVERT: d 30 TRP cc_start: 0.8604 (t60) cc_final: 0.8202 (t60) REVERT: d 34 LYS cc_start: 0.8449 (mmtm) cc_final: 0.8056 (mmmm) REVERT: d 68 ASP cc_start: 0.8286 (t0) cc_final: 0.8057 (t0) REVERT: d 263 LYS cc_start: 0.8271 (mtpt) cc_final: 0.7675 (mtpt) REVERT: e 25 MET cc_start: 0.6020 (mtm) cc_final: 0.5775 (mtm) REVERT: e 224 MET cc_start: -0.2201 (mmt) cc_final: -0.6643 (tmm) REVERT: e 245 MET cc_start: 0.0801 (mtm) cc_final: -0.0079 (mtm) REVERT: f 33 ASP cc_start: 0.7355 (m-30) cc_final: 0.7008 (m-30) REVERT: f 41 GLN cc_start: 0.8268 (mt0) cc_final: 0.8017 (mt0) REVERT: f 59 SER cc_start: 0.8119 (m) cc_final: 0.7737 (p) REVERT: f 78 LYS cc_start: 0.8583 (mmmm) cc_final: 0.8229 (mmtp) REVERT: f 79 THR cc_start: 0.7114 (OUTLIER) cc_final: 0.6909 (p) REVERT: f 100 LYS cc_start: 0.8788 (mtpp) cc_final: 0.8248 (ptpp) REVERT: f 126 LYS cc_start: 0.8074 (mmpt) cc_final: 0.7808 (mmmm) REVERT: f 173 MET cc_start: 0.8510 (mmp) cc_final: 0.8268 (mmm) REVERT: f 218 VAL cc_start: 0.8279 (p) cc_final: 0.7994 (m) REVERT: f 260 LYS cc_start: 0.7986 (mptt) cc_final: 0.7785 (tptt) outliers start: 41 outliers final: 36 residues processed: 412 average time/residue: 0.1089 time to fit residues: 64.3002 Evaluate side-chains 426 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 388 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 241 LEU Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 39 GLU Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 87 GLN Chi-restraints excluded: chain b residue 151 VAL Chi-restraints excluded: chain b residue 198 LYS Chi-restraints excluded: chain b residue 211 ILE Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 62 GLN Chi-restraints excluded: chain c residue 167 ASN Chi-restraints excluded: chain c residue 175 ILE Chi-restraints excluded: chain c residue 182 MET Chi-restraints excluded: chain c residue 197 SER Chi-restraints excluded: chain c residue 216 VAL Chi-restraints excluded: chain c residue 235 PHE Chi-restraints excluded: chain c residue 251 THR Chi-restraints excluded: chain c residue 288 LYS Chi-restraints excluded: chain d residue 20 THR Chi-restraints excluded: chain d residue 44 GLN Chi-restraints excluded: chain d residue 141 THR Chi-restraints excluded: chain d residue 199 VAL Chi-restraints excluded: chain e residue 28 VAL Chi-restraints excluded: chain f residue 23 ARG Chi-restraints excluded: chain f residue 44 GLN Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 79 THR Chi-restraints excluded: chain f residue 93 ILE Chi-restraints excluded: chain f residue 105 ASN Chi-restraints excluded: chain f residue 183 THR Chi-restraints excluded: chain f residue 234 THR Chi-restraints excluded: chain f residue 241 LEU Chi-restraints excluded: chain f residue 266 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 49 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 75 optimal weight: 0.0030 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 158 ASN b 242 GLN c 237 HIS ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.192319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.152292 restraints weight = 23239.886| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 3.08 r_work: 0.3802 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.5997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14076 Z= 0.144 Angle : 0.608 11.469 19165 Z= 0.320 Chirality : 0.046 0.272 2088 Planarity : 0.004 0.045 2351 Dihedral : 14.400 174.197 2062 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.74 % Favored : 96.20 % Rotamer: Outliers : 2.66 % Allowed : 25.74 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.22 (0.21), residues: 1631 helix: 0.92 (0.19), residues: 752 sheet: 0.01 (0.35), residues: 217 loop : -0.62 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG b 252 TYR 0.015 0.001 TYR c 154 PHE 0.020 0.002 PHE a 124 TRP 0.029 0.001 TRP d 131 HIS 0.004 0.001 HIS c 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (14076) covalent geometry : angle 0.60806 / 0.32 (19165) hydrogen bonds : bond 0.03705 / 3.90 ( 572) hydrogen bonds : angle 4.25261 / 4.36 ( 1642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3710.81 seconds wall clock time: 64 minutes 12.92 seconds (3852.92 seconds total)