Starting phenix.real_space_refine on Fri Jul 3 22:14:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rqt_54184/07_2026/9rqt_54184_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rqt_54184/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9rqt_54184/07_2026/9rqt_54184_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rqt_54184/07_2026/9rqt_54184_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rqt_54184/07_2026/9rqt_54184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rqt_54184/07_2026/9rqt_54184.map" } 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-6108/lib/python3.11/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: 3.67, per 1000 atoms: 0.23 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: 1.09 Conformation dependent library (CDL) restraints added in 544.1 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: 1.69 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: 2.30 Time building geometry restraints manager: 1.44 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=" O3B AGS b1000 " pdb=" PB AGS b1000 " ideal model delta sigma weight residual 1.673 1.568 0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" O3A AGS b1000 " pdb=" PA AGS b1000 " ideal model delta sigma weight residual 1.664 1.571 0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" O3B AGS a1000 " pdb=" PB AGS a1000 " ideal model delta sigma weight residual 1.673 1.581 0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" O3A AGS a1000 " pdb=" PA AGS a1000 " ideal model delta sigma weight residual 1.664 1.586 0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" O3B AGS b1000 " pdb=" PG AGS b1000 " ideal model delta sigma weight residual 1.614 1.550 0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 16460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 22110 2.34 - 4.67: 230 4.67 - 7.01: 19 7.01 - 9.35: 21 9.35 - 11.69: 49 Bond angle restraints: 22429 Sorted by residual: angle pdb=" N3 DT H 24 " pdb=" C4 DT H 24 " pdb=" O4 DT H 24 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT H 28 " pdb=" C4 DT H 28 " pdb=" O4 DT H 28 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT H 32 " pdb=" C4 DT H 32 " pdb=" O4 DT H 32 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+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=" C2' AGS a1000 " pdb=" C1' AGS a1000 " pdb=" N9 AGS a1000 " ideal model delta sigma weight residual 111.82 123.51 -11.69 3.00e+00 1.11e-01 1.52e+01 ... (remaining 22424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.93: 9190 28.93 - 57.86: 486 57.86 - 86.80: 47 86.80 - 115.73: 5 115.73 - 144.66: 5 Dihedral angle restraints: 9733 sinusoidal: 4122 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=" O1B AGS a1000 " pdb=" O3B AGS a1000 " pdb=" PB AGS a1000 " pdb=" PG AGS a1000 " ideal model delta sinusoidal sigma weight residual 138.55 -6.11 144.66 1 3.00e+01 1.11e-03 1.94e+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 ... (remaining 9730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 2416 0.181 - 0.362: 4 0.362 - 0.543: 27 0.543 - 0.725: 0 0.725 - 0.906: 1 Chirality restraints: 2448 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 2.43 1.53 0.91 2.00e-01 2.50e+01 2.05e+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 2.34 -2.76 -0.42 2.00e-01 2.50e+01 4.42e+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 2.34 -2.75 -0.42 2.00e-01 2.50e+01 4.40e+00 ... (remaining 2445 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: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.330 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 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:5.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 16465 Z= 0.206 Angle : 0.782 11.686 22429 Z= 0.375 Chirality : 0.065 0.906 2448 Planarity : 0.003 0.089 2747 Dihedral : 16.854 144.661 6093 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/Z covalent geometry : bond 0.00357 / 0.21 (16465) covalent geometry : angle 0.78194 / 0.37 (22429) hydrogen bonds : bond 0.14780 / 15.87 ( 710) hydrogen bonds : angle 5.64180 / 5.79 ( 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 : 0.582 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: 0.6013 time to fit residues: 109.0592 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 : 0.630 ------------------------------------------------------------------------------- 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... b 256 HIS c 69 ASN c 110 GLN d 149 HIS d 210 GLN d 282 HIS e 69 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.121940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.067697 restraints weight = 31671.595| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.17 r_work: 0.2725 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16465 Z= 0.221 Angle : 0.601 8.385 22429 Z= 0.318 Chirality : 0.046 0.169 2448 Planarity : 0.004 0.085 2747 Dihedral : 14.326 167.076 2420 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.44 % Allowed : 13.93 % Favored : 84.62 % 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: 0.96 (0.20), residues: 1902 helix: 1.67 (0.17), residues: 887 sheet: -0.43 (0.34), residues: 247 loop : -0.12 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG e 200 TYR 0.022 0.002 TYR f 99 PHE 0.022 0.002 PHE f 133 TRP 0.029 0.001 TRP d 272 HIS 0.009 0.001 HIS b 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 (16465) covalent geometry : angle 0.60096 / 0.32 (22429) hydrogen bonds : bond 0.04568 / 5.05 ( 710) hydrogen bonds : angle 4.52596 / 4.66 ( 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 188 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.9133 (m) cc_final: 0.8734 (p) REVERT: a 252 ARG cc_start: 0.8494 (tpp-160) cc_final: 0.8258 (tpp-160) REVERT: c 64 LYS cc_start: 0.8879 (tppt) cc_final: 0.8570 (tppt) REVERT: d 137 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.7894 (p) REVERT: d 149 HIS cc_start: 0.9077 (m-70) cc_final: 0.8720 (m-70) REVERT: d 182 MET cc_start: 0.8685 (ttp) cc_final: 0.7587 (pmm) REVERT: d 239 GLN cc_start: 0.9297 (tp40) cc_final: 0.9089 (tm-30) REVERT: d 244 ARG cc_start: 0.8257 (mmt-90) cc_final: 0.7904 (mmm160) REVERT: d 252 ARG cc_start: 0.9024 (tpp80) cc_final: 0.8756 (tpp-160) REVERT: d 254 LEU cc_start: 0.8838 (mm) cc_final: 0.8177 (pp) REVERT: d 265 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.8980 (mt-10) REVERT: e 159 TRP cc_start: 0.8331 (p90) cc_final: 0.8055 (p90) REVERT: e 173 MET cc_start: 0.8499 (tpp) cc_final: 0.8276 (tpp) REVERT: e 177 TRP cc_start: 0.8508 (t-100) cc_final: 0.8239 (t-100) REVERT: e 200 ARG cc_start: 0.8951 (ptm-80) cc_final: 0.8731 (ptm-80) REVERT: e 245 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.6310 (mmp) REVERT: f 173 MET cc_start: 0.8366 (mmm) cc_final: 0.7924 (mtp) REVERT: f 245 MET cc_start: 0.7880 (ttm) cc_final: 0.7454 (tmt) REVERT: g 97 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8347 (mtt90) REVERT: g 149 HIS cc_start: 0.8540 (m90) cc_final: 0.7982 (m90) REVERT: g 159 TRP cc_start: 0.8496 (m100) cc_final: 0.7991 (m100) REVERT: g 176 TRP cc_start: 0.8194 (t60) cc_final: 0.7751 (t-100) REVERT: g 182 MET cc_start: 0.8563 (ttm) cc_final: 0.8194 (tmm) REVERT: g 200 ARG cc_start: 0.8832 (mmp80) cc_final: 0.8490 (mmp80) outliers start: 24 outliers final: 6 residues processed: 181 average time/residue: 0.5804 time to fit residues: 115.8569 Evaluate side-chains 157 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain b residue 77 THR Chi-restraints excluded: chain c residue 156 CYS Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 137 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: 6.9990 chunk 4 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 chunk 159 optimal weight: 0.4980 chunk 91 optimal weight: 0.3980 chunk 150 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 221 ASN b 256 HIS d 210 GLN f 149 HIS g 276 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.123514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.069948 restraints weight = 31889.520| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.15 r_work: 0.2779 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16465 Z= 0.119 Angle : 0.546 9.035 22429 Z= 0.289 Chirality : 0.043 0.150 2448 Planarity : 0.004 0.085 2747 Dihedral : 13.719 159.378 2418 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.74 % Allowed : 15.14 % Favored : 83.12 % 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: 1.04 (0.20), residues: 1902 helix: 1.74 (0.17), residues: 895 sheet: -0.32 (0.34), residues: 246 loop : -0.14 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG e 244 TYR 0.029 0.002 TYR f 99 PHE 0.017 0.001 PHE e 246 TRP 0.043 0.001 TRP e 131 HIS 0.010 0.001 HIS b 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (16465) covalent geometry : angle 0.54579 / 0.29 (22429) hydrogen bonds : bond 0.03735 / 4.06 ( 710) hydrogen bonds : angle 4.20250 / 4.30 ( 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 194 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.9069 (m) cc_final: 0.8566 (p) REVERT: a 252 ARG cc_start: 0.8482 (tpp-160) cc_final: 0.8265 (tpp80) REVERT: b 251 THR cc_start: 0.9190 (m) cc_final: 0.8840 (p) REVERT: c 64 LYS cc_start: 0.8791 (tppt) cc_final: 0.8485 (tppt) REVERT: d 149 HIS cc_start: 0.8965 (m-70) cc_final: 0.8464 (m90) REVERT: d 182 MET cc_start: 0.8668 (ttp) cc_final: 0.7569 (pmm) REVERT: d 239 GLN cc_start: 0.9266 (tp40) cc_final: 0.9063 (tm-30) REVERT: d 244 ARG cc_start: 0.8207 (mmt-90) cc_final: 0.7888 (mmm160) REVERT: d 252 ARG cc_start: 0.9034 (tpp80) cc_final: 0.8734 (tpp-160) REVERT: d 253 ARG cc_start: 0.7399 (tpp-160) cc_final: 0.7123 (tpp-160) REVERT: d 254 LEU cc_start: 0.8808 (mm) cc_final: 0.8307 (pp) REVERT: d 265 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8920 (mt-10) REVERT: d 271 ARG cc_start: 0.8803 (tpt90) cc_final: 0.8584 (tpt90) REVERT: e 131 TRP cc_start: 0.6972 (m100) cc_final: 0.6457 (m100) REVERT: e 132 LEU cc_start: 0.9174 (mm) cc_final: 0.8610 (tt) REVERT: e 159 TRP cc_start: 0.8336 (p90) cc_final: 0.8046 (p90) REVERT: e 173 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8196 (tpp) REVERT: e 176 TRP cc_start: 0.8432 (t60) cc_final: 0.8145 (t60) REVERT: e 177 TRP cc_start: 0.8600 (t-100) cc_final: 0.8234 (t-100) REVERT: e 245 MET cc_start: 0.7870 (mmt) cc_final: 0.7665 (mpm) REVERT: f 173 MET cc_start: 0.8324 (mmm) cc_final: 0.7971 (mtp) REVERT: f 245 MET cc_start: 0.7874 (ttm) cc_final: 0.7470 (tmm) REVERT: f 250 LEU cc_start: 0.8442 (tp) cc_final: 0.8209 (tp) REVERT: g 97 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8351 (mtt90) REVERT: g 149 HIS cc_start: 0.8460 (m90) cc_final: 0.7903 (m90) REVERT: g 159 TRP cc_start: 0.8527 (m100) cc_final: 0.8064 (m100) REVERT: g 176 TRP cc_start: 0.8226 (t60) cc_final: 0.7750 (t-100) REVERT: g 182 MET cc_start: 0.8477 (ttm) cc_final: 0.8101 (tmm) REVERT: g 224 MET cc_start: 0.7798 (mmm) cc_final: 0.7281 (mpm) outliers start: 29 outliers final: 8 residues processed: 188 average time/residue: 0.5737 time to fit residues: 118.7662 Evaluate side-chains 162 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain b residue 77 THR Chi-restraints excluded: chain b residue 130 ILE Chi-restraints excluded: chain b residue 183 THR Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain d residue 265 GLU Chi-restraints excluded: chain e residue 164 PHE Chi-restraints excluded: chain e residue 173 MET Chi-restraints excluded: chain e residue 237 HIS Chi-restraints excluded: chain f residue 216 VAL 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: 4.9990 chunk 98 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 157 optimal weight: 0.3980 chunk 168 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 256 HIS ** d 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 149 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.122310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.068270 restraints weight = 31747.239| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.15 r_work: 0.2719 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1632 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= 0.168 Angle : 0.544 8.817 22429 Z= 0.287 Chirality : 0.044 0.140 2448 Planarity : 0.004 0.089 2747 Dihedral : 13.565 154.364 2414 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.94 % Favored : 97.00 % Rotamer: Outliers : 1.50 % Allowed : 15.92 % Favored : 82.58 % 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: 1.02 (0.20), residues: 1902 helix: 1.76 (0.17), residues: 896 sheet: -0.32 (0.33), residues: 248 loop : -0.20 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG e 200 TYR 0.018 0.002 TYR d 99 PHE 0.012 0.001 PHE e 246 TRP 0.022 0.001 TRP e 131 HIS 0.010 0.001 HIS b 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (16465) covalent geometry : angle 0.54370 / 0.29 (22429) hydrogen bonds : bond 0.03758 / 4.12 ( 710) hydrogen bonds : angle 4.11473 / 4.24 ( 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 181 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.9119 (m) cc_final: 0.8649 (p) REVERT: b 251 THR cc_start: 0.9239 (m) cc_final: 0.8905 (p) REVERT: c 64 LYS cc_start: 0.8868 (tppt) cc_final: 0.8563 (tppt) REVERT: d 137 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8179 (p) REVERT: d 149 HIS cc_start: 0.9028 (m-70) cc_final: 0.8710 (m-70) REVERT: d 182 MET cc_start: 0.8624 (ttp) cc_final: 0.7410 (pmm) REVERT: d 239 GLN cc_start: 0.9221 (tp40) cc_final: 0.9010 (tm-30) REVERT: d 244 ARG cc_start: 0.8275 (mmt-90) cc_final: 0.7941 (mmm160) REVERT: d 252 ARG cc_start: 0.8993 (tpp80) cc_final: 0.8774 (tpp-160) REVERT: d 253 ARG cc_start: 0.7393 (tpp-160) cc_final: 0.6813 (tpp-160) REVERT: d 254 LEU cc_start: 0.8833 (mm) cc_final: 0.8337 (pp) REVERT: d 271 ARG cc_start: 0.8778 (tpt90) cc_final: 0.8516 (tpt90) REVERT: e 25 MET cc_start: 0.9473 (mtm) cc_final: 0.9266 (mtm) REVERT: e 132 LEU cc_start: 0.9145 (mm) cc_final: 0.8550 (tt) REVERT: e 159 TRP cc_start: 0.8320 (p90) cc_final: 0.8033 (p90) REVERT: e 173 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8200 (tpp) REVERT: e 176 TRP cc_start: 0.8481 (t60) cc_final: 0.8216 (t60) REVERT: e 177 TRP cc_start: 0.8655 (t-100) cc_final: 0.8273 (t-100) REVERT: f 173 MET cc_start: 0.8613 (mmm) cc_final: 0.8034 (mtp) REVERT: f 245 MET cc_start: 0.7900 (ttm) cc_final: 0.7468 (tmm) REVERT: f 250 LEU cc_start: 0.8468 (tp) cc_final: 0.8249 (OUTLIER) REVERT: g 97 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8334 (mtt90) REVERT: g 159 TRP cc_start: 0.8544 (m100) cc_final: 0.8095 (m100) REVERT: g 176 TRP cc_start: 0.8286 (t60) cc_final: 0.7834 (t60) REVERT: g 182 MET cc_start: 0.8590 (ttm) cc_final: 0.8233 (tmm) outliers start: 25 outliers final: 10 residues processed: 177 average time/residue: 0.5275 time to fit residues: 102.9890 Evaluate side-chains 159 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain b residue 77 THR Chi-restraints excluded: chain b residue 183 THR Chi-restraints excluded: chain b residue 232 SER 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 e residue 37 THR Chi-restraints excluded: chain e residue 164 PHE Chi-restraints excluded: chain e residue 173 MET 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: 0.4980 chunk 100 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 46 optimal weight: 0.3980 chunk 120 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 126 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 256 HIS ** d 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 149 HIS g 242 GLN g 276 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.123044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.068956 restraints weight = 31542.052| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.16 r_work: 0.2727 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1806 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= 0.131 Angle : 0.533 9.318 22429 Z= 0.281 Chirality : 0.043 0.226 2448 Planarity : 0.004 0.089 2747 Dihedral : 13.544 157.311 2414 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.68 % Favored : 97.27 % Rotamer: Outliers : 1.44 % Allowed : 17.00 % Favored : 81.56 % 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: 1.10 (0.20), residues: 1902 helix: 1.86 (0.18), residues: 893 sheet: -0.24 (0.33), residues: 248 loop : -0.22 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG d 97 TYR 0.018 0.001 TYR g 99 PHE 0.030 0.001 PHE d 258 TRP 0.045 0.001 TRP e 131 HIS 0.011 0.001 HIS b 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (16465) covalent geometry : angle 0.53327 / 0.28 (22429) hydrogen bonds : bond 0.03493 / 3.81 ( 710) hydrogen bonds : angle 4.00952 / 4.12 ( 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 185 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.9115 (m) cc_final: 0.8693 (p) REVERT: a 252 ARG cc_start: 0.8723 (tpp-160) cc_final: 0.8453 (tpp80) REVERT: b 251 THR cc_start: 0.9220 (m) cc_final: 0.8892 (p) REVERT: c 64 LYS cc_start: 0.8802 (tppt) cc_final: 0.8516 (tppt) REVERT: c 156 CYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8844 (m) REVERT: c 178 GLU cc_start: 0.9015 (tp30) cc_final: 0.8804 (tp30) REVERT: d 149 HIS cc_start: 0.9068 (m-70) cc_final: 0.8549 (m90) REVERT: d 182 MET cc_start: 0.8614 (ttp) cc_final: 0.7570 (pmm) REVERT: d 239 GLN cc_start: 0.9215 (tp40) cc_final: 0.9007 (tm-30) REVERT: d 244 ARG cc_start: 0.8250 (mmt-90) cc_final: 0.7947 (mmm160) REVERT: d 271 ARG cc_start: 0.8766 (tpt90) cc_final: 0.8552 (tpt90) REVERT: e 131 TRP cc_start: 0.6975 (m100) cc_final: 0.6735 (m100) REVERT: e 132 LEU cc_start: 0.9218 (mm) cc_final: 0.8661 (tt) REVERT: e 159 TRP cc_start: 0.8338 (p90) cc_final: 0.8059 (p90) REVERT: e 176 TRP cc_start: 0.8418 (t60) cc_final: 0.8161 (t60) REVERT: e 177 TRP cc_start: 0.8697 (t-100) cc_final: 0.8278 (t-100) REVERT: e 201 VAL cc_start: 0.8197 (m) cc_final: 0.7914 (p) REVERT: f 173 MET cc_start: 0.8562 (mmm) cc_final: 0.7956 (mtp) REVERT: f 245 MET cc_start: 0.7849 (ttm) cc_final: 0.7416 (tmm) REVERT: f 250 LEU cc_start: 0.8518 (tp) cc_final: 0.8282 (tp) REVERT: g 97 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8244 (mtt-85) REVERT: g 149 HIS cc_start: 0.8314 (m90) cc_final: 0.7892 (m90) REVERT: g 159 TRP cc_start: 0.8572 (m100) cc_final: 0.8124 (m100) REVERT: g 176 TRP cc_start: 0.8197 (t60) cc_final: 0.7816 (t-100) REVERT: g 182 MET cc_start: 0.8487 (ttm) cc_final: 0.8149 (tmm) outliers start: 24 outliers final: 8 residues processed: 182 average time/residue: 0.5970 time to fit residues: 119.5793 Evaluate side-chains 164 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 251 THR Chi-restraints excluded: chain e residue 15 VAL 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: 3.9990 chunk 128 optimal weight: 8.9990 chunk 172 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 135 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 256 HIS d 54 ASN ** d 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 149 HIS g 276 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.122782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.068592 restraints weight = 31598.735| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.16 r_work: 0.2722 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1996 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= 0.145 Angle : 0.533 9.812 22429 Z= 0.280 Chirality : 0.043 0.209 2448 Planarity : 0.004 0.090 2747 Dihedral : 13.481 158.190 2414 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.84 % Favored : 97.11 % Rotamer: Outliers : 1.50 % Allowed : 17.60 % Favored : 80.90 % 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: 1.10 (0.20), residues: 1902 helix: 1.90 (0.18), residues: 891 sheet: -0.32 (0.32), residues: 258 loop : -0.23 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG e 200 TYR 0.017 0.001 TYR d 99 PHE 0.022 0.001 PHE d 258 TRP 0.024 0.001 TRP e 131 HIS 0.011 0.001 HIS f 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (16465) covalent geometry : angle 0.53350 / 0.28 (22429) hydrogen bonds : bond 0.03511 / 3.84 ( 710) hydrogen bonds : angle 3.97742 / 4.10 ( 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 187 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.9128 (m) cc_final: 0.8759 (t) REVERT: a 252 ARG cc_start: 0.8730 (tpp-160) cc_final: 0.8450 (tpp80) REVERT: b 19 LYS cc_start: 0.8271 (pmmt) cc_final: 0.8037 (ptmt) REVERT: b 162 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8859 (tt0) REVERT: b 251 THR cc_start: 0.9219 (m) cc_final: 0.8904 (p) REVERT: c 64 LYS cc_start: 0.8824 (tppt) cc_final: 0.8539 (tppt) REVERT: c 154 TYR cc_start: 0.9094 (p90) cc_final: 0.8814 (p90) REVERT: c 178 GLU cc_start: 0.9020 (tp30) cc_final: 0.8811 (tp30) REVERT: d 39 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8468 (mt-10) REVERT: d 64 LYS cc_start: 0.8907 (tppp) cc_final: 0.8603 (tppt) REVERT: d 149 HIS cc_start: 0.9055 (m-70) cc_final: 0.8534 (m90) REVERT: d 182 MET cc_start: 0.8660 (ttp) cc_final: 0.7592 (pmm) REVERT: d 244 ARG cc_start: 0.8269 (mmt-90) cc_final: 0.7966 (mmm160) REVERT: d 253 ARG cc_start: 0.7958 (tpp-160) cc_final: 0.7509 (tpp-160) REVERT: d 271 ARG cc_start: 0.8762 (tpt90) cc_final: 0.8514 (tpt90) REVERT: e 132 LEU cc_start: 0.9200 (mm) cc_final: 0.8617 (tt) REVERT: e 159 TRP cc_start: 0.8347 (p90) cc_final: 0.8054 (p90) REVERT: e 176 TRP cc_start: 0.8463 (t60) cc_final: 0.8219 (t60) REVERT: e 177 TRP cc_start: 0.8748 (t-100) cc_final: 0.8367 (t-100) REVERT: e 200 ARG cc_start: 0.8906 (ptm-80) cc_final: 0.8658 (ptm-80) REVERT: e 201 VAL cc_start: 0.8214 (m) cc_final: 0.7849 (p) REVERT: f 173 MET cc_start: 0.8511 (mmm) cc_final: 0.7904 (mtp) REVERT: f 245 MET cc_start: 0.7839 (ttm) cc_final: 0.7410 (tmm) REVERT: f 250 LEU cc_start: 0.8567 (tp) cc_final: 0.8342 (OUTLIER) REVERT: g 97 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8330 (mtt90) REVERT: g 149 HIS cc_start: 0.8354 (m90) cc_final: 0.7902 (m90) REVERT: g 159 TRP cc_start: 0.8589 (m100) cc_final: 0.8155 (m100) REVERT: g 176 TRP cc_start: 0.8227 (t60) cc_final: 0.7817 (t-100) REVERT: g 182 MET cc_start: 0.8496 (ttm) cc_final: 0.8159 (tmm) REVERT: g 224 MET cc_start: 0.7758 (mmm) cc_final: 0.7233 (mpm) outliers start: 25 outliers final: 13 residues processed: 184 average time/residue: 0.5413 time to fit residues: 110.0555 Evaluate side-chains 168 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 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 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 f residue 251 THR 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: 3.9990 chunk 145 optimal weight: 0.5980 chunk 102 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 10 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 256 HIS ** d 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 149 HIS g 167 ASN g 276 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.123403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.069453 restraints weight = 31380.835| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.15 r_work: 0.2736 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16465 Z= 0.121 Angle : 0.537 10.084 22429 Z= 0.282 Chirality : 0.043 0.193 2448 Planarity : 0.004 0.091 2747 Dihedral : 13.417 158.282 2414 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.94 % Favored : 97.00 % Rotamer: Outliers : 1.20 % Allowed : 17.96 % 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: 1.13 (0.20), residues: 1902 helix: 1.90 (0.18), residues: 893 sheet: -0.18 (0.34), residues: 248 loop : -0.24 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG d 252 TYR 0.018 0.001 TYR g 99 PHE 0.017 0.001 PHE e 133 TRP 0.051 0.001 TRP e 131 HIS 0.015 0.001 HIS f 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (16465) covalent geometry : angle 0.53708 / 0.28 (22429) hydrogen bonds : bond 0.03315 / 3.61 ( 710) hydrogen bonds : angle 3.92806 / 4.04 ( 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 180 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.9060 (m) cc_final: 0.8801 (t) REVERT: a 224 MET cc_start: 0.9287 (mmm) cc_final: 0.8843 (tpt) REVERT: a 252 ARG cc_start: 0.8738 (tpp-160) cc_final: 0.8446 (tpp80) REVERT: b 19 LYS cc_start: 0.8287 (pmmt) cc_final: 0.8078 (ptmt) REVERT: b 162 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8565 (tt0) REVERT: b 251 THR cc_start: 0.9213 (m) cc_final: 0.8906 (p) REVERT: c 64 LYS cc_start: 0.8781 (tppt) cc_final: 0.8510 (tppt) REVERT: c 154 TYR cc_start: 0.9082 (p90) cc_final: 0.8674 (p90) REVERT: c 156 CYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8796 (m) REVERT: c 178 GLU cc_start: 0.8998 (tp30) cc_final: 0.8791 (tp30) REVERT: d 39 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8428 (mt-10) REVERT: d 64 LYS cc_start: 0.8897 (tppp) cc_final: 0.8599 (tppt) REVERT: d 149 HIS cc_start: 0.9087 (m-70) cc_final: 0.8562 (m90) REVERT: d 182 MET cc_start: 0.8650 (ttp) cc_final: 0.7610 (pmm) REVERT: d 244 ARG cc_start: 0.8216 (mmt-90) cc_final: 0.7922 (mmm160) REVERT: d 252 ARG cc_start: 0.8944 (tpp80) cc_final: 0.8678 (tpp-160) REVERT: d 253 ARG cc_start: 0.7669 (tpp-160) cc_final: 0.7345 (tpp-160) REVERT: d 271 ARG cc_start: 0.8759 (tpt90) cc_final: 0.8497 (tpt90) REVERT: e 33 ASP cc_start: 0.8794 (t0) cc_final: 0.8545 (t0) REVERT: e 131 TRP cc_start: 0.6757 (m100) cc_final: 0.6392 (m100) REVERT: e 132 LEU cc_start: 0.9222 (mm) cc_final: 0.8720 (tt) REVERT: e 176 TRP cc_start: 0.8427 (t60) cc_final: 0.8196 (t60) REVERT: e 177 TRP cc_start: 0.8768 (t-100) cc_final: 0.8380 (t-100) REVERT: e 250 LEU cc_start: 0.9224 (mt) cc_final: 0.8975 (tt) REVERT: f 173 MET cc_start: 0.8475 (mmm) cc_final: 0.7839 (mtp) REVERT: f 245 MET cc_start: 0.7862 (ttm) cc_final: 0.7377 (tmm) REVERT: f 250 LEU cc_start: 0.8579 (tp) cc_final: 0.8305 (tp) REVERT: g 39 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8513 (mt-10) REVERT: g 97 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8228 (mtt-85) REVERT: g 149 HIS cc_start: 0.8364 (m90) cc_final: 0.7960 (m90) REVERT: g 159 TRP cc_start: 0.8565 (m100) cc_final: 0.8127 (m100) REVERT: g 176 TRP cc_start: 0.8224 (t60) cc_final: 0.7818 (t-100) REVERT: g 182 MET cc_start: 0.8494 (ttm) cc_final: 0.8163 (tmm) REVERT: g 245 MET cc_start: 0.8082 (mtt) cc_final: 0.7663 (mpt) REVERT: g 285 TYR cc_start: 0.8908 (m-80) cc_final: 0.8635 (m-10) outliers start: 20 outliers final: 11 residues processed: 178 average time/residue: 0.5417 time to fit residues: 106.5280 Evaluate side-chains 167 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 39 GLU Chi-restraints excluded: chain d residue 132 LEU Chi-restraints excluded: chain d residue 251 THR Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 40 LYS Chi-restraints excluded: chain e residue 164 PHE Chi-restraints excluded: chain f residue 251 THR Chi-restraints excluded: chain g residue 76 LEU Chi-restraints excluded: chain g residue 97 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 169 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 178 optimal weight: 0.0170 chunk 2 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** d 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 276 HIS ** 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 = 0.3926 r_free = 0.3926 target = 0.123469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.069364 restraints weight = 31647.670| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.16 r_work: 0.2763 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16465 Z= 0.125 Angle : 0.551 17.228 22429 Z= 0.284 Chirality : 0.043 0.190 2448 Planarity : 0.004 0.091 2747 Dihedral : 13.364 155.797 2414 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.84 % Favored : 97.11 % Rotamer: Outliers : 1.08 % Allowed : 18.26 % Favored : 80.66 % 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: 1.94 (0.18), residues: 891 sheet: -0.17 (0.34), residues: 248 loop : -0.23 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG e 200 TYR 0.017 0.001 TYR e 99 PHE 0.028 0.001 PHE g 269 TRP 0.038 0.001 TRP d 272 HIS 0.007 0.001 HIS b 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (16465) covalent geometry : angle 0.55129 / 0.28 (22429) hydrogen bonds : bond 0.03295 / 3.61 ( 710) hydrogen bonds : angle 3.93464 / 4.04 ( 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 175 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.9042 (m) cc_final: 0.8804 (t) REVERT: a 68 ASP cc_start: 0.8928 (t70) cc_final: 0.8724 (t0) REVERT: a 224 MET cc_start: 0.9203 (mmm) cc_final: 0.8814 (tpt) REVERT: a 252 ARG cc_start: 0.8731 (tpp-160) cc_final: 0.8435 (tpp80) REVERT: a 255 ASP cc_start: 0.7786 (m-30) cc_final: 0.7501 (p0) REVERT: b 19 LYS cc_start: 0.8292 (pmmt) cc_final: 0.8091 (ptmt) REVERT: b 162 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8594 (tt0) REVERT: b 251 THR cc_start: 0.9190 (m) cc_final: 0.8896 (p) REVERT: c 64 LYS cc_start: 0.8803 (tppt) cc_final: 0.8514 (tppt) REVERT: c 154 TYR cc_start: 0.9096 (p90) cc_final: 0.8698 (p90) REVERT: c 156 CYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8780 (m) REVERT: c 178 GLU cc_start: 0.9000 (tp30) cc_final: 0.8792 (tp30) REVERT: d 39 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8435 (mt-10) REVERT: d 64 LYS cc_start: 0.8915 (tppp) cc_final: 0.8610 (tppt) REVERT: d 149 HIS cc_start: 0.9088 (m-70) cc_final: 0.8559 (m90) REVERT: d 182 MET cc_start: 0.8666 (ttp) cc_final: 0.7595 (pmm) REVERT: d 244 ARG cc_start: 0.8236 (mmt-90) cc_final: 0.7939 (mmm160) REVERT: d 252 ARG cc_start: 0.8935 (tpp80) cc_final: 0.8707 (tpp-160) REVERT: d 253 ARG cc_start: 0.7718 (tpp-160) cc_final: 0.7447 (tpp-160) REVERT: d 271 ARG cc_start: 0.8744 (tpt90) cc_final: 0.8507 (tpt90) REVERT: e 33 ASP cc_start: 0.8748 (t0) cc_final: 0.8491 (t0) REVERT: e 131 TRP cc_start: 0.6715 (m100) cc_final: 0.6344 (m100) REVERT: e 132 LEU cc_start: 0.9192 (mm) cc_final: 0.8604 (tt) REVERT: e 176 TRP cc_start: 0.8433 (t60) cc_final: 0.8195 (t60) REVERT: e 177 TRP cc_start: 0.8772 (t-100) cc_final: 0.8399 (t-100) REVERT: e 200 ARG cc_start: 0.8921 (ptm-80) cc_final: 0.8692 (ptm-80) REVERT: e 201 VAL cc_start: 0.8198 (m) cc_final: 0.7822 (p) REVERT: f 173 MET cc_start: 0.8458 (mmm) cc_final: 0.7827 (mtp) REVERT: f 245 MET cc_start: 0.7855 (ttm) cc_final: 0.7400 (tmm) REVERT: f 250 LEU cc_start: 0.8628 (tp) cc_final: 0.8367 (tp) REVERT: g 97 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8162 (mtt-85) REVERT: g 149 HIS cc_start: 0.8359 (m90) cc_final: 0.7975 (m90) REVERT: g 159 TRP cc_start: 0.8573 (m100) cc_final: 0.8113 (m100) REVERT: g 176 TRP cc_start: 0.8230 (t60) cc_final: 0.7806 (t-100) REVERT: g 182 MET cc_start: 0.8470 (ttm) cc_final: 0.8129 (tmm) REVERT: g 224 MET cc_start: 0.7770 (mmm) cc_final: 0.7350 (mpm) REVERT: g 285 TYR cc_start: 0.8901 (m-80) cc_final: 0.8672 (m-10) outliers start: 18 outliers final: 11 residues processed: 172 average time/residue: 0.5574 time to fit residues: 105.5057 Evaluate side-chains 167 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 39 GLU Chi-restraints excluded: chain d residue 132 LEU Chi-restraints excluded: chain d residue 254 LEU Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 40 LYS Chi-restraints excluded: chain e residue 164 PHE Chi-restraints excluded: chain f residue 251 THR Chi-restraints excluded: chain g residue 76 LEU Chi-restraints excluded: chain g residue 97 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 132 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 39 optimal weight: 0.4980 chunk 163 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 chunk 146 optimal weight: 0.7980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3909 r_free = 0.3909 target = 0.122629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.068201 restraints weight = 31355.242| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.12 r_work: 0.2723 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16465 Z= 0.162 Angle : 0.564 16.134 22429 Z= 0.291 Chirality : 0.044 0.179 2448 Planarity : 0.004 0.090 2747 Dihedral : 13.310 154.773 2414 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.94 % Favored : 97.00 % Rotamer: Outliers : 1.08 % Allowed : 18.08 % 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: 1.16 (0.20), residues: 1902 helix: 1.96 (0.18), residues: 886 sheet: -0.18 (0.33), residues: 250 loop : -0.26 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG e 200 TYR 0.019 0.001 TYR g 99 PHE 0.024 0.001 PHE g 269 TRP 0.045 0.001 TRP d 272 HIS 0.019 0.001 HIS f 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (16465) covalent geometry : angle 0.56400 / 0.29 (22429) hydrogen bonds : bond 0.03551 / 3.90 ( 710) hydrogen bonds : angle 3.95495 / 4.09 ( 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 179 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.9075 (m) cc_final: 0.8866 (t) REVERT: a 224 MET cc_start: 0.9180 (mmm) cc_final: 0.8810 (tpt) REVERT: a 252 ARG cc_start: 0.8688 (tpp-160) cc_final: 0.8404 (tpp80) REVERT: a 255 ASP cc_start: 0.7830 (m-30) cc_final: 0.7577 (p0) REVERT: b 162 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8778 (tt0) REVERT: b 251 THR cc_start: 0.9193 (m) cc_final: 0.8913 (p) REVERT: c 64 LYS cc_start: 0.8820 (tppt) cc_final: 0.8533 (tppt) REVERT: c 154 TYR cc_start: 0.9113 (p90) cc_final: 0.8687 (p90) REVERT: c 156 CYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8780 (m) REVERT: d 39 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8442 (mt-10) REVERT: d 64 LYS cc_start: 0.8937 (tppp) cc_final: 0.8630 (tppt) REVERT: d 149 HIS cc_start: 0.9086 (m-70) cc_final: 0.8547 (m90) REVERT: d 182 MET cc_start: 0.8686 (ttp) cc_final: 0.7611 (pmm) REVERT: d 244 ARG cc_start: 0.8250 (mmt-90) cc_final: 0.7946 (mmm160) REVERT: d 252 ARG cc_start: 0.8926 (tpp80) cc_final: 0.8724 (tpp-160) REVERT: d 253 ARG cc_start: 0.7711 (tpp-160) cc_final: 0.7428 (tpp-160) REVERT: e 40 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8814 (tmtm) REVERT: e 131 TRP cc_start: 0.6932 (m100) cc_final: 0.6603 (m100) REVERT: e 132 LEU cc_start: 0.9197 (mm) cc_final: 0.8587 (tt) REVERT: e 175 ILE cc_start: 0.9240 (mt) cc_final: 0.9030 (mm) REVERT: e 176 TRP cc_start: 0.8430 (t60) cc_final: 0.8182 (t60) REVERT: e 177 TRP cc_start: 0.8782 (t-100) cc_final: 0.8386 (t-100) REVERT: e 201 VAL cc_start: 0.8255 (m) cc_final: 0.7868 (p) REVERT: f 173 MET cc_start: 0.8491 (mmm) cc_final: 0.7879 (mtp) REVERT: f 245 MET cc_start: 0.7908 (ttm) cc_final: 0.7448 (tmm) REVERT: f 250 LEU cc_start: 0.8639 (tp) cc_final: 0.8367 (tp) REVERT: g 97 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8187 (mtt-85) REVERT: g 149 HIS cc_start: 0.8411 (m90) cc_final: 0.8021 (m90) REVERT: g 159 TRP cc_start: 0.8598 (m100) cc_final: 0.8154 (m100) REVERT: g 176 TRP cc_start: 0.8223 (t60) cc_final: 0.7816 (t-100) REVERT: g 182 MET cc_start: 0.8508 (ttm) cc_final: 0.8192 (tmm) REVERT: g 224 MET cc_start: 0.7823 (mmm) cc_final: 0.7366 (mpm) REVERT: g 245 MET cc_start: 0.8118 (mtt) cc_final: 0.7840 (mpp) REVERT: g 285 TYR cc_start: 0.8870 (m-80) cc_final: 0.8617 (m-10) outliers start: 18 outliers final: 12 residues processed: 176 average time/residue: 0.6130 time to fit residues: 118.8086 Evaluate side-chains 168 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 39 GLU Chi-restraints excluded: chain d residue 132 LEU Chi-restraints excluded: chain d residue 171 ASP Chi-restraints excluded: chain d residue 254 LEU Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 40 LYS Chi-restraints excluded: chain e residue 164 PHE Chi-restraints excluded: chain f residue 251 THR Chi-restraints excluded: chain f residue 285 TYR Chi-restraints excluded: chain g residue 76 LEU Chi-restraints excluded: chain g residue 97 ARG 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: 0.9980 chunk 5 optimal weight: 0.5980 chunk 145 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 124 optimal weight: 0.0670 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** d 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 276 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.122547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.068805 restraints weight = 31239.403| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.07 r_work: 0.2771 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16465 Z= 0.129 Angle : 0.577 16.525 22429 Z= 0.298 Chirality : 0.043 0.215 2448 Planarity : 0.004 0.089 2747 Dihedral : 13.268 155.610 2414 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.05 % Favored : 96.90 % Rotamer: Outliers : 0.96 % Allowed : 18.74 % Favored : 80.30 % 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: 1.96 (0.18), residues: 890 sheet: -0.13 (0.33), residues: 252 loop : -0.28 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG g 200 TYR 0.021 0.001 TYR a 99 PHE 0.025 0.001 PHE g 269 TRP 0.046 0.001 TRP d 272 HIS 0.006 0.001 HIS b 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (16465) covalent geometry : angle 0.57705 / 0.30 (22429) hydrogen bonds : bond 0.03415 / 3.72 ( 710) hydrogen bonds : angle 3.94725 / 4.06 ( 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 179 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 68 ASP cc_start: 0.8924 (t70) cc_final: 0.8720 (t0) REVERT: a 224 MET cc_start: 0.9066 (mmm) cc_final: 0.8702 (tpt) REVERT: a 252 ARG cc_start: 0.8689 (tpp-160) cc_final: 0.8406 (tpp80) REVERT: a 255 ASP cc_start: 0.7779 (m-30) cc_final: 0.7566 (p0) REVERT: b 185 LYS cc_start: 0.9348 (mmmt) cc_final: 0.8980 (tptt) REVERT: b 251 THR cc_start: 0.9188 (m) cc_final: 0.8907 (p) REVERT: c 64 LYS cc_start: 0.8796 (tppt) cc_final: 0.8524 (tppt) REVERT: c 154 TYR cc_start: 0.9102 (p90) cc_final: 0.8671 (p90) REVERT: c 156 CYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8843 (m) REVERT: d 39 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8437 (mt-10) REVERT: d 64 LYS cc_start: 0.8957 (tppp) cc_final: 0.8657 (tppt) REVERT: d 149 HIS cc_start: 0.9078 (m-70) cc_final: 0.8517 (m90) REVERT: d 182 MET cc_start: 0.8679 (ttp) cc_final: 0.7615 (pmm) REVERT: d 244 ARG cc_start: 0.8238 (mmt-90) cc_final: 0.7942 (mmm160) REVERT: e 40 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8824 (tmtm) REVERT: e 131 TRP cc_start: 0.6931 (m100) cc_final: 0.6617 (m100) REVERT: e 132 LEU cc_start: 0.9219 (mm) cc_final: 0.8593 (tt) REVERT: e 175 ILE cc_start: 0.9230 (mt) cc_final: 0.9019 (mm) REVERT: e 176 TRP cc_start: 0.8425 (t60) cc_final: 0.8177 (t60) REVERT: e 177 TRP cc_start: 0.8785 (t-100) cc_final: 0.8390 (t-100) REVERT: e 201 VAL cc_start: 0.8189 (m) cc_final: 0.7816 (p) REVERT: f 173 MET cc_start: 0.8480 (mmm) cc_final: 0.7874 (mtp) REVERT: f 245 MET cc_start: 0.7790 (ttm) cc_final: 0.7350 (tmm) REVERT: f 250 LEU cc_start: 0.8633 (tp) cc_final: 0.8363 (tp) REVERT: g 97 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8216 (mtt-85) REVERT: g 149 HIS cc_start: 0.8357 (m90) cc_final: 0.7977 (m90) REVERT: g 159 TRP cc_start: 0.8587 (m100) cc_final: 0.8119 (m100) REVERT: g 176 TRP cc_start: 0.8216 (t60) cc_final: 0.7836 (t-100) REVERT: g 182 MET cc_start: 0.8512 (ttm) cc_final: 0.8193 (tmm) REVERT: g 224 MET cc_start: 0.7838 (mmm) cc_final: 0.7347 (mpm) REVERT: g 245 MET cc_start: 0.8157 (mtt) cc_final: 0.7752 (mpt) REVERT: g 285 TYR cc_start: 0.8854 (m-80) cc_final: 0.8626 (m-10) outliers start: 16 outliers final: 10 residues processed: 176 average time/residue: 0.5819 time to fit residues: 112.8241 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 : 0.485 ------------------------------------------------------------------------------- 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 39 GLU Chi-restraints excluded: chain d residue 132 LEU Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 40 LYS Chi-restraints excluded: chain e residue 124 PHE Chi-restraints excluded: chain e residue 164 PHE Chi-restraints excluded: chain f residue 251 THR Chi-restraints excluded: chain g residue 76 LEU Chi-restraints excluded: chain g residue 97 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 100 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 124 optimal weight: 0.0770 chunk 84 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3909 r_free = 0.3909 target = 0.122370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.068700 restraints weight = 31141.817| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.05 r_work: 0.2768 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16465 Z= 0.139 Angle : 0.572 16.116 22429 Z= 0.294 Chirality : 0.043 0.202 2448 Planarity : 0.004 0.087 2747 Dihedral : 13.186 154.787 2414 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.89 % Favored : 97.06 % Rotamer: Outliers : 0.96 % Allowed : 18.86 % Favored : 80.18 % 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: 1.15 (0.20), residues: 1902 helix: 1.96 (0.18), residues: 889 sheet: -0.16 (0.33), residues: 251 loop : -0.29 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG e 200 TYR 0.023 0.001 TYR d 99 PHE 0.024 0.001 PHE g 269 TRP 0.064 0.001 TRP d 272 HIS 0.006 0.001 HIS b 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (16465) covalent geometry : angle 0.57184 / 0.29 (22429) hydrogen bonds : bond 0.03422 / 3.75 ( 710) hydrogen bonds : angle 3.95393 / 4.07 ( 2033) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4788.40 seconds wall clock time: 82 minutes 28.95 seconds (4948.95 seconds total)