Starting phenix.real_space_refine on Wed Mar 4 21:28:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rqt_54184/03_2026/9rqt_54184_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rqt_54184/03_2026/9rqt_54184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rqt_54184/03_2026/9rqt_54184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rqt_54184/03_2026/9rqt_54184.map" model { file = "/net/cci-nas-00/data/ceres_data/9rqt_54184/03_2026/9rqt_54184_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rqt_54184/03_2026/9rqt_54184_neut.cif" } resolution = 2.88 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= 0.014 sd= 1.167 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 36 5.49 5 Mg 3 5.21 5 S 69 5.16 5 C 10096 2.51 5 N 2743 2.21 5 O 3089 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 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: 16036 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 574 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} 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: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2210 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 1 Chain: "e" Number of atoms: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2175 Classifications: {'peptide': 273} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 262} 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: "g" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2170 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain breaks: 2 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.01, per 1000 atoms: 0.25 Number of scatterers: 16036 At special positions: 0 Unit cell: (80.85, 138.6, 138.6, 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 69 16.00 P 36 15.00 Mg 3 11.99 O 3089 8.00 N 2743 7.00 C 10096 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: 1.63 Conformation dependent library (CDL) restraints added in 648.1 milliseconds 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3640 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 20 sheets defined 50.9% alpha, 8.2% beta 13 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 1.65 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 53 removed outlier: 3.872A pdb=" N TYR a 50 " --> pdb=" O ASP a 46 " (cutoff:3.500A) Processing helix chain 'a' and resid 56 through 78 removed outlier: 3.812A pdb=" N THR a 77 " --> pdb=" O ILE a 73 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS a 78 " --> pdb=" O MET a 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 79 through 85 removed outlier: 3.724A pdb=" N TYR a 83 " --> pdb=" O THR a 79 " (cutoff:3.500A) Processing helix chain 'a' and resid 96 through 105 Processing helix chain 'a' and resid 108 through 122 Processing helix chain 'a' and resid 139 through 151 removed outlier: 3.745A pdb=" N VAL a 151 " --> pdb=" O ILE a 147 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 195 removed outlier: 3.545A 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 262 through 276 Processing helix chain 'b' and resid 18 through 34 Processing helix chain 'b' and resid 38 through 46 Processing helix chain 'b' and resid 46 through 54 removed outlier: 3.598A pdb=" N ASN b 54 " --> pdb=" O TYR b 50 " (cutoff:3.500A) Processing helix chain 'b' and resid 56 through 75 removed outlier: 3.716A pdb=" N LYS b 64 " --> pdb=" O ARG b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 79 through 85 removed outlier: 3.788A pdb=" N TYR b 83 " --> pdb=" O THR b 79 " (cutoff:3.500A) Processing helix chain 'b' and resid 96 through 105 Processing helix chain 'b' and resid 108 through 122 Processing helix chain 'b' and resid 139 through 151 removed outlier: 3.856A pdb=" N VAL b 151 " --> pdb=" O ILE b 147 " (cutoff:3.500A) Processing helix chain 'b' and resid 186 through 195 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 54 removed outlier: 3.504A pdb=" N ASN c 54 " --> pdb=" O TYR c 50 " (cutoff:3.500A) Processing helix chain 'c' and resid 57 through 78 removed outlier: 3.706A pdb=" N LYS c 64 " --> pdb=" O ARG c 60 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 85 Processing helix chain 'c' and resid 96 through 105 Processing helix chain 'c' and resid 108 through 121 Processing helix chain 'c' and resid 139 through 151 removed outlier: 3.769A pdb=" N VAL c 151 " --> pdb=" O ILE c 147 " (cutoff:3.500A) Processing helix chain 'c' and resid 166 through 170 removed outlier: 4.295A pdb=" N VAL c 170 " --> pdb=" O ASN c 167 " (cutoff:3.500A) Processing helix chain 'c' and resid 183 through 195 removed outlier: 4.728A pdb=" N GLU c 188 " --> pdb=" O ALA c 184 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER c 189 " --> pdb=" O LYS c 185 " (cutoff:3.500A) 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 35 Processing helix chain 'd' and resid 38 through 46 Processing helix chain 'd' and resid 46 through 54 removed outlier: 4.095A pdb=" N TYR d 50 " --> pdb=" O ASP d 46 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 78 removed outlier: 4.021A pdb=" N LYS d 64 " --> pdb=" O ARG d 60 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA d 65 " --> pdb=" O SER d 61 " (cutoff:3.500A) Processing helix chain 'd' and resid 80 through 85 Processing helix chain 'd' and resid 96 through 105 Processing helix chain 'd' and resid 108 through 122 Processing helix chain 'd' and resid 139 through 151 removed outlier: 3.773A pdb=" N VAL d 151 " --> pdb=" O ILE d 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 183 through 185 No H-bonds generated for 'chain 'd' and resid 183 through 185' Processing helix chain 'd' and resid 186 through 195 Processing helix chain 'd' and resid 237 through 243 Processing helix chain 'd' and resid 255 through 259 removed outlier: 3.639A pdb=" N GLY d 259 " --> pdb=" O HIS d 256 " (cutoff:3.500A) Processing helix chain 'd' and resid 262 through 276 Processing helix chain 'e' and resid 18 through 35 Processing helix chain 'e' and resid 38 through 46 Processing helix chain 'e' and resid 46 through 53 Processing helix chain 'e' and resid 56 through 78 removed outlier: 4.125A pdb=" N LYS e 64 " --> pdb=" O ARG e 60 " (cutoff:3.500A) Processing helix chain 'e' and resid 79 through 85 removed outlier: 4.019A pdb=" N TYR e 83 " --> pdb=" O THR e 79 " (cutoff:3.500A) Processing helix chain 'e' and resid 96 through 105 Processing helix chain 'e' and resid 108 through 122 Processing helix chain 'e' and resid 141 through 151 removed outlier: 3.765A pdb=" N ALA e 146 " --> pdb=" O ASN e 142 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL e 151 " --> pdb=" O ILE e 147 " (cutoff:3.500A) Processing helix chain 'e' and resid 164 through 170 removed outlier: 3.898A pdb=" N ASP e 168 " --> pdb=" O PRO e 165 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL e 170 " --> pdb=" O ASN e 167 " (cutoff:3.500A) Processing helix chain 'e' and resid 190 through 195 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 Processing helix chain 'f' and resid 38 through 46 Processing helix chain 'f' and resid 46 through 53 Processing helix chain 'f' and resid 56 through 78 removed outlier: 3.607A pdb=" N LYS f 64 " --> pdb=" O ARG f 60 " (cutoff:3.500A) Processing helix chain 'f' and resid 79 through 85 removed outlier: 4.061A 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 122 Processing helix chain 'f' and resid 142 through 151 removed outlier: 3.572A pdb=" N VAL f 151 " --> pdb=" O ILE f 147 " (cutoff:3.500A) Processing helix chain 'f' and resid 164 through 170 removed outlier: 4.118A pdb=" N ASP f 168 " --> pdb=" O PRO f 165 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL f 170 " --> pdb=" O ASN f 167 " (cutoff:3.500A) Processing helix chain 'f' and resid 186 through 195 removed outlier: 3.740A pdb=" N ALA f 190 " --> pdb=" O VAL f 186 " (cutoff:3.500A) 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 244 Processing helix chain 'f' and resid 255 through 259 removed outlier: 3.664A pdb=" N GLY f 259 " --> pdb=" O HIS f 256 " (cutoff:3.500A) Processing helix chain 'f' and resid 262 through 276 Processing helix chain 'g' and resid 18 through 35 Processing helix chain 'g' and resid 38 through 46 Processing helix chain 'g' and resid 46 through 54 removed outlier: 3.868A pdb=" N TYR g 50 " --> pdb=" O ASP g 46 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 78 Processing helix chain 'g' and resid 80 through 85 Processing helix chain 'g' and resid 96 through 106 Processing helix chain 'g' and resid 108 through 122 Processing helix chain 'g' and resid 138 through 151 removed outlier: 3.550A pdb=" N ALA g 146 " --> pdb=" O ASN g 142 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL g 151 " --> pdb=" O ILE g 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 164 through 169 removed outlier: 4.615A pdb=" N ASP g 168 " --> pdb=" O PRO g 165 " (cutoff:3.500A) Processing helix chain 'g' and resid 186 through 195 Processing helix chain 'g' and resid 237 through 243 Processing helix chain 'g' and resid 262 through 276 Processing sheet with id=AA1, first strand: chain 'a' and resid 154 through 156 removed outlier: 6.316A pdb=" N GLY a 155 " --> pdb=" O TRP a 176 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE a 175 " --> pdb=" O ILE a 217 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N THR a 219 " --> pdb=" O ILE a 175 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TRP a 177 " --> pdb=" O THR a 219 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE a 130 " --> pdb=" O VAL a 218 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N SER a 220 " --> pdb=" O ILE a 130 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU a 132 " --> pdb=" O SER a 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 199 through 203 removed outlier: 3.650A pdb=" N VAL a 199 " --> pdb=" O ILE a 211 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLN a 203 " --> pdb=" O SER a 207 " (cutoff:3.500A) removed outlier: 5.353A 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: 6.396A pdb=" N GLY b 155 " --> pdb=" O TRP b 176 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLU b 178 " --> pdb=" O GLY b 155 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE b 175 " --> pdb=" O ILE b 217 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N THR b 219 " --> pdb=" O ILE b 175 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TRP b 177 " --> pdb=" O THR b 219 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE b 130 " --> pdb=" O VAL b 218 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N SER b 220 " --> pdb=" O ILE b 130 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU b 132 " --> pdb=" O SER b 220 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 199 through 203 removed outlier: 3.656A pdb=" N VAL b 199 " --> pdb=" O ILE b 211 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLN b 203 " --> pdb=" O SER b 207 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N SER b 207 " --> pdb=" O GLN b 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 227 through 228 Processing sheet with id=AA7, first strand: chain 'c' and resid 155 through 156 removed outlier: 6.587A pdb=" N GLY c 155 " --> pdb=" O TRP c 176 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLU c 178 " --> pdb=" O GLY c 155 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE c 175 " --> pdb=" O ILE c 217 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N THR c 219 " --> pdb=" O ILE c 175 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TRP c 177 " --> pdb=" O THR c 219 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE c 130 " --> pdb=" O VAL c 218 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N SER c 220 " --> pdb=" O ILE c 130 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU c 132 " --> pdb=" O SER c 220 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'c' and resid 199 through 203 removed outlier: 3.688A pdb=" N VAL c 199 " --> pdb=" O ILE c 211 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN c 203 " --> pdb=" O SER c 207 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N SER c 207 " --> pdb=" O GLN c 203 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'c' and resid 227 through 229 Processing sheet with id=AB1, first strand: chain 'd' and resid 155 through 156 removed outlier: 6.621A pdb=" N GLY d 155 " --> pdb=" O TRP d 176 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE d 175 " --> pdb=" O ILE d 217 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'd' and resid 199 through 202 removed outlier: 3.635A pdb=" N VAL d 199 " --> pdb=" O ILE d 211 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'd' and resid 227 through 228 Processing sheet with id=AB4, first strand: chain 'e' and resid 129 through 133 Processing sheet with id=AB5, first strand: chain 'e' and resid 154 through 156 removed outlier: 6.358A pdb=" N GLY e 155 " --> pdb=" O TRP e 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'e' and resid 200 through 201 Processing sheet with id=AB7, first strand: chain 'f' and resid 154 through 156 removed outlier: 6.564A pdb=" N GLY f 155 " --> pdb=" O TRP f 176 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE f 130 " --> pdb=" O VAL f 218 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR f 129 " --> pdb=" O PHE f 246 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N PHE f 248 " --> pdb=" O THR f 129 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP f 131 " --> pdb=" O PHE f 248 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'f' and resid 199 through 201 Processing sheet with id=AB9, first strand: chain 'g' and resid 155 through 157 removed outlier: 6.310A pdb=" N ILE g 175 " --> pdb=" O ILE g 217 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE g 130 " --> pdb=" O VAL g 218 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'g' and resid 182 through 183 removed outlier: 7.349A pdb=" N MET g 182 " --> pdb=" O ILE g 228 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'g' and resid 199 through 201 removed outlier: 3.582A pdb=" N VAL g 199 " --> pdb=" O ILE g 211 " (cutoff:3.500A) 673 hydrogen bonds defined for protein. 1959 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 2.00 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: 5178 1.36 - 1.51: 4830 1.51 - 1.65: 6346 1.65 - 1.80: 51 1.80 - 1.95: 60 Bond restraints: 16465 Sorted by residual: 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 3.19e+00 bond pdb=" N ASP d 12 " pdb=" CA ASP d 12 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.16e+00 bond pdb=" N ASP f 12 " pdb=" CA ASP f 12 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 bond pdb=" N ASP c 12 " pdb=" CA ASP c 12 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N ASP a 12 " pdb=" CA ASP a 12 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 ... (remaining 16460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 22132 2.14 - 4.27: 221 4.27 - 6.41: 16 6.41 - 8.54: 7 8.54 - 10.68: 53 Bond angle restraints: 22429 Sorted by residual: angle pdb=" C2' AGS a1000 " pdb=" C1' AGS a1000 " pdb=" N9 AGS a1000 " ideal model delta sigma weight residual 114.04 123.51 -9.47 1.55e+00 4.14e-01 3.71e+01 angle pdb=" N9 AGS a1000 " pdb=" C1' AGS a1000 " pdb=" O4' AGS a1000 " ideal model delta sigma weight residual 108.44 115.04 -6.60 1.32e+00 5.75e-01 2.50e+01 angle pdb=" N VAL e 227 " pdb=" CA VAL e 227 " pdb=" C VAL e 227 " ideal model delta sigma weight residual 111.56 108.08 3.48 8.60e-01 1.35e+00 1.64e+01 angle pdb=" N ASN f 142 " pdb=" CA ASN f 142 " pdb=" C ASN f 142 " ideal model delta sigma weight residual 113.18 108.11 5.07 1.33e+00 5.65e-01 1.45e+01 angle pdb=" OP1 DC H 25 " pdb=" P DC H 25 " pdb=" OP2 DC H 25 " ideal model delta sigma weight residual 120.00 109.32 10.68 3.00e+00 1.11e-01 1.27e+01 ... (remaining 22424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 8503 17.84 - 35.68: 869 35.68 - 53.52: 252 53.52 - 71.36: 55 71.36 - 89.20: 18 Dihedral angle restraints: 9697 sinusoidal: 4086 harmonic: 5611 Sorted by residual: dihedral pdb=" CA MET c 245 " pdb=" C MET c 245 " pdb=" N PHE c 246 " pdb=" CA PHE c 246 " ideal model delta harmonic sigma weight residual 180.00 157.52 22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA MET b 245 " pdb=" C MET b 245 " pdb=" N PHE b 246 " pdb=" CA PHE b 246 " ideal model delta harmonic sigma weight residual 180.00 158.13 21.87 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA MET d 245 " pdb=" C MET d 245 " pdb=" N PHE d 246 " pdb=" CA PHE d 246 " ideal model delta harmonic sigma weight residual 180.00 159.98 20.02 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 9694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.176: 2422 0.176 - 0.352: 2 0.352 - 0.528: 27 0.528 - 0.704: 0 0.704 - 0.880: 1 Chirality restraints: 2452 Sorted by residual: chirality pdb=" C1' AGS a1000 " pdb=" C2' AGS a1000 " pdb=" N9 AGS a1000 " pdb=" O4' AGS a1000 " both_signs ideal model delta sigma weight residual False 2.41 1.53 0.88 2.00e-01 2.50e+01 1.94e+01 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 -0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" P DG H 22 " pdb=" OP1 DG H 22 " pdb=" OP2 DG H 22 " pdb=" O5' DG H 22 " both_signs ideal model delta sigma weight residual True 2.35 -2.75 -0.41 2.00e-01 2.50e+01 4.19e+00 ... (remaining 2449 not shown) Planarity restraints: 2747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG a 252 " -0.199 9.50e-02 1.11e+02 8.93e-02 5.15e+00 pdb=" NE ARG a 252 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG a 252 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG a 252 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG a 252 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP b 171 " -0.008 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C ASP b 171 " 0.030 2.00e-02 2.50e+03 pdb=" O ASP b 171 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS b 172 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP e 212 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO e 213 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO e 213 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO e 213 " -0.021 5.00e-02 4.00e+02 ... (remaining 2744 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 11 2.43 - 3.05: 11000 3.05 - 3.67: 24384 3.67 - 4.28: 37583 4.28 - 4.90: 60720 Nonbonded interactions: 133698 Sorted by model distance: nonbonded pdb=" O3B ADP c1000 " pdb="MG MG c1001 " model vdw 1.818 2.170 nonbonded pdb=" OG1 THR b 141 " pdb="MG MG b1001 " model vdw 1.854 2.170 nonbonded pdb=" OG1 THR a 141 " pdb="MG MG a1001 " model vdw 1.882 2.170 nonbonded pdb=" O2B AGS b1000 " pdb="MG MG b1001 " model vdw 1.920 2.170 nonbonded pdb=" O3B AGS a1000 " pdb="MG MG a1001 " model vdw 1.932 2.170 ... (remaining 133693 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 202 or resid 208 through 228 or (resid 232 and \ (name N or name CA or name C or name O or name CB )) or resid 233 through 288)) selection = (chain 'b' and (resid 12 through 202 or resid 208 through 228 or (resid 232 and \ (name N or name CA or name C or name O or name CB )) or resid 233 through 288)) selection = (chain 'c' and (resid 12 through 202 or resid 208 through 228 or (resid 232 and \ (name N or name CA or name C or name O or name CB )) or resid 233 through 288)) selection = (chain 'd' and (resid 12 through 202 or resid 208 through 228 or (resid 232 and \ (name N or name CA or name C or name O or name CB )) or resid 233 through 288)) selection = (chain 'e' and (resid 12 through 228 or (resid 232 and (name N or name CA or nam \ e C or name O or name CB )) or resid 233 through 288)) selection = (chain 'f' and (resid 12 through 202 or resid 208 through 228 or resid 232 throu \ gh 288)) selection = (chain 'g' and (resid 12 through 202 or resid 208 through 228 or (resid 232 and \ (name N or name CA or name C or name O or name CB )) or resid 233 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: 3.390 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.000 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16465 Z= 0.129 Angle : 0.730 10.676 22429 Z= 0.344 Chirality : 0.062 0.880 2452 Planarity : 0.003 0.089 2747 Dihedral : 16.159 89.201 6057 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.36 % Allowed : 12.79 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.20), residues: 1902 helix: 1.80 (0.18), residues: 879 sheet: -0.70 (0.32), residues: 260 loop : -0.07 (0.24), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG a 252 TYR 0.025 0.001 TYR e 154 PHE 0.012 0.001 PHE e 246 TRP 0.013 0.001 TRP e 131 HIS 0.009 0.001 HIS b 256 Details of bonding type rmsd covalent geometry : bond 0.00271 (16465) covalent geometry : angle 0.73042 (22429) hydrogen bonds : bond 0.14780 ( 710) hydrogen bonds : angle 5.64180 ( 2033) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 162 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.8984 (m) cc_final: 0.8556 (p) REVERT: a 200 ARG cc_start: 0.8615 (mtp85) cc_final: 0.8396 (ttt90) REVERT: c 64 LYS cc_start: 0.8634 (tppt) cc_final: 0.8320 (tppt) REVERT: d 182 MET cc_start: 0.8703 (ttp) cc_final: 0.7577 (pmm) REVERT: d 244 ARG cc_start: 0.8057 (mmt-90) cc_final: 0.7755 (mmm160) REVERT: d 254 LEU cc_start: 0.8784 (mm) cc_final: 0.7809 (pp) REVERT: d 271 ARG cc_start: 0.8988 (tpt-90) cc_final: 0.8713 (tpt90) REVERT: e 159 TRP cc_start: 0.8295 (p90) cc_final: 0.8016 (p90) REVERT: e 245 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.6805 (mmp) REVERT: f 173 MET cc_start: 0.8263 (mmm) cc_final: 0.7710 (mtp) REVERT: f 245 MET cc_start: 0.7605 (ttm) cc_final: 0.7137 (tmm) REVERT: g 17 ARG cc_start: 0.9512 (mtp85) cc_final: 0.9270 (mmm-85) REVERT: g 97 ARG cc_start: 0.8855 (mmt-90) cc_final: 0.8358 (mtt90) REVERT: g 145 GLU cc_start: 0.8457 (tp30) cc_final: 0.7939 (tm-30) REVERT: g 149 HIS cc_start: 0.8467 (m90) cc_final: 0.7942 (m90) REVERT: g 182 MET cc_start: 0.8600 (ttm) cc_final: 0.8127 (tmm) REVERT: g 224 MET cc_start: 0.7609 (mmm) cc_final: 0.7211 (mpm) outliers start: 6 outliers final: 2 residues processed: 166 average time/residue: 0.7459 time to fit residues: 134.7980 Evaluate side-chains 143 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 140 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 245 MET Chi-restraints excluded: chain f residue 194 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.0570 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 256 HIS c 69 ASN c 110 GLN d 69 ASN d 149 HIS d 210 GLN d 282 HIS e 69 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.121615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.067627 restraints weight = 31636.684| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.14 r_work: 0.2703 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16465 Z= 0.219 Angle : 0.583 8.242 22429 Z= 0.309 Chirality : 0.046 0.165 2452 Planarity : 0.004 0.083 2747 Dihedral : 12.755 85.975 2384 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.56 % Allowed : 13.99 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.20), residues: 1902 helix: 1.65 (0.17), residues: 895 sheet: -0.55 (0.34), residues: 247 loop : -0.09 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG e 200 TYR 0.024 0.002 TYR f 99 PHE 0.019 0.002 PHE f 133 TRP 0.031 0.001 TRP d 272 HIS 0.009 0.001 HIS b 256 Details of bonding type rmsd covalent geometry : bond 0.00512 (16465) covalent geometry : angle 0.58267 (22429) hydrogen bonds : bond 0.04328 ( 710) hydrogen bonds : angle 4.44844 ( 2033) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.9141 (m) cc_final: 0.8684 (p) REVERT: b 251 THR cc_start: 0.9232 (m) cc_final: 0.8874 (p) REVERT: c 64 LYS cc_start: 0.8908 (tppt) cc_final: 0.8611 (tppt) REVERT: d 149 HIS cc_start: 0.9111 (m-70) cc_final: 0.8815 (m-70) REVERT: d 182 MET cc_start: 0.8714 (ttp) cc_final: 0.7609 (pmm) REVERT: d 239 GLN cc_start: 0.9255 (tp40) cc_final: 0.9045 (tm-30) REVERT: d 244 ARG cc_start: 0.8358 (mmt-90) cc_final: 0.8090 (mmm160) REVERT: d 252 ARG cc_start: 0.9034 (tpp80) cc_final: 0.8766 (tpp-160) REVERT: d 254 LEU cc_start: 0.8862 (mm) cc_final: 0.8234 (pp) REVERT: d 265 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.8989 (mt-10) REVERT: e 159 TRP cc_start: 0.8323 (p90) cc_final: 0.8045 (p90) REVERT: e 176 TRP cc_start: 0.8453 (t60) cc_final: 0.8249 (t60) REVERT: e 177 TRP cc_start: 0.8540 (t-100) cc_final: 0.8290 (t-100) REVERT: e 245 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.6474 (mmp) REVERT: f 173 MET cc_start: 0.8422 (mmm) cc_final: 0.7960 (mtp) REVERT: f 245 MET cc_start: 0.7898 (ttm) cc_final: 0.7486 (tmt) REVERT: g 97 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8387 (mtt90) REVERT: g 149 HIS cc_start: 0.8553 (m90) cc_final: 0.7984 (m90) REVERT: g 159 TRP cc_start: 0.8530 (m100) cc_final: 0.8060 (m100) REVERT: g 176 TRP cc_start: 0.8208 (t60) cc_final: 0.7774 (t-100) REVERT: g 182 MET cc_start: 0.8560 (ttm) cc_final: 0.8212 (tmm) REVERT: g 200 ARG cc_start: 0.8831 (mmp80) cc_final: 0.8609 (mmp80) outliers start: 26 outliers final: 5 residues processed: 181 average time/residue: 0.6990 time to fit residues: 138.0350 Evaluate side-chains 153 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain b residue 77 THR Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 265 GLU Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 164 PHE Chi-restraints excluded: chain e residue 245 MET Chi-restraints excluded: chain g residue 97 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 105 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 167 optimal weight: 0.6980 chunk 131 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 chunk 159 optimal weight: 0.2980 chunk 91 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 256 HIS f 149 HIS g 276 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.123169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.069170 restraints weight = 31936.685| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.17 r_work: 0.2737 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16465 Z= 0.124 Angle : 0.534 8.771 22429 Z= 0.279 Chirality : 0.043 0.222 2452 Planarity : 0.004 0.087 2747 Dihedral : 12.629 81.290 2382 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.50 % Allowed : 15.14 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.20), residues: 1902 helix: 1.82 (0.18), residues: 895 sheet: -0.32 (0.34), residues: 248 loop : -0.11 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG e 200 TYR 0.028 0.001 TYR f 99 PHE 0.019 0.001 PHE f 133 TRP 0.036 0.001 TRP e 131 HIS 0.010 0.001 HIS b 256 Details of bonding type rmsd covalent geometry : bond 0.00280 (16465) covalent geometry : angle 0.53360 (22429) hydrogen bonds : bond 0.03516 ( 710) hydrogen bonds : angle 4.11750 ( 2033) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.9112 (m) cc_final: 0.8641 (p) REVERT: b 251 THR cc_start: 0.9222 (m) cc_final: 0.8886 (p) REVERT: c 64 LYS cc_start: 0.8813 (tppt) cc_final: 0.8522 (tppt) REVERT: d 64 LYS cc_start: 0.8870 (tppp) cc_final: 0.8573 (tppt) REVERT: d 137 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8684 (p) REVERT: d 149 HIS cc_start: 0.9080 (m-70) cc_final: 0.8762 (m-70) REVERT: d 182 MET cc_start: 0.8653 (ttp) cc_final: 0.7593 (pmm) REVERT: d 239 GLN cc_start: 0.9209 (tp40) cc_final: 0.9001 (tm-30) REVERT: d 244 ARG cc_start: 0.8291 (mmt-90) cc_final: 0.7952 (mmm160) REVERT: d 252 ARG cc_start: 0.9005 (tpp80) cc_final: 0.8791 (tpp-160) REVERT: d 271 ARG cc_start: 0.8805 (tpt90) cc_final: 0.8557 (tpt90) REVERT: e 25 MET cc_start: 0.9461 (mtm) cc_final: 0.9248 (mtm) REVERT: e 132 LEU cc_start: 0.9200 (mm) cc_final: 0.8811 (pp) REVERT: e 159 TRP cc_start: 0.8314 (p90) cc_final: 0.8023 (p90) REVERT: e 173 MET cc_start: 0.8404 (tpp) cc_final: 0.8145 (tpp) REVERT: e 176 TRP cc_start: 0.8466 (t60) cc_final: 0.8214 (t60) REVERT: e 177 TRP cc_start: 0.8620 (t-100) cc_final: 0.8247 (t-100) REVERT: f 173 MET cc_start: 0.8373 (mmm) cc_final: 0.7976 (mtp) REVERT: f 245 MET cc_start: 0.7910 (ttm) cc_final: 0.7480 (tmt) REVERT: f 250 LEU cc_start: 0.8554 (tp) cc_final: 0.8309 (tp) REVERT: g 39 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8514 (mt-10) REVERT: g 97 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8340 (mtt90) REVERT: g 149 HIS cc_start: 0.8484 (m90) cc_final: 0.7899 (m90) REVERT: g 159 TRP cc_start: 0.8568 (m100) cc_final: 0.8119 (m100) REVERT: g 176 TRP cc_start: 0.8234 (t60) cc_final: 0.7792 (t60) REVERT: g 182 MET cc_start: 0.8494 (ttm) cc_final: 0.8139 (tmm) outliers start: 25 outliers final: 8 residues processed: 189 average time/residue: 0.6578 time to fit residues: 136.2322 Evaluate side-chains 162 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain b residue 183 THR Chi-restraints excluded: chain c residue 156 CYS Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 251 THR Chi-restraints excluded: chain e residue 164 PHE Chi-restraints excluded: chain e residue 237 HIS Chi-restraints excluded: chain g residue 97 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 77 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 chunk 168 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 221 ASN b 256 HIS ** d 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 149 HIS g 167 ASN g 242 GLN g 276 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.120477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.065782 restraints weight = 31661.612| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.13 r_work: 0.2666 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 16465 Z= 0.269 Angle : 0.596 9.211 22429 Z= 0.311 Chirality : 0.046 0.150 2452 Planarity : 0.004 0.089 2747 Dihedral : 12.860 86.364 2378 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.31 % Favored : 96.64 % Rotamer: Outliers : 2.04 % Allowed : 16.22 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.20), residues: 1902 helix: 1.69 (0.17), residues: 884 sheet: -0.44 (0.32), residues: 260 loop : -0.20 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG e 200 TYR 0.017 0.002 TYR d 99 PHE 0.018 0.002 PHE e 246 TRP 0.037 0.001 TRP e 131 HIS 0.010 0.001 HIS b 256 Details of bonding type rmsd covalent geometry : bond 0.00632 (16465) covalent geometry : angle 0.59576 (22429) hydrogen bonds : bond 0.04424 ( 710) hydrogen bonds : angle 4.20559 ( 2033) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.9208 (m) cc_final: 0.8813 (t) REVERT: b 162 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8812 (tt0) REVERT: b 251 THR cc_start: 0.9209 (m) cc_final: 0.8897 (p) REVERT: c 64 LYS cc_start: 0.8921 (tppt) cc_final: 0.8599 (tppt) REVERT: d 39 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8488 (mt-10) REVERT: d 64 LYS cc_start: 0.9026 (tppp) cc_final: 0.8684 (tppt) REVERT: d 137 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8205 (p) REVERT: d 149 HIS cc_start: 0.9108 (m-70) cc_final: 0.8784 (m-70) REVERT: d 182 MET cc_start: 0.8710 (ttp) cc_final: 0.7625 (pmm) REVERT: d 244 ARG cc_start: 0.8351 (mmt-90) cc_final: 0.8016 (mmm160) REVERT: d 253 ARG cc_start: 0.7941 (tpp-160) cc_final: 0.7380 (tpp-160) REVERT: d 254 LEU cc_start: 0.8628 (tm) cc_final: 0.8035 (pp) REVERT: d 271 ARG cc_start: 0.8779 (tpt90) cc_final: 0.8484 (tpt90) REVERT: e 132 LEU cc_start: 0.9174 (mm) cc_final: 0.8563 (tt) REVERT: e 159 TRP cc_start: 0.8343 (p90) cc_final: 0.8052 (p90) REVERT: e 176 TRP cc_start: 0.8506 (t60) cc_final: 0.8192 (t60) REVERT: e 177 TRP cc_start: 0.8729 (t-100) cc_final: 0.8334 (t-100) REVERT: e 200 ARG cc_start: 0.8936 (ptm-80) cc_final: 0.8728 (ptm-80) REVERT: f 173 MET cc_start: 0.8714 (mmm) cc_final: 0.8026 (mtp) REVERT: f 245 MET cc_start: 0.7947 (ttm) cc_final: 0.7519 (tmm) REVERT: f 250 LEU cc_start: 0.8590 (tp) cc_final: 0.8344 (OUTLIER) REVERT: g 97 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8313 (mtt90) REVERT: g 149 HIS cc_start: 0.8454 (m90) cc_final: 0.7865 (m90) REVERT: g 159 TRP cc_start: 0.8634 (m100) cc_final: 0.8241 (m100) REVERT: g 176 TRP cc_start: 0.8285 (t60) cc_final: 0.7815 (t60) REVERT: g 182 MET cc_start: 0.8597 (ttm) cc_final: 0.8237 (tmm) outliers start: 34 outliers final: 12 residues processed: 200 average time/residue: 0.6823 time to fit residues: 149.6592 Evaluate side-chains 169 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 68 ASP Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain b residue 183 THR Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain b residue 232 SER Chi-restraints excluded: chain c residue 156 CYS Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 39 GLU Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 251 THR Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 164 PHE Chi-restraints excluded: chain e residue 237 HIS Chi-restraints excluded: chain g residue 97 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 221 ASN f 149 HIS g 276 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.121751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.068018 restraints weight = 31296.127| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.07 r_work: 0.2752 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16465 Z= 0.127 Angle : 0.547 9.706 22429 Z= 0.285 Chirality : 0.043 0.208 2452 Planarity : 0.004 0.089 2747 Dihedral : 12.783 80.769 2378 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.79 % Favored : 97.16 % Rotamer: Outliers : 1.26 % Allowed : 17.90 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.20), residues: 1902 helix: 1.84 (0.18), residues: 891 sheet: -0.30 (0.33), residues: 248 loop : -0.21 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG e 200 TYR 0.018 0.001 TYR g 99 PHE 0.014 0.001 PHE f 133 TRP 0.034 0.001 TRP e 131 HIS 0.010 0.001 HIS f 149 Details of bonding type rmsd covalent geometry : bond 0.00287 (16465) covalent geometry : angle 0.54682 (22429) hydrogen bonds : bond 0.03495 ( 710) hydrogen bonds : angle 3.99401 ( 2033) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.9115 (m) cc_final: 0.8800 (t) REVERT: b 251 THR cc_start: 0.9200 (m) cc_final: 0.8901 (p) REVERT: c 64 LYS cc_start: 0.8853 (tppt) cc_final: 0.8566 (tppt) REVERT: c 156 CYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8891 (m) REVERT: d 64 LYS cc_start: 0.8954 (tppp) cc_final: 0.8641 (tppt) REVERT: d 97 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8221 (mtp85) REVERT: d 137 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8562 (p) REVERT: d 149 HIS cc_start: 0.9074 (m-70) cc_final: 0.8683 (m-70) REVERT: d 182 MET cc_start: 0.8687 (ttp) cc_final: 0.7638 (pmm) REVERT: d 244 ARG cc_start: 0.8229 (mmt-90) cc_final: 0.7909 (mmm160) REVERT: d 254 LEU cc_start: 0.8602 (tm) cc_final: 0.8272 (mm) REVERT: d 271 ARG cc_start: 0.8806 (tpt90) cc_final: 0.8583 (tpt90) REVERT: e 131 TRP cc_start: 0.7103 (m100) cc_final: 0.6851 (m100) REVERT: e 132 LEU cc_start: 0.9194 (mm) cc_final: 0.8605 (tt) REVERT: e 176 TRP cc_start: 0.8501 (t60) cc_final: 0.8271 (t60) REVERT: e 177 TRP cc_start: 0.8762 (t-100) cc_final: 0.8462 (t-100) REVERT: f 173 MET cc_start: 0.8594 (mmm) cc_final: 0.7998 (mtp) REVERT: f 245 MET cc_start: 0.7929 (ttm) cc_final: 0.7454 (tmm) REVERT: f 250 LEU cc_start: 0.8595 (tp) cc_final: 0.8352 (OUTLIER) REVERT: g 97 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8395 (mtt90) REVERT: g 159 TRP cc_start: 0.8609 (m100) cc_final: 0.8186 (m100) REVERT: g 176 TRP cc_start: 0.8260 (t60) cc_final: 0.7880 (t60) REVERT: g 182 MET cc_start: 0.8518 (ttm) cc_final: 0.8136 (tmm) REVERT: g 224 MET cc_start: 0.7789 (mmm) cc_final: 0.7286 (mpm) outliers start: 21 outliers final: 10 residues processed: 179 average time/residue: 0.6671 time to fit residues: 130.9138 Evaluate side-chains 167 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain b residue 232 SER Chi-restraints excluded: chain c residue 156 CYS Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 97 ARG Chi-restraints excluded: chain d residue 132 LEU Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 251 THR Chi-restraints excluded: chain e residue 40 LYS Chi-restraints excluded: chain e residue 164 PHE Chi-restraints excluded: chain e residue 237 HIS Chi-restraints excluded: chain g residue 97 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 103 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 172 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 53 optimal weight: 0.0050 chunk 115 optimal weight: 0.6980 chunk 183 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 54 ASN f 149 HIS g 276 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.122666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.069006 restraints weight = 31346.755| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.06 r_work: 0.2773 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16465 Z= 0.118 Angle : 0.539 9.779 22429 Z= 0.279 Chirality : 0.043 0.214 2452 Planarity : 0.004 0.086 2747 Dihedral : 12.521 80.299 2378 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.05 % Favored : 96.90 % Rotamer: Outliers : 1.50 % Allowed : 17.36 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.20), residues: 1902 helix: 1.97 (0.18), residues: 891 sheet: -0.26 (0.33), residues: 248 loop : -0.23 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG d 252 TYR 0.015 0.001 TYR e 99 PHE 0.013 0.001 PHE f 133 TRP 0.023 0.001 TRP e 131 HIS 0.014 0.001 HIS f 149 Details of bonding type rmsd covalent geometry : bond 0.00267 (16465) covalent geometry : angle 0.53927 (22429) hydrogen bonds : bond 0.03205 ( 710) hydrogen bonds : angle 3.89504 ( 2033) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.9077 (m) cc_final: 0.8840 (t) REVERT: b 185 LYS cc_start: 0.9345 (mmmt) cc_final: 0.8965 (tptt) REVERT: b 251 THR cc_start: 0.9163 (m) cc_final: 0.8900 (p) REVERT: c 64 LYS cc_start: 0.8788 (tppt) cc_final: 0.8513 (tppt) REVERT: c 156 CYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8885 (m) REVERT: c 178 GLU cc_start: 0.9026 (tp30) cc_final: 0.8822 (tp30) REVERT: d 39 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8426 (mt-10) REVERT: d 64 LYS cc_start: 0.8972 (tppp) cc_final: 0.8679 (tppt) REVERT: d 97 ARG cc_start: 0.8556 (mmt90) cc_final: 0.8205 (mtp180) REVERT: d 149 HIS cc_start: 0.9095 (m-70) cc_final: 0.8693 (m-70) REVERT: d 182 MET cc_start: 0.8714 (ttp) cc_final: 0.7637 (pmm) REVERT: d 244 ARG cc_start: 0.8217 (mmt-90) cc_final: 0.7905 (mmm160) REVERT: d 252 ARG cc_start: 0.8952 (tpp80) cc_final: 0.8727 (tpp-160) REVERT: d 253 ARG cc_start: 0.7959 (tpp-160) cc_final: 0.7495 (tpp-160) REVERT: e 25 MET cc_start: 0.9385 (mtm) cc_final: 0.9160 (mpp) REVERT: e 132 LEU cc_start: 0.9167 (mm) cc_final: 0.8572 (tt) REVERT: e 176 TRP cc_start: 0.8456 (t60) cc_final: 0.8223 (t60) REVERT: e 177 TRP cc_start: 0.8781 (t-100) cc_final: 0.8394 (t-100) REVERT: f 173 MET cc_start: 0.8511 (mmm) cc_final: 0.7924 (mtp) REVERT: f 245 MET cc_start: 0.7894 (ttm) cc_final: 0.7406 (tmm) REVERT: f 250 LEU cc_start: 0.8613 (tp) cc_final: 0.8381 (OUTLIER) REVERT: g 39 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8490 (mt-10) REVERT: g 97 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8266 (mtt-85) REVERT: g 159 TRP cc_start: 0.8590 (m100) cc_final: 0.8147 (m100) REVERT: g 176 TRP cc_start: 0.8281 (t60) cc_final: 0.7865 (t60) REVERT: g 182 MET cc_start: 0.8461 (ttm) cc_final: 0.8126 (tmm) outliers start: 25 outliers final: 11 residues processed: 187 average time/residue: 0.6389 time to fit residues: 131.4821 Evaluate side-chains 168 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain b residue 232 SER Chi-restraints excluded: chain c residue 156 CYS Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 39 GLU Chi-restraints excluded: chain d residue 132 LEU Chi-restraints excluded: chain d residue 251 THR Chi-restraints excluded: chain e residue 40 LYS Chi-restraints excluded: chain e residue 164 PHE Chi-restraints excluded: chain g residue 76 LEU Chi-restraints excluded: chain g residue 97 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 2 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 175 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 83 optimal weight: 0.0370 chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 221 ASN d 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.123108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.069490 restraints weight = 31186.676| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.06 r_work: 0.2787 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16465 Z= 0.113 Angle : 0.536 10.207 22429 Z= 0.277 Chirality : 0.042 0.232 2452 Planarity : 0.004 0.087 2747 Dihedral : 12.442 80.726 2378 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.73 % Favored : 97.21 % Rotamer: Outliers : 1.32 % Allowed : 18.32 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.20), residues: 1902 helix: 2.01 (0.18), residues: 891 sheet: -0.19 (0.33), residues: 252 loop : -0.24 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG d 252 TYR 0.021 0.001 TYR d 99 PHE 0.015 0.001 PHE e 133 TRP 0.038 0.001 TRP e 131 HIS 0.005 0.001 HIS b 256 Details of bonding type rmsd covalent geometry : bond 0.00251 (16465) covalent geometry : angle 0.53616 (22429) hydrogen bonds : bond 0.03118 ( 710) hydrogen bonds : angle 3.82526 ( 2033) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.9045 (m) cc_final: 0.8835 (t) REVERT: b 185 LYS cc_start: 0.9343 (mmmt) cc_final: 0.8980 (tptt) REVERT: b 251 THR cc_start: 0.9165 (m) cc_final: 0.8897 (p) REVERT: c 64 LYS cc_start: 0.8776 (tppt) cc_final: 0.8493 (tppt) REVERT: c 154 TYR cc_start: 0.9071 (p90) cc_final: 0.8742 (p90) REVERT: c 156 CYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8919 (m) REVERT: c 178 GLU cc_start: 0.9012 (tp30) cc_final: 0.8811 (tp30) REVERT: d 39 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8463 (mt-10) REVERT: d 64 LYS cc_start: 0.8972 (tppp) cc_final: 0.8683 (tppt) REVERT: d 97 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8241 (mtp180) REVERT: d 149 HIS cc_start: 0.9100 (m-70) cc_final: 0.8677 (m-70) REVERT: d 182 MET cc_start: 0.8715 (ttp) cc_final: 0.7641 (pmm) REVERT: d 244 ARG cc_start: 0.8184 (mmt-90) cc_final: 0.7878 (mmm160) REVERT: d 254 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8148 (mm) REVERT: e 33 ASP cc_start: 0.8815 (t0) cc_final: 0.8590 (t0) REVERT: e 131 TRP cc_start: 0.6914 (m100) cc_final: 0.6594 (m100) REVERT: e 132 LEU cc_start: 0.9217 (mm) cc_final: 0.8686 (tt) REVERT: e 175 ILE cc_start: 0.9238 (mt) cc_final: 0.9037 (mm) REVERT: e 176 TRP cc_start: 0.8453 (t60) cc_final: 0.8199 (t60) REVERT: e 177 TRP cc_start: 0.8809 (t-100) cc_final: 0.8420 (t-100) REVERT: e 250 LEU cc_start: 0.9189 (mt) cc_final: 0.8942 (tt) REVERT: f 173 MET cc_start: 0.8441 (mmm) cc_final: 0.7858 (mtp) REVERT: f 245 MET cc_start: 0.7911 (ttm) cc_final: 0.7433 (tmm) REVERT: f 250 LEU cc_start: 0.8612 (tp) cc_final: 0.8378 (OUTLIER) REVERT: g 97 ARG cc_start: 0.8796 (mmt-90) cc_final: 0.8310 (mtt90) REVERT: g 149 HIS cc_start: 0.8017 (m90) cc_final: 0.7722 (m170) REVERT: g 159 TRP cc_start: 0.8595 (m100) cc_final: 0.8136 (m100) REVERT: g 176 TRP cc_start: 0.8240 (t60) cc_final: 0.7841 (t-100) REVERT: g 182 MET cc_start: 0.8437 (ttm) cc_final: 0.8084 (tmm) REVERT: g 224 MET cc_start: 0.7805 (mmm) cc_final: 0.7309 (mpm) REVERT: g 285 TYR cc_start: 0.8874 (m-80) cc_final: 0.8622 (m-10) outliers start: 22 outliers final: 12 residues processed: 187 average time/residue: 0.6598 time to fit residues: 135.3493 Evaluate side-chains 171 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain b residue 232 SER Chi-restraints excluded: chain c residue 156 CYS Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 39 GLU Chi-restraints excluded: chain d residue 97 ARG Chi-restraints excluded: chain d residue 254 LEU Chi-restraints excluded: chain e residue 40 LYS Chi-restraints excluded: chain e residue 164 PHE Chi-restraints excluded: chain e residue 237 HIS Chi-restraints excluded: chain e residue 280 VAL Chi-restraints excluded: chain g residue 76 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 169 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 178 optimal weight: 4.9990 chunk 2 optimal weight: 0.2980 chunk 184 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 76 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: ** d 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 149 HIS g 276 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.123051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.069609 restraints weight = 31424.646| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.07 r_work: 0.2788 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16465 Z= 0.116 Angle : 0.555 17.440 22429 Z= 0.282 Chirality : 0.042 0.201 2452 Planarity : 0.004 0.086 2747 Dihedral : 12.412 81.381 2378 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.21 % Favored : 96.74 % Rotamer: Outliers : 1.14 % Allowed : 18.92 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.20), residues: 1902 helix: 2.02 (0.18), residues: 892 sheet: -0.17 (0.33), residues: 252 loop : -0.23 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG f 252 TYR 0.018 0.001 TYR g 99 PHE 0.029 0.001 PHE g 269 TRP 0.032 0.001 TRP e 131 HIS 0.019 0.001 HIS f 149 Details of bonding type rmsd covalent geometry : bond 0.00263 (16465) covalent geometry : angle 0.55456 (22429) hydrogen bonds : bond 0.03064 ( 710) hydrogen bonds : angle 3.77561 ( 2033) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 185 LYS cc_start: 0.9351 (mmmt) cc_final: 0.9000 (tptt) REVERT: b 251 THR cc_start: 0.9159 (m) cc_final: 0.8893 (p) REVERT: c 64 LYS cc_start: 0.8768 (tppt) cc_final: 0.8499 (tppt) REVERT: c 154 TYR cc_start: 0.9082 (p90) cc_final: 0.8757 (p90) REVERT: c 156 CYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8931 (m) REVERT: d 39 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8455 (mt-10) REVERT: d 64 LYS cc_start: 0.8985 (tppp) cc_final: 0.8694 (tppt) REVERT: d 97 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8263 (mtp85) REVERT: d 149 HIS cc_start: 0.9108 (m-70) cc_final: 0.8664 (m-70) REVERT: d 182 MET cc_start: 0.8690 (ttp) cc_final: 0.7635 (pmm) REVERT: d 244 ARG cc_start: 0.8205 (mmt-90) cc_final: 0.7901 (mmm160) REVERT: d 254 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8138 (mm) REVERT: e 33 ASP cc_start: 0.8783 (t0) cc_final: 0.8559 (t0) REVERT: e 131 TRP cc_start: 0.7008 (m100) cc_final: 0.6685 (m100) REVERT: e 132 LEU cc_start: 0.9210 (mm) cc_final: 0.8591 (tt) REVERT: e 175 ILE cc_start: 0.9238 (mt) cc_final: 0.9037 (mm) REVERT: e 176 TRP cc_start: 0.8448 (t60) cc_final: 0.8199 (t60) REVERT: e 177 TRP cc_start: 0.8825 (t-100) cc_final: 0.8451 (t-100) REVERT: f 173 MET cc_start: 0.8422 (mmm) cc_final: 0.7844 (mtp) REVERT: f 245 MET cc_start: 0.7896 (ttm) cc_final: 0.7421 (tmm) REVERT: f 250 LEU cc_start: 0.8643 (tp) cc_final: 0.8380 (OUTLIER) REVERT: g 97 ARG cc_start: 0.8727 (mmt-90) cc_final: 0.8205 (mtt-85) REVERT: g 149 HIS cc_start: 0.8220 (m90) cc_final: 0.7860 (m170) REVERT: g 159 TRP cc_start: 0.8569 (m100) cc_final: 0.8089 (m100) REVERT: g 182 MET cc_start: 0.8442 (ttm) cc_final: 0.8144 (tmm) outliers start: 19 outliers final: 12 residues processed: 176 average time/residue: 0.6911 time to fit residues: 132.9688 Evaluate side-chains 171 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 232 SER Chi-restraints excluded: chain c residue 156 CYS Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 39 GLU Chi-restraints excluded: chain d residue 97 ARG Chi-restraints excluded: chain d residue 254 LEU Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 40 LYS Chi-restraints excluded: chain e residue 164 PHE Chi-restraints excluded: chain f residue 285 TYR Chi-restraints excluded: chain g residue 76 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 132 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 163 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 171 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.122756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.069082 restraints weight = 31390.081| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.07 r_work: 0.2778 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16465 Z= 0.137 Angle : 0.571 17.539 22429 Z= 0.291 Chirality : 0.043 0.190 2452 Planarity : 0.004 0.087 2747 Dihedral : 12.429 82.156 2378 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.15 % Favored : 96.79 % Rotamer: Outliers : 1.02 % Allowed : 19.28 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.20), residues: 1902 helix: 2.00 (0.18), residues: 890 sheet: -0.12 (0.33), residues: 255 loop : -0.25 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG f 252 TYR 0.025 0.001 TYR f 285 PHE 0.022 0.001 PHE g 269 TRP 0.057 0.001 TRP d 272 HIS 0.006 0.001 HIS b 256 Details of bonding type rmsd covalent geometry : bond 0.00318 (16465) covalent geometry : angle 0.57058 (22429) hydrogen bonds : bond 0.03171 ( 710) hydrogen bonds : angle 3.81674 ( 2033) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 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: b 185 LYS cc_start: 0.9355 (mmmt) cc_final: 0.9011 (tptt) REVERT: b 251 THR cc_start: 0.9163 (m) cc_final: 0.8894 (p) REVERT: c 64 LYS cc_start: 0.8776 (tppt) cc_final: 0.8502 (tppt) REVERT: c 154 TYR cc_start: 0.9105 (p90) cc_final: 0.8759 (p90) REVERT: c 156 CYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8924 (m) REVERT: d 39 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8465 (mt-10) REVERT: d 64 LYS cc_start: 0.9025 (tppp) cc_final: 0.8720 (tppt) REVERT: d 97 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8257 (mtp85) REVERT: d 149 HIS cc_start: 0.9116 (m-70) cc_final: 0.8519 (m90) REVERT: d 182 MET cc_start: 0.8691 (ttp) cc_final: 0.7637 (pmm) REVERT: d 244 ARG cc_start: 0.8192 (mmt-90) cc_final: 0.7889 (mmm160) REVERT: e 33 ASP cc_start: 0.8770 (t0) cc_final: 0.8539 (t0) REVERT: e 131 TRP cc_start: 0.6944 (m100) cc_final: 0.6645 (m100) REVERT: e 132 LEU cc_start: 0.9214 (mm) cc_final: 0.8591 (tt) REVERT: e 175 ILE cc_start: 0.9235 (mt) cc_final: 0.9022 (mm) REVERT: e 176 TRP cc_start: 0.8463 (t60) cc_final: 0.8210 (t60) REVERT: e 177 TRP cc_start: 0.8843 (t-100) cc_final: 0.8468 (t-100) REVERT: f 173 MET cc_start: 0.8440 (mmm) cc_final: 0.7864 (mtp) REVERT: f 245 MET cc_start: 0.7823 (ttm) cc_final: 0.7364 (tmm) REVERT: f 250 LEU cc_start: 0.8630 (tp) cc_final: 0.8380 (OUTLIER) REVERT: g 97 ARG cc_start: 0.8734 (mmt-90) cc_final: 0.8130 (mtt-85) REVERT: g 149 HIS cc_start: 0.8211 (m90) cc_final: 0.7969 (m170) REVERT: g 159 TRP cc_start: 0.8591 (m100) cc_final: 0.8110 (m100) REVERT: g 182 MET cc_start: 0.8442 (ttm) cc_final: 0.8126 (tmm) REVERT: g 224 MET cc_start: 0.7814 (mmm) cc_final: 0.7461 (mpm) outliers start: 17 outliers final: 11 residues processed: 166 average time/residue: 0.6963 time to fit residues: 126.2474 Evaluate side-chains 163 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain b residue 232 SER Chi-restraints excluded: chain c residue 156 CYS Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 39 GLU Chi-restraints excluded: chain d residue 97 ARG Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 40 LYS Chi-restraints excluded: chain e residue 164 PHE Chi-restraints excluded: chain g residue 76 LEU Chi-restraints excluded: chain g residue 143 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 175 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 149 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.122094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.068441 restraints weight = 31276.495| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.06 r_work: 0.2763 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16465 Z= 0.150 Angle : 0.573 16.601 22429 Z= 0.292 Chirality : 0.043 0.188 2452 Planarity : 0.004 0.086 2747 Dihedral : 12.489 83.027 2378 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.00 % Favored : 96.95 % Rotamer: Outliers : 0.96 % Allowed : 19.28 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.20), residues: 1902 helix: 1.98 (0.18), residues: 890 sheet: -0.08 (0.33), residues: 254 loop : -0.29 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG d 17 TYR 0.024 0.001 TYR d 99 PHE 0.025 0.001 PHE g 269 TRP 0.032 0.001 TRP d 272 HIS 0.022 0.001 HIS f 149 Details of bonding type rmsd covalent geometry : bond 0.00350 (16465) covalent geometry : angle 0.57347 (22429) hydrogen bonds : bond 0.03381 ( 710) hydrogen bonds : angle 3.82906 ( 2033) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 255 ASP cc_start: 0.7815 (m-30) cc_final: 0.7603 (p0) REVERT: b 185 LYS cc_start: 0.9363 (mmmt) cc_final: 0.9025 (tptt) REVERT: b 251 THR cc_start: 0.9163 (m) cc_final: 0.8889 (p) REVERT: c 64 LYS cc_start: 0.8787 (tppt) cc_final: 0.8522 (tppt) REVERT: c 154 TYR cc_start: 0.9119 (p90) cc_final: 0.8766 (p90) REVERT: c 156 CYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8928 (m) REVERT: d 39 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8441 (mt-10) REVERT: d 64 LYS cc_start: 0.9067 (tppp) cc_final: 0.8762 (tppt) REVERT: d 97 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8237 (mtp180) REVERT: d 149 HIS cc_start: 0.9115 (m-70) cc_final: 0.8522 (m90) REVERT: d 182 MET cc_start: 0.8640 (ttp) cc_final: 0.7626 (pmm) REVERT: d 244 ARG cc_start: 0.8292 (mmt-90) cc_final: 0.7988 (mmm160) REVERT: d 254 LEU cc_start: 0.8673 (tm) cc_final: 0.8300 (mm) REVERT: e 131 TRP cc_start: 0.6924 (m100) cc_final: 0.6648 (m100) REVERT: e 132 LEU cc_start: 0.9208 (mm) cc_final: 0.8546 (tt) REVERT: e 175 ILE cc_start: 0.9223 (mt) cc_final: 0.8997 (mm) REVERT: e 176 TRP cc_start: 0.8486 (t60) cc_final: 0.8228 (t60) REVERT: e 177 TRP cc_start: 0.8868 (t-100) cc_final: 0.8476 (t-100) REVERT: f 173 MET cc_start: 0.8500 (mmm) cc_final: 0.7910 (mtp) REVERT: f 245 MET cc_start: 0.7885 (ttm) cc_final: 0.7392 (tmm) REVERT: f 250 LEU cc_start: 0.8657 (tp) cc_final: 0.8386 (OUTLIER) REVERT: g 97 ARG cc_start: 0.8724 (mmt-90) cc_final: 0.8206 (mtt-85) REVERT: g 149 HIS cc_start: 0.8323 (m90) cc_final: 0.8096 (m170) REVERT: g 159 TRP cc_start: 0.8607 (m100) cc_final: 0.8144 (m100) REVERT: g 169 CYS cc_start: 0.9101 (m) cc_final: 0.8802 (t) REVERT: g 176 TRP cc_start: 0.8290 (t60) cc_final: 0.7931 (t-100) REVERT: g 182 MET cc_start: 0.8476 (ttm) cc_final: 0.8245 (tmm) REVERT: g 224 MET cc_start: 0.7900 (mmm) cc_final: 0.7485 (mpm) outliers start: 16 outliers final: 12 residues processed: 168 average time/residue: 0.6655 time to fit residues: 122.7883 Evaluate side-chains 164 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain b residue 232 SER Chi-restraints excluded: chain c residue 156 CYS Chi-restraints excluded: chain c residue 189 SER Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 39 GLU Chi-restraints excluded: chain d residue 97 ARG Chi-restraints excluded: chain d residue 251 THR Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 164 PHE Chi-restraints excluded: chain f residue 285 TYR Chi-restraints excluded: chain g residue 76 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 100 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 171 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 124 optimal weight: 0.0270 chunk 84 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 96 ASN ** d 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.123066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.069207 restraints weight = 31275.644| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.09 r_work: 0.2782 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16465 Z= 0.120 Angle : 0.570 16.178 22429 Z= 0.291 Chirality : 0.042 0.183 2452 Planarity : 0.004 0.086 2747 Dihedral : 12.457 81.283 2378 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 0.96 % Allowed : 19.22 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.20), residues: 1902 helix: 2.01 (0.18), residues: 890 sheet: -0.04 (0.33), residues: 254 loop : -0.28 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG f 252 TYR 0.019 0.001 TYR f 285 PHE 0.023 0.001 PHE g 269 TRP 0.039 0.001 TRP d 272 HIS 0.005 0.001 HIS b 256 Details of bonding type rmsd covalent geometry : bond 0.00272 (16465) covalent geometry : angle 0.57021 (22429) hydrogen bonds : bond 0.03174 ( 710) hydrogen bonds : angle 3.79537 ( 2033) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5706.31 seconds wall clock time: 97 minutes 47.91 seconds (5867.91 seconds total)