Starting phenix.real_space_refine on Wed Mar 4 14:12:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s10_54429/03_2026/9s10_54429_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s10_54429/03_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_54429/03_2026/9s10_54429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s10_54429/03_2026/9s10_54429.map" model { file = "/net/cci-nas-00/data/ceres_data/9s10_54429/03_2026/9s10_54429_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s10_54429/03_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-dev-5986/lib/python3.9/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: 3.67, per 1000 atoms: 0.27 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: 1.19 Conformation dependent library (CDL) restraints added in 672.9 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: 1.92 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: 2.44 Time building geometry restraints manager: 1.59 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=" CB ASN e 158 " pdb=" CG ASN e 158 " ideal model delta sigma weight residual 1.516 1.602 -0.086 2.50e-02 1.60e+03 1.17e+01 bond pdb=" N ASP c 12 " pdb=" CA ASP c 12 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.44e+00 bond pdb=" N ASP f 12 " pdb=" CA ASP f 12 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.34e+00 bond pdb=" N ASP b 12 " pdb=" CA ASP b 12 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.30e+00 bond pdb=" N ASP a 12 " pdb=" CA ASP a 12 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.16e+00 ... (remaining 14071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 18626 2.32 - 4.65: 442 4.65 - 6.97: 55 6.97 - 9.30: 16 9.30 - 11.62: 26 Bond angle restraints: 19165 Sorted by residual: angle pdb=" N ALA d 48 " pdb=" CA ALA d 48 " pdb=" C ALA d 48 " ideal model delta sigma weight residual 112.87 117.84 -4.97 1.20e+00 6.94e-01 1.71e+01 angle pdb=" C2' DC H 29 " pdb=" C1' DC H 29 " pdb=" N1 DC H 29 " ideal model delta sigma weight residual 113.50 119.67 -6.17 1.50e+00 4.44e-01 1.69e+01 angle pdb=" O3' DG H 22 " pdb=" P DC H 23 " pdb=" OP1 DC H 23 " ideal model delta sigma weight residual 108.00 119.62 -11.62 3.00e+00 1.11e-01 1.50e+01 angle pdb=" N TRP e 159 " pdb=" CA TRP e 159 " pdb=" C TRP e 159 " ideal model delta sigma weight residual 110.80 118.88 -8.08 2.13e+00 2.20e-01 1.44e+01 angle pdb=" OP1 DA H 94 " pdb=" P DA H 94 " pdb=" OP2 DA H 94 " ideal model delta sigma weight residual 120.00 109.16 10.84 3.00e+00 1.11e-01 1.31e+01 ... (remaining 19160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.42: 8007 33.42 - 66.85: 248 66.85 - 100.27: 46 100.27 - 133.70: 2 133.70 - 167.12: 1 Dihedral angle restraints: 8304 sinusoidal: 3497 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 8301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1811 0.084 - 0.168: 251 0.168 - 0.252: 7 0.252 - 0.335: 4 0.335 - 0.419: 19 Chirality restraints: 2092 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 2.35 -2.76 -0.42 2.00e-01 2.50e+01 4.39e+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 2.35 -2.76 -0.42 2.00e-01 2.50e+01 4.34e+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 2.35 -2.76 -0.42 2.00e-01 2.50e+01 4.32e+00 ... (remaining 2089 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: 3.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.970 Find NCS groups from input model: 0.350 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 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 : 0.004 0.086 14076 Z= 0.191 Angle : 0.963 11.622 19165 Z= 0.517 Chirality : 0.064 0.419 2092 Planarity : 0.009 0.123 2351 Dihedral : 16.821 167.122 5186 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 covalent geometry : bond 0.00385 (14076) covalent geometry : angle 0.96318 (19165) hydrogen bonds : bond 0.15516 ( 572) hydrogen bonds : angle 6.35857 ( 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 : 0.500 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: 0.1187 time to fit residues: 69.1874 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 : 0.431 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4516 r_free = 0.4516 target = 0.201324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.161664 restraints weight = 23814.316| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 3.16 r_work: 0.3929 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 14076 Z= 0.189 Angle : 0.692 9.592 19165 Z= 0.384 Chirality : 0.049 0.201 2092 Planarity : 0.004 0.045 2351 Dihedral : 14.908 164.697 2044 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.79 % Allowed : 14.17 % Favored : 82.05 % 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: 0.03 (0.20), residues: 1631 helix: 0.36 (0.19), residues: 726 sheet: 0.40 (0.34), residues: 231 loop : -0.35 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 200 TYR 0.020 0.002 TYR b 99 PHE 0.024 0.002 PHE f 246 TRP 0.028 0.002 TRP f 176 HIS 0.005 0.001 HIS b 282 Details of bonding type rmsd covalent geometry : bond 0.00409 (14076) covalent geometry : angle 0.69223 (19165) hydrogen bonds : bond 0.04499 ( 572) hydrogen bonds : angle 4.67843 ( 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 461 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 407 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 20 THR cc_start: 0.9002 (m) cc_final: 0.8725 (t) REVERT: a 32 VAL cc_start: 0.8571 (t) cc_final: 0.8305 (m) REVERT: a 83 TYR cc_start: 0.7530 (m-80) cc_final: 0.7135 (m-80) REVERT: a 88 GLN cc_start: 0.6648 (mm-40) cc_final: 0.6287 (mm-40) REVERT: a 153 PHE cc_start: 0.8594 (m-80) cc_final: 0.8304 (m-80) REVERT: a 170 VAL cc_start: 0.8137 (t) cc_final: 0.7774 (m) REVERT: a 177 TRP cc_start: 0.7662 (t60) cc_final: 0.7447 (t60) REVERT: a 194 LEU cc_start: 0.8333 (mt) cc_final: 0.8129 (mt) REVERT: a 267 LYS cc_start: 0.8833 (mttt) cc_final: 0.8599 (mttp) REVERT: a 275 ASP cc_start: 0.8123 (m-30) cc_final: 0.7790 (m-30) REVERT: a 283 GLU cc_start: 0.6068 (mm-30) cc_final: 0.5643 (tm-30) REVERT: b 59 SER cc_start: 0.7620 (m) cc_final: 0.7347 (p) REVERT: b 74 MET cc_start: 0.7644 (mtt) cc_final: 0.7356 (mtp) REVERT: b 171 ASP cc_start: 0.7348 (t0) cc_final: 0.7009 (t0) REVERT: b 179 GLU cc_start: 0.8241 (mm-30) cc_final: 0.8022 (mm-30) REVERT: b 224 MET cc_start: 0.8012 (mmm) cc_final: 0.7738 (mmm) REVERT: c 21 SER cc_start: 0.8116 (m) cc_final: 0.7219 (p) REVERT: c 74 MET cc_start: 0.8222 (mtp) cc_final: 0.8005 (mtp) REVERT: c 175 ILE cc_start: 0.7608 (mt) cc_final: 0.7268 (mt) REVERT: c 198 LYS cc_start: 0.8053 (mttt) cc_final: 0.7771 (mttt) REVERT: c 224 MET cc_start: 0.7974 (mmm) cc_final: 0.7736 (mmm) REVERT: c 253 ARG cc_start: 0.7238 (mtp180) cc_final: 0.6952 (mtt-85) REVERT: c 264 GLN cc_start: 0.7474 (tp40) cc_final: 0.7087 (tp40) REVERT: c 268 ASP cc_start: 0.7212 (m-30) cc_final: 0.6146 (m-30) REVERT: c 271 ARG cc_start: 0.8038 (tpt-90) cc_final: 0.7802 (tpp80) REVERT: d 21 SER cc_start: 0.7827 (m) cc_final: 0.7343 (p) REVERT: d 34 LYS cc_start: 0.8422 (mmtm) cc_final: 0.8156 (mmmm) REVERT: d 263 LYS cc_start: 0.8257 (mtpt) cc_final: 0.7781 (mtpt) REVERT: d 267 LYS cc_start: 0.6961 (mttm) cc_final: 0.6685 (mttm) REVERT: e 182 MET cc_start: 0.0930 (mmm) cc_final: 0.0716 (mmt) REVERT: f 33 ASP cc_start: 0.7269 (m-30) cc_final: 0.7026 (m-30) REVERT: f 47 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: f 59 SER cc_start: 0.7971 (m) cc_final: 0.7700 (p) REVERT: f 78 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8521 (mmmm) REVERT: f 93 ILE cc_start: 0.8213 (tp) cc_final: 0.7952 (tp) REVERT: f 100 LYS cc_start: 0.8891 (ttmm) cc_final: 0.8643 (ttmm) REVERT: f 173 MET cc_start: 0.8488 (mmp) cc_final: 0.8237 (mmm) REVERT: f 218 VAL cc_start: 0.8106 (p) cc_final: 0.7808 (m) outliers start: 54 outliers final: 30 residues processed: 428 average time/residue: 0.1226 time to fit residues: 74.6994 Evaluate side-chains 409 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 378 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 137 THR Chi-restraints excluded: chain a residue 199 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 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 61 SER Chi-restraints excluded: chain d residue 63 ILE 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 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: 1.9990 chunk 24 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 81 optimal weight: 0.0170 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 0.0870 chunk 110 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 39 optimal weight: 0.3980 chunk 101 optimal weight: 4.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 44 GLN ** a 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 238 GLN b 242 GLN b 282 HIS c 105 ASN ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 238 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.201115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.161741 restraints weight = 23997.049| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 3.15 r_work: 0.3927 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14076 Z= 0.128 Angle : 0.586 10.718 19165 Z= 0.311 Chirality : 0.045 0.169 2092 Planarity : 0.003 0.035 2351 Dihedral : 14.610 172.612 2028 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.70 % Favored : 97.24 % Rotamer: Outliers : 2.52 % Allowed : 20.62 % Favored : 76.86 % 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: 0.40 (0.21), residues: 1631 helix: 0.79 (0.19), residues: 736 sheet: 0.56 (0.35), residues: 225 loop : -0.32 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG e 23 TYR 0.020 0.001 TYR c 99 PHE 0.016 0.001 PHE b 53 TRP 0.015 0.001 TRP a 119 HIS 0.005 0.000 HIS b 282 Details of bonding type rmsd covalent geometry : bond 0.00279 (14076) covalent geometry : angle 0.58558 (19165) hydrogen bonds : bond 0.03895 ( 572) hydrogen bonds : angle 4.39392 ( 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 429 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 393 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 20 THR cc_start: 0.8954 (m) cc_final: 0.8671 (t) REVERT: a 26 GLU cc_start: 0.8216 (tt0) cc_final: 0.7985 (tm-30) REVERT: a 52 SER cc_start: 0.8176 (p) cc_final: 0.7655 (t) REVERT: a 88 GLN cc_start: 0.6594 (mm-40) cc_final: 0.6260 (mm-40) REVERT: a 107 TYR cc_start: 0.8175 (m-80) cc_final: 0.7736 (m-80) REVERT: a 170 VAL cc_start: 0.8264 (t) cc_final: 0.7865 (m) REVERT: a 221 ASN cc_start: 0.7746 (t0) cc_final: 0.7539 (t0) REVERT: a 267 LYS cc_start: 0.8791 (mttt) cc_final: 0.8524 (mmmm) REVERT: a 275 ASP cc_start: 0.8064 (m-30) cc_final: 0.7751 (m-30) REVERT: a 283 GLU cc_start: 0.6192 (mm-30) cc_final: 0.5771 (tm-30) REVERT: b 59 SER cc_start: 0.7579 (m) cc_final: 0.7204 (p) REVERT: b 171 ASP cc_start: 0.7406 (t0) cc_final: 0.7077 (t0) REVERT: b 200 ARG cc_start: 0.7905 (mtp85) cc_final: 0.7594 (mtp85) REVERT: b 224 MET cc_start: 0.8003 (mmm) cc_final: 0.7404 (mpp) REVERT: c 21 SER cc_start: 0.8134 (m) cc_final: 0.7212 (p) REVERT: c 103 GLU cc_start: 0.7710 (tt0) cc_final: 0.7327 (pp20) REVERT: c 171 ASP cc_start: 0.7571 (t70) cc_final: 0.7243 (t0) REVERT: c 175 ILE cc_start: 0.7745 (mt) cc_final: 0.7471 (mt) REVERT: c 198 LYS cc_start: 0.8137 (mttt) cc_final: 0.7847 (mttt) REVERT: c 253 ARG cc_start: 0.7300 (mtp180) cc_final: 0.7080 (mtt-85) REVERT: c 271 ARG cc_start: 0.8067 (tpt-90) cc_final: 0.7812 (tpp80) REVERT: d 21 SER cc_start: 0.7910 (m) cc_final: 0.7548 (p) REVERT: d 34 LYS cc_start: 0.8363 (mmtm) cc_final: 0.8032 (mmmm) REVERT: d 45 GLU cc_start: 0.7231 (tp30) cc_final: 0.6926 (tp30) REVERT: d 263 LYS cc_start: 0.8227 (mtpt) cc_final: 0.7756 (mtpt) REVERT: d 267 LYS cc_start: 0.7047 (mttm) cc_final: 0.6766 (mttm) REVERT: e 173 MET cc_start: 0.1994 (mtp) cc_final: 0.1500 (ptp) REVERT: e 224 MET cc_start: -0.2992 (mmt) cc_final: -0.5219 (tmm) REVERT: f 27 LEU cc_start: 0.8815 (tp) cc_final: 0.8614 (tt) REVERT: f 33 ASP cc_start: 0.7159 (m-30) cc_final: 0.6850 (m-30) REVERT: f 41 GLN cc_start: 0.8388 (mt0) cc_final: 0.8112 (mt0) REVERT: f 47 GLN cc_start: 0.8303 (mt0) cc_final: 0.8069 (tt0) REVERT: f 59 SER cc_start: 0.7947 (m) cc_final: 0.7701 (p) REVERT: f 78 LYS cc_start: 0.8728 (mmtt) cc_final: 0.8470 (mmmm) REVERT: f 93 ILE cc_start: 0.8192 (tp) cc_final: 0.7906 (tp) REVERT: f 100 LYS cc_start: 0.8861 (ttmm) cc_final: 0.8589 (ttmm) REVERT: f 153 PHE cc_start: 0.8000 (m-80) cc_final: 0.7751 (m-80) REVERT: f 173 MET cc_start: 0.8453 (mmp) cc_final: 0.8219 (mmm) REVERT: f 218 VAL cc_start: 0.8228 (p) cc_final: 0.7908 (m) outliers start: 36 outliers final: 25 residues processed: 408 average time/residue: 0.1245 time to fit residues: 72.9641 Evaluate side-chains 405 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 380 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 186 VAL Chi-restraints excluded: chain a residue 197 SER 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 216 VAL Chi-restraints excluded: chain c residue 27 LEU 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 182 MET Chi-restraints excluded: chain c residue 197 SER Chi-restraints excluded: chain d residue 20 THR Chi-restraints excluded: chain d residue 44 GLN Chi-restraints excluded: chain d residue 61 SER 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 105 ASN 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: 2.9990 chunk 120 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 58 ASN ** a 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 88 GLN c 105 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 f 238 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.195449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.155535 restraints weight = 23270.218| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 3.05 r_work: 0.3852 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 14076 Z= 0.185 Angle : 0.617 8.993 19165 Z= 0.331 Chirality : 0.047 0.181 2092 Planarity : 0.004 0.069 2351 Dihedral : 14.399 171.261 2026 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.94 % Favored : 97.00 % Rotamer: Outliers : 4.63 % Allowed : 19.71 % Favored : 75.67 % 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: 0.18 (0.21), residues: 1631 helix: 0.75 (0.19), residues: 742 sheet: 0.34 (0.35), residues: 225 loop : -0.57 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 200 TYR 0.021 0.002 TYR b 99 PHE 0.019 0.002 PHE a 248 TRP 0.020 0.002 TRP a 119 HIS 0.004 0.001 HIS a 237 Details of bonding type rmsd covalent geometry : bond 0.00416 (14076) covalent geometry : angle 0.61713 (19165) hydrogen bonds : bond 0.04237 ( 572) hydrogen bonds : angle 4.38614 ( 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 491 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 425 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 20 THR cc_start: 0.8990 (m) cc_final: 0.8754 (t) REVERT: a 26 GLU cc_start: 0.8119 (tt0) cc_final: 0.7877 (tm-30) REVERT: a 52 SER cc_start: 0.8453 (p) cc_final: 0.8101 (t) REVERT: a 54 ASN cc_start: 0.8038 (OUTLIER) cc_final: 0.7699 (m-40) REVERT: a 88 GLN cc_start: 0.6677 (mm-40) cc_final: 0.6400 (mm-40) REVERT: a 107 TYR cc_start: 0.8282 (m-80) cc_final: 0.7849 (m-80) REVERT: a 170 VAL cc_start: 0.8652 (t) cc_final: 0.8350 (m) REVERT: a 172 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7703 (mmtm) REVERT: a 204 LYS cc_start: 0.7569 (mttm) cc_final: 0.7237 (mttm) REVERT: a 263 LYS cc_start: 0.8479 (ttpt) cc_final: 0.8260 (mtpp) REVERT: a 275 ASP cc_start: 0.8184 (m-30) cc_final: 0.7868 (m-30) REVERT: a 283 GLU cc_start: 0.6365 (mm-30) cc_final: 0.5953 (tm-30) REVERT: a 287 LYS cc_start: 0.8306 (ptmm) cc_final: 0.8003 (ptmm) REVERT: b 59 SER cc_start: 0.7856 (m) cc_final: 0.7482 (p) REVERT: b 61 SER cc_start: 0.8826 (m) cc_final: 0.8364 (p) REVERT: b 99 TYR cc_start: 0.8337 (t80) cc_final: 0.8115 (t80) REVERT: b 100 LYS cc_start: 0.8409 (mtmm) cc_final: 0.7932 (mttm) REVERT: b 145 GLU cc_start: 0.7422 (tt0) cc_final: 0.7044 (tt0) REVERT: b 153 PHE cc_start: 0.8359 (m-80) cc_final: 0.8004 (m-80) REVERT: b 171 ASP cc_start: 0.7501 (t0) cc_final: 0.7198 (t0) REVERT: b 200 ARG cc_start: 0.8365 (mtp85) cc_final: 0.8154 (mtp85) REVERT: b 264 GLN cc_start: 0.7926 (tp40) cc_final: 0.7662 (tp40) REVERT: c 33 ASP cc_start: 0.7631 (m-30) cc_final: 0.7283 (m-30) REVERT: c 171 ASP cc_start: 0.7839 (t70) cc_final: 0.7513 (t0) REVERT: c 173 MET cc_start: 0.8214 (mtm) cc_final: 0.7996 (mtt) REVERT: c 183 THR cc_start: 0.7820 (p) cc_final: 0.7601 (p) REVERT: c 197 SER cc_start: 0.8687 (OUTLIER) cc_final: 0.8377 (p) REVERT: c 253 ARG cc_start: 0.7759 (mtp180) cc_final: 0.7473 (mtp-110) REVERT: d 27 LEU cc_start: 0.8670 (tp) cc_final: 0.8441 (tp) REVERT: d 30 TRP cc_start: 0.8542 (t60) cc_final: 0.8192 (t60) REVERT: d 34 LYS cc_start: 0.8434 (mmtm) cc_final: 0.8072 (mmmm) REVERT: d 182 MET cc_start: 0.2482 (OUTLIER) cc_final: 0.2036 (ptp) REVERT: d 263 LYS cc_start: 0.8251 (mtpt) cc_final: 0.7740 (mtpt) REVERT: d 267 LYS cc_start: 0.7254 (mttm) cc_final: 0.6962 (mttm) REVERT: e 224 MET cc_start: -0.2821 (mmt) cc_final: -0.5147 (tmm) REVERT: f 33 ASP cc_start: 0.7289 (m-30) cc_final: 0.6924 (m-30) REVERT: f 41 GLN cc_start: 0.8313 (mt0) cc_final: 0.8029 (mt0) REVERT: f 47 GLN cc_start: 0.8519 (mt0) cc_final: 0.8314 (tt0) REVERT: f 59 SER cc_start: 0.8160 (m) cc_final: 0.7839 (p) REVERT: f 78 LYS cc_start: 0.8695 (mmtt) cc_final: 0.8432 (mmmm) REVERT: f 100 LYS cc_start: 0.8807 (ttmm) cc_final: 0.8553 (ttmm) REVERT: f 173 MET cc_start: 0.8449 (mmp) cc_final: 0.8189 (mmm) REVERT: f 177 TRP cc_start: 0.7469 (t-100) cc_final: 0.7241 (t60) REVERT: f 218 VAL cc_start: 0.8249 (p) cc_final: 0.7915 (m) REVERT: f 284 PHE cc_start: 0.7839 (t80) cc_final: 0.7198 (t80) outliers start: 66 outliers final: 42 residues processed: 458 average time/residue: 0.1266 time to fit residues: 82.3374 Evaluate side-chains 447 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 401 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 54 ASN Chi-restraints excluded: chain a residue 172 LYS 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 217 ILE 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 87 GLN Chi-restraints excluded: chain b residue 90 VAL Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain b residue 137 THR 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 20 THR Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 37 THR Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 167 ASN 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 222 THR 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 52 SER Chi-restraints excluded: chain d residue 59 SER Chi-restraints excluded: chain d residue 141 THR Chi-restraints excluded: chain d residue 182 MET 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 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 277 VAL 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: 0.5980 chunk 30 optimal weight: 0.9990 chunk 126 optimal weight: 0.0370 chunk 140 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 95 optimal weight: 0.0970 chunk 92 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 64 optimal weight: 0.0980 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 105 ASN ** a 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 221 ASN b 110 GLN b 221 ASN b 238 GLN b 242 GLN c 105 ASN d 41 GLN d 167 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 f 238 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.196859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.157025 restraints weight = 23407.856| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 3.05 r_work: 0.3865 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14076 Z= 0.119 Angle : 0.560 8.982 19165 Z= 0.295 Chirality : 0.044 0.144 2092 Planarity : 0.003 0.049 2351 Dihedral : 14.295 173.879 2026 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.88 % Favored : 97.06 % Rotamer: Outliers : 3.79 % Allowed : 22.23 % Favored : 73.98 % 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: 0.37 (0.21), residues: 1631 helix: 0.89 (0.19), residues: 745 sheet: 0.44 (0.35), residues: 226 loop : -0.45 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 23 TYR 0.017 0.001 TYR b 99 PHE 0.028 0.001 PHE b 164 TRP 0.026 0.001 TRP b 177 HIS 0.002 0.000 HIS b 149 Details of bonding type rmsd covalent geometry : bond 0.00266 (14076) covalent geometry : angle 0.55999 (19165) hydrogen bonds : bond 0.03407 ( 572) hydrogen bonds : angle 4.16780 ( 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 459 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 405 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 20 THR cc_start: 0.8956 (m) cc_final: 0.8756 (t) REVERT: a 26 GLU cc_start: 0.8076 (tt0) cc_final: 0.7811 (tm-30) REVERT: a 40 LYS cc_start: 0.8123 (ttmm) cc_final: 0.7894 (ttmt) REVERT: a 88 GLN cc_start: 0.6766 (mm-40) cc_final: 0.6480 (mm-40) REVERT: a 107 TYR cc_start: 0.8227 (m-80) cc_final: 0.7775 (m-80) REVERT: a 170 VAL cc_start: 0.8584 (t) cc_final: 0.8354 (m) REVERT: a 172 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7711 (mmtm) REVERT: a 204 LYS cc_start: 0.7559 (mttm) cc_final: 0.7179 (mttm) REVERT: a 263 LYS cc_start: 0.8380 (ttpt) cc_final: 0.8113 (mtpp) REVERT: a 267 LYS cc_start: 0.8800 (mttt) cc_final: 0.8479 (mmmm) REVERT: a 283 GLU cc_start: 0.6478 (mm-30) cc_final: 0.6050 (tm-30) REVERT: a 287 LYS cc_start: 0.8340 (ptmm) cc_final: 0.8041 (ptmm) REVERT: b 59 SER cc_start: 0.7746 (m) cc_final: 0.7445 (p) REVERT: b 61 SER cc_start: 0.8827 (m) cc_final: 0.8384 (p) REVERT: b 94 SER cc_start: 0.8744 (OUTLIER) cc_final: 0.8461 (p) REVERT: b 100 LYS cc_start: 0.8315 (mtmm) cc_final: 0.7833 (mtmm) REVERT: b 145 GLU cc_start: 0.7354 (tt0) cc_final: 0.6995 (tt0) REVERT: b 153 PHE cc_start: 0.8335 (m-80) cc_final: 0.8041 (m-80) REVERT: b 171 ASP cc_start: 0.7519 (t0) cc_final: 0.7211 (t0) REVERT: b 200 ARG cc_start: 0.8400 (mtp85) cc_final: 0.8031 (mtp-110) REVERT: c 21 SER cc_start: 0.8683 (m) cc_final: 0.7849 (p) REVERT: c 32 VAL cc_start: 0.8585 (t) cc_final: 0.8354 (m) REVERT: c 33 ASP cc_start: 0.7590 (m-30) cc_final: 0.7176 (m-30) REVERT: c 59 SER cc_start: 0.7114 (m) cc_final: 0.6815 (p) REVERT: c 68 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7383 (t0) REVERT: c 143 ILE cc_start: 0.7938 (mt) cc_final: 0.7171 (mm) REVERT: c 171 ASP cc_start: 0.7767 (t70) cc_final: 0.7432 (t0) REVERT: c 172 LYS cc_start: 0.8402 (mmtm) cc_final: 0.8167 (mmtm) REVERT: c 183 THR cc_start: 0.7918 (p) cc_final: 0.7679 (p) REVERT: c 197 SER cc_start: 0.8757 (OUTLIER) cc_final: 0.8466 (p) REVERT: c 200 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7815 (mtp-110) REVERT: d 27 LEU cc_start: 0.8672 (tp) cc_final: 0.8465 (tp) REVERT: d 34 LYS cc_start: 0.8369 (mmtm) cc_final: 0.8048 (mmmm) REVERT: d 45 GLU cc_start: 0.7332 (tp30) cc_final: 0.7001 (tp30) REVERT: d 54 ASN cc_start: 0.8552 (m-40) cc_final: 0.8303 (m-40) REVERT: d 68 ASP cc_start: 0.8149 (t0) cc_final: 0.7896 (t0) REVERT: d 263 LYS cc_start: 0.8230 (mtpt) cc_final: 0.7645 (mtpt) REVERT: e 60 ARG cc_start: 0.7251 (ttp-170) cc_final: 0.7024 (ttp-110) REVERT: e 224 MET cc_start: -0.2630 (mmt) cc_final: -0.5091 (tmm) REVERT: e 245 MET cc_start: 0.0848 (mtm) cc_final: -0.0146 (mtm) REVERT: f 33 ASP cc_start: 0.7130 (m-30) cc_final: 0.6765 (m-30) REVERT: f 34 LYS cc_start: 0.8601 (mmmm) cc_final: 0.8376 (mmmm) REVERT: f 41 GLN cc_start: 0.8301 (mt0) cc_final: 0.7981 (mt0) REVERT: f 47 GLN cc_start: 0.8586 (mt0) cc_final: 0.8339 (tt0) REVERT: f 59 SER cc_start: 0.8114 (m) cc_final: 0.7753 (p) REVERT: f 78 LYS cc_start: 0.8648 (mmtt) cc_final: 0.8406 (mmmm) REVERT: f 100 LYS cc_start: 0.8807 (ttmm) cc_final: 0.8565 (ttmm) REVERT: f 101 ILE cc_start: 0.8710 (tt) cc_final: 0.8190 (pt) REVERT: f 173 MET cc_start: 0.8425 (mmp) cc_final: 0.8160 (mmm) REVERT: f 218 VAL cc_start: 0.8235 (p) cc_final: 0.7958 (m) REVERT: f 264 GLN cc_start: 0.7711 (tp-100) cc_final: 0.7505 (tp-100) outliers start: 54 outliers final: 33 residues processed: 430 average time/residue: 0.1229 time to fit residues: 75.0875 Evaluate side-chains 421 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 383 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 138 THR Chi-restraints excluded: chain a residue 172 LYS Chi-restraints excluded: chain a residue 197 SER 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 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 b residue 245 MET Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 68 ASP Chi-restraints excluded: chain c residue 167 ASN Chi-restraints excluded: chain c residue 182 MET Chi-restraints excluded: chain c residue 189 SER Chi-restraints excluded: chain c residue 197 SER Chi-restraints excluded: chain c residue 200 ARG Chi-restraints excluded: chain c residue 235 PHE Chi-restraints excluded: chain c residue 251 THR Chi-restraints excluded: chain d residue 18 SER Chi-restraints excluded: chain d residue 20 THR Chi-restraints excluded: chain d residue 44 GLN Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain f residue 23 ARG Chi-restraints excluded: chain f residue 40 LYS 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 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: 0.4980 chunk 109 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 62 GLN ** a 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 105 ASN b 238 GLN b 242 GLN c 105 ASN ** d 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.192531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.152131 restraints weight = 23082.594| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 3.04 r_work: 0.3802 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.5557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14076 Z= 0.175 Angle : 0.603 10.068 19165 Z= 0.322 Chirality : 0.046 0.149 2092 Planarity : 0.004 0.044 2351 Dihedral : 14.264 172.686 2026 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.69 % Rotamer: Outliers : 3.93 % Allowed : 22.44 % Favored : 73.63 % 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: 0.18 (0.21), residues: 1631 helix: 0.77 (0.19), residues: 741 sheet: 0.19 (0.34), residues: 234 loop : -0.55 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 200 TYR 0.014 0.001 TYR c 83 PHE 0.018 0.002 PHE e 246 TRP 0.019 0.002 TRP b 177 HIS 0.004 0.001 HIS a 237 Details of bonding type rmsd covalent geometry : bond 0.00389 (14076) covalent geometry : angle 0.60256 (19165) hydrogen bonds : bond 0.04152 ( 572) hydrogen bonds : angle 4.32771 ( 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 467 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 411 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 26 GLU cc_start: 0.8008 (tt0) cc_final: 0.7768 (tm-30) REVERT: a 40 LYS cc_start: 0.8392 (ttmm) cc_final: 0.8071 (ttmt) REVERT: a 88 GLN cc_start: 0.6815 (mm-40) cc_final: 0.6553 (mm-40) REVERT: a 107 TYR cc_start: 0.8245 (m-80) cc_final: 0.7847 (m-80) REVERT: a 119 TRP cc_start: 0.7888 (t60) cc_final: 0.7419 (t60) REVERT: a 163 ASN cc_start: 0.8160 (t0) cc_final: 0.7887 (m-40) REVERT: a 170 VAL cc_start: 0.8682 (t) cc_final: 0.8424 (m) REVERT: a 172 LYS cc_start: 0.8061 (mmtm) cc_final: 0.7829 (mmtm) REVERT: a 204 LYS cc_start: 0.7668 (mttm) cc_final: 0.7284 (mttm) REVERT: a 258 PHE cc_start: 0.8357 (t80) cc_final: 0.8109 (t80) REVERT: a 283 GLU cc_start: 0.6461 (mm-30) cc_final: 0.6051 (tm-30) REVERT: a 287 LYS cc_start: 0.8473 (ptmm) cc_final: 0.8158 (ptmm) REVERT: b 59 SER cc_start: 0.8045 (m) cc_final: 0.7748 (p) REVERT: b 61 SER cc_start: 0.8799 (m) cc_final: 0.8472 (p) REVERT: b 62 GLN cc_start: 0.8150 (mt0) cc_final: 0.7945 (tt0) REVERT: b 94 SER cc_start: 0.8727 (OUTLIER) cc_final: 0.8363 (p) REVERT: b 100 LYS cc_start: 0.8456 (mtmm) cc_final: 0.7977 (mttm) REVERT: b 171 ASP cc_start: 0.7594 (t0) cc_final: 0.7310 (t0) REVERT: b 204 LYS cc_start: 0.8299 (mtpt) cc_final: 0.7664 (mtmt) REVERT: b 206 LYS cc_start: 0.8606 (mppt) cc_final: 0.8196 (mppt) REVERT: b 243 ASP cc_start: 0.8000 (m-30) cc_final: 0.7767 (m-30) REVERT: b 260 LYS cc_start: 0.8331 (mtmt) cc_final: 0.8041 (mtpp) REVERT: b 264 GLN cc_start: 0.8193 (tp40) cc_final: 0.7823 (tp40) REVERT: c 21 SER cc_start: 0.8788 (m) cc_final: 0.8033 (p) REVERT: c 32 VAL cc_start: 0.8762 (t) cc_final: 0.8551 (m) REVERT: c 33 ASP cc_start: 0.7809 (m-30) cc_final: 0.7473 (m-30) REVERT: c 59 SER cc_start: 0.7448 (m) cc_final: 0.7145 (p) REVERT: c 68 ASP cc_start: 0.7806 (t0) cc_final: 0.7545 (t0) REVERT: c 171 ASP cc_start: 0.7876 (t70) cc_final: 0.7613 (t0) REVERT: c 175 ILE cc_start: 0.8496 (mt) cc_final: 0.8271 (mt) REVERT: c 197 SER cc_start: 0.8795 (OUTLIER) cc_final: 0.8494 (p) REVERT: c 222 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7698 (p) REVERT: d 27 LEU cc_start: 0.8794 (tp) cc_final: 0.8574 (tp) REVERT: d 30 TRP cc_start: 0.8621 (t60) cc_final: 0.8397 (t60) REVERT: d 34 LYS cc_start: 0.8469 (mmtm) cc_final: 0.8152 (mmmm) REVERT: d 68 ASP cc_start: 0.8312 (t0) cc_final: 0.8083 (t0) REVERT: d 263 LYS cc_start: 0.8266 (mtpt) cc_final: 0.7702 (mtpt) REVERT: e 245 MET cc_start: 0.0927 (mtm) cc_final: 0.0293 (mtm) REVERT: f 33 ASP cc_start: 0.7363 (m-30) cc_final: 0.6987 (m-30) REVERT: f 41 GLN cc_start: 0.8362 (mt0) cc_final: 0.8073 (mt0) REVERT: f 47 GLN cc_start: 0.8544 (mt0) cc_final: 0.8305 (tt0) REVERT: f 59 SER cc_start: 0.8190 (m) cc_final: 0.7817 (p) REVERT: f 78 LYS cc_start: 0.8561 (mmtt) cc_final: 0.7926 (mmmm) REVERT: f 122 LYS cc_start: 0.7165 (mtmm) cc_final: 0.6946 (mttp) REVERT: f 126 LYS cc_start: 0.8169 (mmpt) cc_final: 0.7923 (mmpt) REVERT: f 140 LYS cc_start: 0.7175 (ttpt) cc_final: 0.6953 (ptpt) REVERT: f 172 LYS cc_start: 0.8584 (mmtp) cc_final: 0.8244 (mmtm) REVERT: f 173 MET cc_start: 0.8482 (mmp) cc_final: 0.8279 (mmm) REVERT: f 218 VAL cc_start: 0.8209 (p) cc_final: 0.7948 (m) outliers start: 56 outliers final: 38 residues processed: 440 average time/residue: 0.1297 time to fit residues: 80.5397 Evaluate side-chains 439 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 398 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 54 ASN Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 138 THR Chi-restraints excluded: chain a residue 197 SER Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain a residue 279 GLU 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 211 ILE Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain b residue 245 MET Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 62 GLN Chi-restraints excluded: chain c residue 76 LEU Chi-restraints excluded: chain c residue 182 MET Chi-restraints excluded: chain c residue 197 SER Chi-restraints excluded: chain c residue 201 VAL Chi-restraints excluded: chain c residue 222 THR Chi-restraints excluded: chain c residue 235 PHE Chi-restraints excluded: chain c residue 251 THR Chi-restraints excluded: chain c residue 262 THR Chi-restraints excluded: chain c residue 288 LYS Chi-restraints excluded: chain d residue 20 THR 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 d residue 199 VAL Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain e residue 28 VAL Chi-restraints excluded: chain f residue 23 ARG Chi-restraints excluded: chain f residue 72 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 47 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 97 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 140 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 58 ASN a 62 GLN ** a 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 105 ASN b 110 GLN b 158 ASN b 238 GLN b 242 GLN c 237 HIS e 41 GLN ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 62 GLN ** 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** ** f 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.192585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.152605 restraints weight = 22979.715| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.99 r_work: 0.3804 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.5911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14076 Z= 0.151 Angle : 0.581 9.358 19165 Z= 0.307 Chirality : 0.045 0.145 2092 Planarity : 0.004 0.068 2351 Dihedral : 14.345 175.880 2026 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.93 % Rotamer: Outliers : 4.14 % Allowed : 22.72 % Favored : 73.14 % 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: 0.82 (0.19), residues: 741 sheet: 0.17 (0.34), residues: 230 loop : -0.53 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 252 TYR 0.014 0.001 TYR c 99 PHE 0.024 0.002 PHE c 124 TRP 0.013 0.001 TRP c 159 HIS 0.002 0.001 HIS a 237 Details of bonding type rmsd covalent geometry : bond 0.00339 (14076) covalent geometry : angle 0.58064 (19165) hydrogen bonds : bond 0.03697 ( 572) hydrogen bonds : angle 4.22415 ( 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 462 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 403 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 26 GLU cc_start: 0.7991 (tt0) cc_final: 0.7745 (tm-30) REVERT: a 40 LYS cc_start: 0.8368 (ttmm) cc_final: 0.7984 (ttmt) REVERT: a 88 GLN cc_start: 0.6806 (mm-40) cc_final: 0.6575 (mm-40) REVERT: a 107 TYR cc_start: 0.8196 (m-80) cc_final: 0.7760 (m-80) REVERT: a 119 TRP cc_start: 0.7806 (t60) cc_final: 0.7241 (t60) REVERT: a 163 ASN cc_start: 0.8205 (t0) cc_final: 0.7937 (m-40) REVERT: a 172 LYS cc_start: 0.8057 (mmtm) cc_final: 0.7782 (mmtm) REVERT: a 258 PHE cc_start: 0.8244 (t80) cc_final: 0.7934 (t80) REVERT: a 263 LYS cc_start: 0.8350 (ttpt) cc_final: 0.8002 (mtpp) REVERT: a 267 LYS cc_start: 0.8763 (mttt) cc_final: 0.8498 (mmmt) REVERT: a 283 GLU cc_start: 0.6613 (mm-30) cc_final: 0.6167 (tm-30) REVERT: a 287 LYS cc_start: 0.8480 (ptmm) cc_final: 0.8157 (ptmm) REVERT: b 53 PHE cc_start: 0.8169 (m-80) cc_final: 0.7861 (m-80) REVERT: b 59 SER cc_start: 0.8024 (m) cc_final: 0.7761 (p) REVERT: b 61 SER cc_start: 0.8747 (m) cc_final: 0.8467 (p) REVERT: b 94 SER cc_start: 0.8685 (OUTLIER) cc_final: 0.8319 (p) REVERT: b 100 LYS cc_start: 0.8472 (mtmm) cc_final: 0.7968 (mttm) REVERT: b 171 ASP cc_start: 0.7652 (t0) cc_final: 0.7369 (t0) REVERT: b 200 ARG cc_start: 0.8603 (mtp85) cc_final: 0.8381 (mtp85) REVERT: b 204 LYS cc_start: 0.8366 (mtpt) cc_final: 0.7731 (mtmt) REVERT: b 206 LYS cc_start: 0.8621 (mppt) cc_final: 0.8235 (mppt) REVERT: b 260 LYS cc_start: 0.8303 (mtmt) cc_final: 0.7994 (mtpp) REVERT: c 21 SER cc_start: 0.8757 (m) cc_final: 0.8056 (p) REVERT: c 32 VAL cc_start: 0.8791 (t) cc_final: 0.8546 (p) REVERT: c 33 ASP cc_start: 0.7832 (m-30) cc_final: 0.7448 (m-30) REVERT: c 59 SER cc_start: 0.7469 (m) cc_final: 0.7182 (p) REVERT: c 68 ASP cc_start: 0.7818 (t0) cc_final: 0.7568 (t0) REVERT: c 171 ASP cc_start: 0.7838 (t70) cc_final: 0.7601 (t0) REVERT: c 197 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8525 (p) REVERT: c 222 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7820 (p) REVERT: d 27 LEU cc_start: 0.8806 (tp) cc_final: 0.8584 (tp) REVERT: d 30 TRP cc_start: 0.8567 (t60) cc_final: 0.8271 (t60) REVERT: d 33 ASP cc_start: 0.8044 (t0) cc_final: 0.7786 (t0) REVERT: d 34 LYS cc_start: 0.8436 (mmtm) cc_final: 0.7976 (mmmm) REVERT: d 68 ASP cc_start: 0.8268 (t0) cc_final: 0.8043 (t0) REVERT: d 182 MET cc_start: 0.3062 (OUTLIER) cc_final: 0.2856 (ptp) REVERT: d 263 LYS cc_start: 0.8252 (mtpt) cc_final: 0.7679 (mtpt) REVERT: e 41 GLN cc_start: 0.8279 (mt0) cc_final: 0.8068 (mt0) REVERT: e 69 ASN cc_start: 0.7783 (m-40) cc_final: 0.7567 (m-40) REVERT: e 224 MET cc_start: -0.3090 (mmt) cc_final: -0.6487 (tmm) REVERT: e 245 MET cc_start: 0.0882 (mtm) cc_final: 0.0046 (mtm) REVERT: f 33 ASP cc_start: 0.7333 (m-30) cc_final: 0.6927 (m-30) REVERT: f 34 LYS cc_start: 0.8640 (mmmm) cc_final: 0.8397 (ttmm) REVERT: f 41 GLN cc_start: 0.8321 (mt0) cc_final: 0.8024 (mt0) REVERT: f 47 GLN cc_start: 0.8497 (mt0) cc_final: 0.8250 (tt0) REVERT: f 59 SER cc_start: 0.8160 (m) cc_final: 0.7752 (p) REVERT: f 78 LYS cc_start: 0.8561 (mmtt) cc_final: 0.7890 (mmmm) REVERT: f 122 LYS cc_start: 0.7115 (mtmm) cc_final: 0.6851 (mttp) REVERT: f 126 LYS cc_start: 0.8102 (mmpt) cc_final: 0.7838 (mmpt) REVERT: f 140 LYS cc_start: 0.7160 (ttpt) cc_final: 0.6922 (ptpt) REVERT: f 172 LYS cc_start: 0.8604 (mmtp) cc_final: 0.8203 (mmtm) REVERT: f 173 MET cc_start: 0.8409 (mmp) cc_final: 0.8197 (mmm) REVERT: f 218 VAL cc_start: 0.8188 (p) cc_final: 0.7945 (m) outliers start: 59 outliers final: 42 residues processed: 432 average time/residue: 0.1357 time to fit residues: 82.3777 Evaluate side-chains 443 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 397 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 54 ASN Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 138 THR Chi-restraints excluded: chain a residue 179 GLU Chi-restraints excluded: chain a residue 197 SER Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain a residue 279 GLU 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 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 b residue 245 MET Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain c residue 16 ILE 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 103 GLU Chi-restraints excluded: chain c residue 158 ASN Chi-restraints excluded: chain c residue 182 MET Chi-restraints excluded: chain c residue 186 VAL Chi-restraints excluded: chain c residue 197 SER Chi-restraints excluded: chain c residue 222 THR Chi-restraints excluded: chain c residue 235 PHE Chi-restraints excluded: chain c residue 262 THR Chi-restraints excluded: chain d residue 20 THR Chi-restraints excluded: chain d residue 59 SER Chi-restraints excluded: chain d residue 64 LYS Chi-restraints excluded: chain d residue 182 MET Chi-restraints excluded: chain d residue 199 VAL Chi-restraints excluded: chain d residue 222 THR 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 72 LYS Chi-restraints excluded: chain f residue 84 LEU 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 277 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 64 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 110 optimal weight: 0.6980 chunk 141 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 62 GLN ** a 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 105 ASN b 158 ASN b 221 ASN b 242 GLN ** c 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 237 HIS d 41 GLN ** 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** f 238 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.191941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.151967 restraints weight = 22997.506| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 3.01 r_work: 0.3795 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.6219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14076 Z= 0.143 Angle : 0.572 7.682 19165 Z= 0.303 Chirality : 0.045 0.161 2092 Planarity : 0.004 0.044 2351 Dihedral : 14.335 175.611 2026 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 3.79 % Allowed : 23.07 % Favored : 73.14 % 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: 0.27 (0.21), residues: 1631 helix: 0.92 (0.19), residues: 740 sheet: 0.17 (0.33), residues: 234 loop : -0.58 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG b 252 TYR 0.013 0.001 TYR c 99 PHE 0.020 0.002 PHE c 124 TRP 0.015 0.001 TRP c 159 HIS 0.002 0.001 HIS c 237 Details of bonding type rmsd covalent geometry : bond 0.00319 (14076) covalent geometry : angle 0.57225 (19165) hydrogen bonds : bond 0.03634 ( 572) hydrogen bonds : angle 4.18051 ( 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 464 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 410 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 26 GLU cc_start: 0.7935 (tt0) cc_final: 0.7695 (tm-30) REVERT: a 40 LYS cc_start: 0.8354 (ttmm) cc_final: 0.8006 (ttmt) REVERT: a 88 GLN cc_start: 0.6815 (mm-40) cc_final: 0.6591 (mm-40) REVERT: a 119 TRP cc_start: 0.7728 (t60) cc_final: 0.7177 (t60) REVERT: a 163 ASN cc_start: 0.8229 (t0) cc_final: 0.7986 (m-40) REVERT: a 172 LYS cc_start: 0.7997 (mmtm) cc_final: 0.7712 (mmtm) REVERT: a 263 LYS cc_start: 0.8347 (ttpt) cc_final: 0.8073 (mtpp) REVERT: a 283 GLU cc_start: 0.6672 (mm-30) cc_final: 0.6233 (tm-30) REVERT: a 287 LYS cc_start: 0.8509 (ptmm) cc_final: 0.8155 (ptmm) REVERT: b 59 SER cc_start: 0.8037 (m) cc_final: 0.7801 (p) REVERT: b 62 GLN cc_start: 0.8178 (mt0) cc_final: 0.7933 (tt0) REVERT: b 64 LYS cc_start: 0.8793 (tppt) cc_final: 0.8584 (tppt) REVERT: b 94 SER cc_start: 0.8659 (OUTLIER) cc_final: 0.8312 (p) REVERT: b 100 LYS cc_start: 0.8439 (mtmm) cc_final: 0.7951 (mttm) REVERT: b 171 ASP cc_start: 0.7637 (t0) cc_final: 0.7332 (t0) REVERT: b 200 ARG cc_start: 0.8581 (mtp85) cc_final: 0.8169 (mtp-110) REVERT: b 204 LYS cc_start: 0.8382 (mtpt) cc_final: 0.7755 (mtmt) REVERT: b 206 LYS cc_start: 0.8660 (mppt) cc_final: 0.8288 (mppt) REVERT: b 260 LYS cc_start: 0.8263 (mtmt) cc_final: 0.7992 (mtpp) REVERT: b 264 GLN cc_start: 0.8130 (tp40) cc_final: 0.7815 (tp40) REVERT: c 21 SER cc_start: 0.8779 (m) cc_final: 0.8086 (p) REVERT: c 32 VAL cc_start: 0.8819 (t) cc_final: 0.8589 (p) REVERT: c 33 ASP cc_start: 0.7841 (m-30) cc_final: 0.7492 (m-30) REVERT: c 59 SER cc_start: 0.7575 (m) cc_final: 0.7292 (p) REVERT: c 68 ASP cc_start: 0.7765 (t0) cc_final: 0.7522 (t0) REVERT: c 69 ASN cc_start: 0.8148 (m-40) cc_final: 0.7896 (m-40) REVERT: c 171 ASP cc_start: 0.7819 (t70) cc_final: 0.7592 (t0) REVERT: c 197 SER cc_start: 0.8767 (OUTLIER) cc_final: 0.8516 (p) REVERT: c 222 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.7952 (p) REVERT: d 27 LEU cc_start: 0.8805 (tp) cc_final: 0.8601 (tp) REVERT: d 30 TRP cc_start: 0.8600 (t60) cc_final: 0.8306 (t60) REVERT: d 34 LYS cc_start: 0.8468 (mmtm) cc_final: 0.8075 (mmmm) REVERT: d 68 ASP cc_start: 0.8296 (t0) cc_final: 0.8073 (t0) REVERT: d 263 LYS cc_start: 0.8246 (mtpt) cc_final: 0.7670 (mtpt) REVERT: e 224 MET cc_start: -0.2552 (mmt) cc_final: -0.6729 (tmm) REVERT: e 245 MET cc_start: 0.1045 (mtm) cc_final: 0.0317 (mtm) REVERT: f 33 ASP cc_start: 0.7369 (m-30) cc_final: 0.6957 (m-30) REVERT: f 34 LYS cc_start: 0.8646 (mmmm) cc_final: 0.8438 (ttmm) REVERT: f 41 GLN cc_start: 0.8289 (mt0) cc_final: 0.7966 (mt0) REVERT: f 47 GLN cc_start: 0.8500 (mt0) cc_final: 0.8260 (tt0) REVERT: f 59 SER cc_start: 0.8170 (m) cc_final: 0.7767 (p) REVERT: f 78 LYS cc_start: 0.8508 (mmtt) cc_final: 0.7843 (mmmm) REVERT: f 101 ILE cc_start: 0.8738 (tt) cc_final: 0.8171 (pt) REVERT: f 122 LYS cc_start: 0.7163 (mtmm) cc_final: 0.6959 (mttp) REVERT: f 126 LYS cc_start: 0.8131 (mmpt) cc_final: 0.7845 (mmpt) REVERT: f 140 LYS cc_start: 0.7096 (ttpt) cc_final: 0.6872 (ptpt) REVERT: f 172 LYS cc_start: 0.8586 (mmtp) cc_final: 0.8185 (mmtm) REVERT: f 173 MET cc_start: 0.8394 (mmp) cc_final: 0.8189 (mmm) REVERT: f 218 VAL cc_start: 0.8216 (p) cc_final: 0.7969 (m) outliers start: 54 outliers final: 38 residues processed: 436 average time/residue: 0.1370 time to fit residues: 84.0138 Evaluate side-chains 447 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 406 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 54 ASN Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 79 THR Chi-restraints excluded: chain a residue 138 THR Chi-restraints excluded: chain a residue 179 GLU Chi-restraints excluded: chain a residue 197 SER Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain a residue 279 GLU 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 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 b residue 262 THR Chi-restraints excluded: chain c residue 16 ILE Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 62 GLN Chi-restraints excluded: chain c residue 103 GLU Chi-restraints excluded: chain c residue 186 VAL Chi-restraints excluded: chain c residue 197 SER Chi-restraints excluded: chain c residue 222 THR Chi-restraints excluded: chain c residue 235 PHE Chi-restraints excluded: chain c residue 251 THR Chi-restraints excluded: chain c residue 262 THR Chi-restraints excluded: chain d residue 20 THR 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 199 VAL Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain e residue 262 THR Chi-restraints excluded: chain f residue 23 ARG Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 105 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 112 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 144 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 105 ASN b 158 ASN b 242 GLN ** c 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 69 ASN d 54 ASN ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 69 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.190435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.150784 restraints weight = 22949.233| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.95 r_work: 0.3777 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.6530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14076 Z= 0.166 Angle : 0.596 9.660 19165 Z= 0.317 Chirality : 0.045 0.176 2092 Planarity : 0.004 0.082 2351 Dihedral : 14.350 175.607 2026 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.56 % Favored : 96.38 % Rotamer: Outliers : 3.23 % Allowed : 24.61 % Favored : 72.16 % 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: 0.21 (0.21), residues: 1631 helix: 0.91 (0.19), residues: 739 sheet: 0.22 (0.34), residues: 224 loop : -0.69 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG b 252 TYR 0.014 0.001 TYR c 99 PHE 0.017 0.002 PHE b 246 TRP 0.023 0.001 TRP b 30 HIS 0.002 0.001 HIS c 149 Details of bonding type rmsd covalent geometry : bond 0.00371 (14076) covalent geometry : angle 0.59628 (19165) hydrogen bonds : bond 0.03806 ( 572) hydrogen bonds : angle 4.23628 ( 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 453 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 407 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 26 GLU cc_start: 0.7928 (tt0) cc_final: 0.7685 (tm-30) REVERT: a 40 LYS cc_start: 0.8355 (ttmm) cc_final: 0.7904 (ttmt) REVERT: a 119 TRP cc_start: 0.7659 (t60) cc_final: 0.7111 (t60) REVERT: a 163 ASN cc_start: 0.8263 (t0) cc_final: 0.8031 (m-40) REVERT: a 172 LYS cc_start: 0.8069 (mmtm) cc_final: 0.7815 (mmtm) REVERT: a 263 LYS cc_start: 0.8332 (ttpt) cc_final: 0.8053 (mtpp) REVERT: a 283 GLU cc_start: 0.6719 (mm-30) cc_final: 0.6252 (mm-30) REVERT: a 287 LYS cc_start: 0.8482 (ptmm) cc_final: 0.8125 (ptmm) REVERT: b 59 SER cc_start: 0.8137 (m) cc_final: 0.7888 (p) REVERT: b 64 LYS cc_start: 0.8786 (tppt) cc_final: 0.8579 (tppt) REVERT: b 94 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8397 (p) REVERT: b 99 TYR cc_start: 0.8397 (t80) cc_final: 0.8185 (t80) REVERT: b 100 LYS cc_start: 0.8503 (mtmm) cc_final: 0.7958 (mtmm) REVERT: b 108 ASP cc_start: 0.8126 (t0) cc_final: 0.7914 (t0) REVERT: b 168 ASP cc_start: 0.7899 (t0) cc_final: 0.7270 (t0) REVERT: b 200 ARG cc_start: 0.8639 (mtp85) cc_final: 0.8251 (mtp85) REVERT: b 204 LYS cc_start: 0.8440 (mtpt) cc_final: 0.7826 (mtmt) REVERT: b 206 LYS cc_start: 0.8691 (mppt) cc_final: 0.8284 (mppt) REVERT: b 260 LYS cc_start: 0.8277 (mtmt) cc_final: 0.7981 (mtpp) REVERT: c 21 SER cc_start: 0.8803 (m) cc_final: 0.8186 (p) REVERT: c 33 ASP cc_start: 0.7938 (m-30) cc_final: 0.7626 (m-30) REVERT: c 34 LYS cc_start: 0.8670 (mmtp) cc_final: 0.8386 (mppt) REVERT: c 59 SER cc_start: 0.7709 (m) cc_final: 0.7421 (p) REVERT: c 68 ASP cc_start: 0.7852 (t0) cc_final: 0.7451 (t0) REVERT: c 69 ASN cc_start: 0.8187 (m110) cc_final: 0.7980 (m-40) REVERT: c 162 GLU cc_start: 0.8036 (pm20) cc_final: 0.7788 (pm20) REVERT: c 171 ASP cc_start: 0.7866 (t70) cc_final: 0.7658 (t0) REVERT: c 197 SER cc_start: 0.8770 (m) cc_final: 0.8529 (p) REVERT: c 222 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.8037 (p) REVERT: c 224 MET cc_start: 0.8505 (mmm) cc_final: 0.8162 (mmm) REVERT: c 252 ARG cc_start: 0.7573 (mmm-85) cc_final: 0.7159 (mtm-85) REVERT: c 253 ARG cc_start: 0.7870 (mtp180) cc_final: 0.7299 (mtp180) REVERT: c 264 GLN cc_start: 0.8240 (tp40) cc_final: 0.7961 (tp-100) REVERT: d 30 TRP cc_start: 0.8635 (t60) cc_final: 0.8333 (t60) REVERT: d 34 LYS cc_start: 0.8502 (mmtm) cc_final: 0.8100 (mmmm) REVERT: d 68 ASP cc_start: 0.8324 (t0) cc_final: 0.8105 (t0) REVERT: d 74 MET cc_start: 0.7894 (ptp) cc_final: 0.7664 (mtm) REVERT: d 263 LYS cc_start: 0.8227 (mtpt) cc_final: 0.7654 (mtpt) REVERT: e 224 MET cc_start: -0.2008 (mmt) cc_final: -0.6749 (tmm) REVERT: e 245 MET cc_start: 0.1060 (mtm) cc_final: 0.0306 (mtm) REVERT: f 33 ASP cc_start: 0.7419 (m-30) cc_final: 0.7010 (m-30) REVERT: f 34 LYS cc_start: 0.8663 (mmmm) cc_final: 0.8461 (ttmm) REVERT: f 41 GLN cc_start: 0.8295 (mt0) cc_final: 0.7988 (mt0) REVERT: f 47 GLN cc_start: 0.8439 (mt0) cc_final: 0.8193 (tt0) REVERT: f 59 SER cc_start: 0.8218 (m) cc_final: 0.7778 (p) REVERT: f 78 LYS cc_start: 0.8457 (mmtt) cc_final: 0.7742 (mmmm) REVERT: f 101 ILE cc_start: 0.8748 (tt) cc_final: 0.8192 (pt) REVERT: f 126 LYS cc_start: 0.8094 (mmpt) cc_final: 0.7788 (mmpt) REVERT: f 140 LYS cc_start: 0.7172 (ttpt) cc_final: 0.6915 (ptpt) REVERT: f 172 LYS cc_start: 0.8609 (mmtp) cc_final: 0.8198 (mmtm) REVERT: f 218 VAL cc_start: 0.8185 (p) cc_final: 0.7952 (m) outliers start: 46 outliers final: 39 residues processed: 430 average time/residue: 0.1384 time to fit residues: 83.3481 Evaluate side-chains 443 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 402 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 54 ASN Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 138 THR Chi-restraints excluded: chain a residue 179 GLU 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 87 GLN 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 b residue 262 THR Chi-restraints excluded: chain c residue 16 ILE Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 76 LEU Chi-restraints excluded: chain c residue 103 GLU Chi-restraints excluded: chain c residue 181 LYS Chi-restraints excluded: chain c residue 186 VAL Chi-restraints excluded: chain c residue 222 THR Chi-restraints excluded: chain c residue 227 VAL Chi-restraints excluded: chain c residue 235 PHE Chi-restraints excluded: chain c residue 251 THR Chi-restraints excluded: chain d residue 20 THR Chi-restraints excluded: chain d residue 54 ASN 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 199 VAL Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain e residue 262 THR Chi-restraints excluded: chain f residue 23 ARG Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 105 ASN 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: 0.9990 chunk 104 optimal weight: 0.0020 chunk 28 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 163 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 62 GLN ** a 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 105 ASN b 110 GLN b 158 ASN b 242 GLN ** c 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.190785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.150781 restraints weight = 22914.692| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.96 r_work: 0.3782 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.6676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14076 Z= 0.146 Angle : 0.595 9.299 19165 Z= 0.314 Chirality : 0.045 0.166 2092 Planarity : 0.004 0.042 2351 Dihedral : 14.340 175.848 2026 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.32 % Rotamer: Outliers : 2.88 % Allowed : 25.74 % Favored : 71.39 % 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: 0.87 (0.19), residues: 741 sheet: 0.23 (0.35), residues: 215 loop : -0.72 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG b 252 TYR 0.014 0.001 TYR c 99 PHE 0.019 0.002 PHE b 246 TRP 0.034 0.001 TRP b 30 HIS 0.002 0.000 HIS b 149 Details of bonding type rmsd covalent geometry : bond 0.00328 (14076) covalent geometry : angle 0.59478 (19165) hydrogen bonds : bond 0.03623 ( 572) hydrogen bonds : angle 4.26271 ( 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 448 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 407 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 26 GLU cc_start: 0.7875 (tt0) cc_final: 0.7637 (tm-30) REVERT: a 40 LYS cc_start: 0.8278 (ttmm) cc_final: 0.7765 (ttmt) REVERT: a 119 TRP cc_start: 0.7602 (t60) cc_final: 0.6989 (t60) REVERT: a 163 ASN cc_start: 0.8250 (t0) cc_final: 0.8037 (m-40) REVERT: a 172 LYS cc_start: 0.8063 (mmtm) cc_final: 0.7805 (mmtm) REVERT: a 263 LYS cc_start: 0.8336 (ttpt) cc_final: 0.8056 (mtpp) REVERT: a 283 GLU cc_start: 0.6681 (mm-30) cc_final: 0.6233 (mm-30) REVERT: a 287 LYS cc_start: 0.8488 (ptmm) cc_final: 0.8134 (ptmm) REVERT: b 59 SER cc_start: 0.8197 (m) cc_final: 0.7905 (p) REVERT: b 64 LYS cc_start: 0.8806 (tppt) cc_final: 0.8601 (tppt) REVERT: b 94 SER cc_start: 0.8622 (OUTLIER) cc_final: 0.8278 (p) REVERT: b 100 LYS cc_start: 0.8464 (mtmm) cc_final: 0.7953 (mttm) REVERT: b 108 ASP cc_start: 0.8086 (t0) cc_final: 0.7876 (t0) REVERT: b 168 ASP cc_start: 0.7918 (t0) cc_final: 0.7317 (t0) REVERT: b 171 ASP cc_start: 0.7830 (t0) cc_final: 0.7626 (m-30) REVERT: b 200 ARG cc_start: 0.8633 (mtp85) cc_final: 0.8197 (mtp85) REVERT: b 204 LYS cc_start: 0.8436 (mtpt) cc_final: 0.7506 (mtmt) REVERT: b 206 LYS cc_start: 0.8699 (mppt) cc_final: 0.8282 (mppt) REVERT: b 236 GLU cc_start: 0.7950 (tp30) cc_final: 0.7745 (tp30) REVERT: b 260 LYS cc_start: 0.8251 (mtmt) cc_final: 0.7968 (mtpp) REVERT: c 21 SER cc_start: 0.8780 (m) cc_final: 0.8169 (p) REVERT: c 33 ASP cc_start: 0.7860 (m-30) cc_final: 0.7525 (m-30) REVERT: c 59 SER cc_start: 0.7709 (m) cc_final: 0.7440 (p) REVERT: c 68 ASP cc_start: 0.7734 (t0) cc_final: 0.7426 (t0) REVERT: c 69 ASN cc_start: 0.8219 (m110) cc_final: 0.7975 (m-40) REVERT: c 162 GLU cc_start: 0.8072 (pm20) cc_final: 0.7817 (pm20) REVERT: c 171 ASP cc_start: 0.7875 (t70) cc_final: 0.7672 (t0) REVERT: c 197 SER cc_start: 0.8713 (m) cc_final: 0.8501 (p) REVERT: c 204 LYS cc_start: 0.8192 (mttt) cc_final: 0.7922 (mttt) REVERT: c 222 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.8079 (p) REVERT: c 224 MET cc_start: 0.8442 (mmm) cc_final: 0.8185 (mmm) REVERT: c 252 ARG cc_start: 0.7576 (mmm-85) cc_final: 0.7083 (mtm-85) REVERT: c 253 ARG cc_start: 0.7821 (mtp180) cc_final: 0.7242 (mtp180) REVERT: c 264 GLN cc_start: 0.8217 (tp40) cc_final: 0.7934 (tp-100) REVERT: d 30 TRP cc_start: 0.8627 (t60) cc_final: 0.8313 (t60) REVERT: d 34 LYS cc_start: 0.8488 (mmtm) cc_final: 0.8093 (mmmm) REVERT: d 68 ASP cc_start: 0.8345 (t0) cc_final: 0.8127 (t0) REVERT: d 74 MET cc_start: 0.7896 (ptp) cc_final: 0.7657 (mtm) REVERT: d 263 LYS cc_start: 0.8245 (mtpt) cc_final: 0.7680 (mtpt) REVERT: e 224 MET cc_start: -0.1810 (mmt) cc_final: -0.6800 (tmm) REVERT: e 245 MET cc_start: 0.1053 (mtm) cc_final: 0.0046 (mtm) REVERT: f 33 ASP cc_start: 0.7362 (m-30) cc_final: 0.6968 (m-30) REVERT: f 34 LYS cc_start: 0.8642 (mmmm) cc_final: 0.8222 (mtpp) REVERT: f 41 GLN cc_start: 0.8269 (mt0) cc_final: 0.7902 (mt0) REVERT: f 47 GLN cc_start: 0.8421 (mt0) cc_final: 0.8185 (tt0) REVERT: f 59 SER cc_start: 0.8202 (m) cc_final: 0.7768 (p) REVERT: f 78 LYS cc_start: 0.8403 (mmtt) cc_final: 0.7725 (mmmm) REVERT: f 101 ILE cc_start: 0.8721 (tt) cc_final: 0.8149 (pt) REVERT: f 126 LYS cc_start: 0.8113 (mmpt) cc_final: 0.7805 (mmpt) REVERT: f 140 LYS cc_start: 0.7081 (ttpt) cc_final: 0.6841 (ptpt) REVERT: f 218 VAL cc_start: 0.8207 (p) cc_final: 0.7961 (m) outliers start: 41 outliers final: 34 residues processed: 426 average time/residue: 0.1364 time to fit residues: 81.3349 Evaluate side-chains 428 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 392 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 54 ASN Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 138 THR Chi-restraints excluded: chain a residue 179 GLU 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 76 LEU Chi-restraints excluded: chain b residue 87 GLN 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 b residue 262 THR Chi-restraints excluded: chain c residue 16 ILE Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 103 GLU Chi-restraints excluded: chain c residue 186 VAL Chi-restraints excluded: chain c residue 222 THR Chi-restraints excluded: chain c residue 235 PHE Chi-restraints excluded: chain c residue 251 THR Chi-restraints excluded: chain d residue 20 THR 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 d residue 222 THR Chi-restraints excluded: chain e residue 262 THR Chi-restraints excluded: chain f residue 23 ARG Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 105 ASN 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: 0.8980 chunk 22 optimal weight: 0.0670 chunk 96 optimal weight: 6.9990 chunk 127 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 chunk 95 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 62 GLN ** a 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 158 ASN b 242 GLN ** c 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 237 HIS d 41 GLN d 54 ASN ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 69 ASN ** 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** f 237 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.190985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.151107 restraints weight = 22963.511| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.96 r_work: 0.3783 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.6873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14076 Z= 0.133 Angle : 0.582 11.705 19165 Z= 0.307 Chirality : 0.045 0.252 2092 Planarity : 0.004 0.040 2351 Dihedral : 14.314 175.918 2026 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.68 % Favored : 96.26 % Rotamer: Outliers : 3.02 % Allowed : 24.96 % Favored : 72.02 % 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: 0.90 (0.19), residues: 748 sheet: 0.37 (0.35), residues: 211 loop : -0.72 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG e 23 TYR 0.015 0.001 TYR b 24 PHE 0.019 0.002 PHE b 246 TRP 0.035 0.001 TRP b 30 HIS 0.002 0.000 HIS b 149 Details of bonding type rmsd covalent geometry : bond 0.00301 (14076) covalent geometry : angle 0.58230 (19165) hydrogen bonds : bond 0.03427 ( 572) hydrogen bonds : angle 4.21694 ( 1642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4126.45 seconds wall clock time: 71 minutes 17.27 seconds (4277.27 seconds total)