Starting phenix.real_space_refine on Thu Aug 6 17:52:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rqt_54184/08_2026/9rqt_54184_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rqt_54184/08_2026/9rqt_54184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rqt_54184/08_2026/9rqt_54184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rqt_54184/08_2026/9rqt_54184.map" model { file = "/net/cci-nas-00/data/ceres_data/9rqt_54184/08_2026/9rqt_54184_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rqt_54184/08_2026/9rqt_54184_neut.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 1.167 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 3 5.21 5 S 69 5.16 5 C 10096 2.51 5 N 2743 2.21 5 O 3089 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.84, per 1000 atoms: 0.24 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: 1.38 Conformation dependent library (CDL) restraints added in 686.0 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: 2.04 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: 3.01 Time building geometry restraints manager: 1.79 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: 4.060 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.930 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.280 ------------------------------------------------------------------------------- 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 0.78219 / 0.38 (22429) hydrogen bonds : bond 0.14780 / 15.93 ( 710) hydrogen bonds : angle 5.64180 / 5.80 ( 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 : 0.659 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: 0.7490 time to fit residues: 135.8407 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 : 0.646 ------------------------------------------------------------------------------- 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 = 0.121924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.067669 restraints weight = 31665.212| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.17 r_work: 0.2724 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16465 Z= 0.221 Angle : 0.600 8.343 22429 Z= 0.318 Chirality : 0.046 0.161 2448 Planarity : 0.004 0.085 2747 Dihedral : 14.321 166.548 2420 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 3.97 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: 0.97 (0.20), residues: 1902 helix: 1.68 (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 0.009 0.001 ARG e 200 TYR 0.022 0.002 TYR f 99 PHE 0.021 0.002 PHE f 133 TRP 0.030 0.001 TRP d 272 HIS 0.009 0.001 HIS b 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.22 (16465) covalent geometry : angle 0.59999 / 0.32 (22429) hydrogen bonds : bond 0.04591 / 5.08 ( 710) hydrogen bonds : angle 4.53045 / 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 186 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.9132 (m) cc_final: 0.8734 (p) REVERT: a 252 ARG cc_start: 0.8492 (tpp-160) cc_final: 0.8256 (tpp-160) REVERT: c 64 LYS cc_start: 0.8882 (tppt) cc_final: 0.8579 (tppt) REVERT: d 137 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.7874 (p) REVERT: d 149 HIS cc_start: 0.9079 (m-70) cc_final: 0.8726 (m-70) REVERT: d 182 MET cc_start: 0.8686 (ttp) cc_final: 0.7588 (pmm) REVERT: d 239 GLN cc_start: 0.9298 (tp40) cc_final: 0.9088 (tm-30) REVERT: d 244 ARG cc_start: 0.8262 (mmt-90) cc_final: 0.7909 (mmm160) REVERT: d 252 ARG cc_start: 0.9019 (tpp80) cc_final: 0.8750 (tpp-160) REVERT: d 254 LEU cc_start: 0.8832 (mm) cc_final: 0.8168 (pp) REVERT: d 265 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8976 (mt-10) REVERT: e 159 TRP cc_start: 0.8332 (p90) cc_final: 0.8057 (p90) REVERT: e 173 MET cc_start: 0.8504 (tpp) cc_final: 0.8281 (tpp) REVERT: e 177 TRP cc_start: 0.8509 (t-100) cc_final: 0.8238 (t-100) REVERT: e 200 ARG cc_start: 0.8925 (ptm-80) cc_final: 0.8700 (ptm-80) REVERT: e 245 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.6340 (mmp) REVERT: f 173 MET cc_start: 0.8365 (mmm) cc_final: 0.7924 (mtp) REVERT: f 245 MET cc_start: 0.7876 (ttm) cc_final: 0.7452 (tmt) REVERT: g 97 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8342 (mtt90) REVERT: g 149 HIS cc_start: 0.8540 (m90) cc_final: 0.7984 (m90) REVERT: g 159 TRP cc_start: 0.8492 (m100) cc_final: 0.7990 (m100) REVERT: g 176 TRP cc_start: 0.8195 (t60) cc_final: 0.7753 (t-100) REVERT: g 182 MET cc_start: 0.8564 (ttm) cc_final: 0.8196 (tmm) REVERT: g 200 ARG cc_start: 0.8818 (mmp80) cc_final: 0.8496 (mmp80) outliers start: 24 outliers final: 7 residues processed: 179 average time/residue: 0.7139 time to fit residues: 140.7835 Evaluate side-chains 157 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 232 SER 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: 5.9990 chunk 4 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 182 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 150 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 221 ASN b 256 HIS 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 = 0.122417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.069043 restraints weight = 31873.533| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.11 r_work: 0.2750 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16465 Z= 0.152 Angle : 0.555 8.720 22429 Z= 0.293 Chirality : 0.044 0.189 2448 Planarity : 0.004 0.088 2747 Dihedral : 13.828 162.773 2418 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.56 % Allowed : 15.50 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.20), residues: 1902 helix: 1.74 (0.17), residues: 889 sheet: -0.35 (0.34), residues: 248 loop : -0.14 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG e 244 TYR 0.025 0.002 TYR f 99 PHE 0.020 0.001 PHE e 246 TRP 0.051 0.001 TRP e 131 HIS 0.010 0.001 HIS b 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (16465) covalent geometry : angle 0.55473 / 0.29 (22429) hydrogen bonds : bond 0.04008 / 4.40 ( 710) hydrogen bonds : angle 4.28116 / 4.41 ( 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 184 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.9132 (m) cc_final: 0.8655 (p) REVERT: a 252 ARG cc_start: 0.8504 (tpp-160) cc_final: 0.8292 (tpp80) REVERT: b 251 THR cc_start: 0.9233 (m) cc_final: 0.8879 (p) REVERT: c 64 LYS cc_start: 0.8874 (tppt) cc_final: 0.8576 (tppt) REVERT: d 149 HIS cc_start: 0.8990 (m-70) cc_final: 0.8689 (m-70) REVERT: d 182 MET cc_start: 0.8694 (ttp) cc_final: 0.7605 (pmm) REVERT: d 239 GLN cc_start: 0.9278 (tp40) cc_final: 0.9075 (tm-30) REVERT: d 244 ARG cc_start: 0.8269 (mmt-90) cc_final: 0.7936 (mmm160) REVERT: d 252 ARG cc_start: 0.8997 (tpp80) cc_final: 0.8761 (tpp-160) REVERT: d 253 ARG cc_start: 0.7384 (tpp-160) cc_final: 0.7081 (tpp-160) REVERT: d 254 LEU cc_start: 0.8829 (mm) cc_final: 0.8271 (pp) REVERT: d 265 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8954 (mt-10) REVERT: d 271 ARG cc_start: 0.8803 (tpt90) cc_final: 0.8563 (tpt90) REVERT: e 132 LEU cc_start: 0.9147 (mm) cc_final: 0.8573 (tt) REVERT: e 159 TRP cc_start: 0.8323 (p90) cc_final: 0.8043 (p90) REVERT: e 173 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8275 (tpp) REVERT: e 177 TRP cc_start: 0.8593 (t-100) cc_final: 0.8213 (t-100) REVERT: f 173 MET cc_start: 0.8402 (mmm) cc_final: 0.8041 (mtp) REVERT: f 245 MET cc_start: 0.7914 (ttm) cc_final: 0.7511 (tmm) REVERT: g 97 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8358 (mtt90) REVERT: g 149 HIS cc_start: 0.8492 (m90) cc_final: 0.7937 (m90) REVERT: g 159 TRP cc_start: 0.8527 (m100) cc_final: 0.8070 (m100) REVERT: g 176 TRP cc_start: 0.8252 (t60) cc_final: 0.7766 (t-100) REVERT: g 182 MET cc_start: 0.8504 (ttm) cc_final: 0.8159 (tmm) REVERT: g 224 MET cc_start: 0.7762 (mmm) cc_final: 0.7265 (mpm) outliers start: 26 outliers final: 8 residues processed: 179 average time/residue: 0.7058 time to fit residues: 138.8995 Evaluate side-chains 157 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 211 ILE Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 265 GLU Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 164 PHE Chi-restraints excluded: chain e residue 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: 3.9990 chunk 98 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 185 optimal weight: 40.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.120708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.066411 restraints weight = 31891.319| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.15 r_work: 0.2695 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 16465 Z= 0.248 Angle : 0.588 8.956 22429 Z= 0.310 Chirality : 0.045 0.158 2448 Planarity : 0.004 0.087 2747 Dihedral : 13.702 158.545 2415 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.26 % Favored : 96.69 % Rotamer: Outliers : 1.74 % Allowed : 16.52 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 1902 helix: 1.65 (0.17), residues: 884 sheet: -0.43 (0.33), residues: 251 loop : -0.22 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG e 200 TYR 0.018 0.002 TYR d 99 PHE 0.023 0.001 PHE e 246 TRP 0.046 0.001 TRP e 131 HIS 0.010 0.001 HIS b 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.25 (16465) covalent geometry : angle 0.58823 / 0.31 (22429) hydrogen bonds : bond 0.04268 / 4.73 ( 710) hydrogen bonds : angle 4.25494 / 4.43 ( 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 188 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.9177 (m) cc_final: 0.8716 (p) REVERT: b 251 THR cc_start: 0.9229 (m) cc_final: 0.8900 (p) REVERT: c 64 LYS cc_start: 0.8901 (tppt) cc_final: 0.8589 (tppt) REVERT: d 137 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8163 (p) REVERT: d 149 HIS cc_start: 0.9056 (m-70) cc_final: 0.8567 (m90) REVERT: d 182 MET cc_start: 0.8687 (ttp) cc_final: 0.7605 (pmm) REVERT: d 244 ARG cc_start: 0.8335 (mmt-90) cc_final: 0.7996 (mmm160) REVERT: d 252 ARG cc_start: 0.9014 (tpp80) cc_final: 0.8814 (tpp-160) REVERT: d 253 ARG cc_start: 0.7429 (tpp-160) cc_final: 0.6868 (tpp-160) REVERT: d 254 LEU cc_start: 0.8823 (mm) cc_final: 0.8284 (pp) REVERT: d 271 ARG cc_start: 0.8777 (tpt90) cc_final: 0.8515 (tpt90) REVERT: e 132 LEU cc_start: 0.9167 (mm) cc_final: 0.8589 (tt) REVERT: e 159 TRP cc_start: 0.8343 (p90) cc_final: 0.8058 (p90) REVERT: e 173 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8265 (tpp) REVERT: e 176 TRP cc_start: 0.8456 (t60) cc_final: 0.8212 (t60) REVERT: e 177 TRP cc_start: 0.8676 (t-100) cc_final: 0.8278 (t-100) REVERT: f 173 MET cc_start: 0.8640 (mmm) cc_final: 0.8038 (mtp) REVERT: f 245 MET cc_start: 0.7909 (ttm) cc_final: 0.7480 (tmm) REVERT: f 250 LEU cc_start: 0.8465 (tp) cc_final: 0.8208 (tp) REVERT: g 97 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8362 (mtt90) REVERT: g 149 HIS cc_start: 0.8444 (m90) cc_final: 0.7956 (m90) REVERT: g 159 TRP cc_start: 0.8585 (m100) cc_final: 0.8148 (m100) REVERT: g 176 TRP cc_start: 0.8286 (t60) cc_final: 0.7794 (t60) REVERT: g 182 MET cc_start: 0.8617 (ttm) cc_final: 0.8274 (tmm) outliers start: 29 outliers final: 10 residues processed: 185 average time/residue: 0.6839 time to fit residues: 139.3923 Evaluate side-chains 159 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 199 VAL Chi-restraints excluded: chain c residue 156 CYS Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 251 THR Chi-restraints excluded: chain e residue 164 PHE Chi-restraints excluded: chain e residue 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: 0.2980 chunk 100 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 46 optimal weight: 0.0370 chunk 120 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 126 optimal weight: 6.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 276 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.122840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.068979 restraints weight = 31464.697| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 3.12 r_work: 0.2726 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16465 Z= 0.115 Angle : 0.537 9.605 22429 Z= 0.283 Chirality : 0.043 0.167 2448 Planarity : 0.004 0.088 2747 Dihedral : 13.566 162.284 2414 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.63 % Favored : 97.32 % Rotamer: Outliers : 1.44 % Allowed : 17.42 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.20), residues: 1902 helix: 1.82 (0.18), residues: 892 sheet: -0.32 (0.33), residues: 248 loop : -0.24 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG e 200 TYR 0.020 0.002 TYR g 99 PHE 0.019 0.001 PHE e 246 TRP 0.045 0.001 TRP e 131 HIS 0.010 0.001 HIS f 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (16465) covalent geometry : angle 0.53652 / 0.28 (22429) hydrogen bonds : bond 0.03502 / 3.85 ( 710) hydrogen bonds : angle 4.05031 / 4.18 ( 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 : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.9125 (m) cc_final: 0.8714 (p) REVERT: a 252 ARG cc_start: 0.8707 (tpp-160) cc_final: 0.8467 (tpp80) REVERT: b 251 THR cc_start: 0.9229 (m) cc_final: 0.8905 (p) REVERT: c 64 LYS cc_start: 0.8833 (tppt) cc_final: 0.8556 (tppt) REVERT: d 39 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8416 (mt-10) REVERT: d 149 HIS cc_start: 0.9043 (m-70) cc_final: 0.8517 (m90) REVERT: d 182 MET cc_start: 0.8706 (ttp) cc_final: 0.7623 (pmm) REVERT: d 244 ARG cc_start: 0.8215 (mmt-90) cc_final: 0.7896 (mmm160) REVERT: d 271 ARG cc_start: 0.8800 (tpt90) cc_final: 0.8592 (tpt90) REVERT: e 131 TRP cc_start: 0.7084 (m100) cc_final: 0.6859 (m100) REVERT: e 132 LEU cc_start: 0.9215 (mm) cc_final: 0.8659 (tt) REVERT: e 159 TRP cc_start: 0.8320 (p90) cc_final: 0.8019 (p90) REVERT: e 176 TRP cc_start: 0.8411 (t60) cc_final: 0.8139 (t60) REVERT: e 177 TRP cc_start: 0.8721 (t-100) cc_final: 0.8292 (t-100) REVERT: f 173 MET cc_start: 0.8593 (mmm) cc_final: 0.8031 (mtp) REVERT: f 245 MET cc_start: 0.7889 (ttm) cc_final: 0.7452 (tmm) REVERT: f 250 LEU cc_start: 0.8484 (tp) cc_final: 0.8257 (tp) REVERT: g 39 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8564 (mt-10) REVERT: g 97 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8366 (mtt90) REVERT: g 159 TRP cc_start: 0.8555 (m100) cc_final: 0.8115 (m100) REVERT: g 176 TRP cc_start: 0.8257 (t60) cc_final: 0.7789 (t60) REVERT: g 182 MET cc_start: 0.8492 (ttm) cc_final: 0.8120 (tmm) REVERT: g 224 MET cc_start: 0.7784 (mmm) cc_final: 0.7221 (mpm) outliers start: 24 outliers final: 8 residues processed: 182 average time/residue: 0.6736 time to fit residues: 135.2127 Evaluate side-chains 161 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 39 GLU Chi-restraints excluded: chain d residue 132 LEU Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 164 PHE Chi-restraints excluded: chain e residue 237 HIS Chi-restraints excluded: chain g residue 97 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 103 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 172 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 135 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 183 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 54 ASN 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 = 0.3918 r_free = 0.3918 target = 0.122843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.069112 restraints weight = 31521.547| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.12 r_work: 0.2730 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16465 Z= 0.122 Angle : 0.533 9.533 22429 Z= 0.279 Chirality : 0.043 0.158 2448 Planarity : 0.004 0.090 2747 Dihedral : 13.482 160.537 2414 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.00 % Favored : 96.95 % Rotamer: Outliers : 1.26 % Allowed : 17.96 % Favored : 80.78 % 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: 1.07 (0.20), residues: 1902 helix: 1.86 (0.18), residues: 892 sheet: -0.27 (0.33), residues: 249 loop : -0.26 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG e 200 TYR 0.017 0.001 TYR d 99 PHE 0.016 0.001 PHE e 246 TRP 0.025 0.001 TRP e 131 HIS 0.012 0.001 HIS f 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (16465) covalent geometry : angle 0.53310 / 0.28 (22429) hydrogen bonds : bond 0.03405 / 3.74 ( 710) hydrogen bonds : angle 3.98366 / 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 181 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.9113 (m) cc_final: 0.8763 (t) REVERT: a 252 ARG cc_start: 0.8741 (tpp-160) cc_final: 0.8481 (tpp80) REVERT: b 162 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8575 (tt0) REVERT: b 251 THR cc_start: 0.9229 (m) cc_final: 0.8924 (p) REVERT: c 64 LYS cc_start: 0.8812 (tppt) cc_final: 0.8538 (tppt) REVERT: d 64 LYS cc_start: 0.8907 (tppp) cc_final: 0.8617 (tppt) REVERT: d 137 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8596 (p) REVERT: d 149 HIS cc_start: 0.9060 (m-70) cc_final: 0.8533 (m90) REVERT: d 182 MET cc_start: 0.8697 (ttp) cc_final: 0.7623 (pmm) REVERT: d 244 ARG cc_start: 0.8227 (mmt-90) cc_final: 0.7918 (mmm160) REVERT: d 254 LEU cc_start: 0.8666 (tm) cc_final: 0.8368 (mm) REVERT: d 271 ARG cc_start: 0.8769 (tpt90) cc_final: 0.8539 (tpt90) REVERT: e 132 LEU cc_start: 0.9223 (mm) cc_final: 0.8633 (tt) REVERT: e 159 TRP cc_start: 0.8348 (p90) cc_final: 0.8061 (p90) REVERT: e 176 TRP cc_start: 0.8419 (t60) cc_final: 0.8208 (t60) REVERT: e 177 TRP cc_start: 0.8773 (t-100) cc_final: 0.8375 (t-100) REVERT: f 173 MET cc_start: 0.8514 (mmm) cc_final: 0.7919 (mtp) REVERT: f 245 MET cc_start: 0.7883 (ttm) cc_final: 0.7431 (tmm) REVERT: f 250 LEU cc_start: 0.8582 (tp) cc_final: 0.8342 (tp) REVERT: g 97 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8219 (mtt-85) REVERT: g 149 HIS cc_start: 0.8333 (m90) cc_final: 0.8007 (m170) REVERT: g 159 TRP cc_start: 0.8580 (m100) cc_final: 0.8155 (m100) REVERT: g 176 TRP cc_start: 0.8212 (t60) cc_final: 0.7844 (t60) REVERT: g 182 MET cc_start: 0.8505 (ttm) cc_final: 0.8158 (tmm) outliers start: 21 outliers final: 12 residues processed: 180 average time/residue: 0.6382 time to fit residues: 126.6054 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 : 0.630 ------------------------------------------------------------------------------- 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 211 ILE Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 132 LEU Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain e residue 15 VAL 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 e residue 237 HIS 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: 5.9990 chunk 145 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 83 optimal weight: 0.0970 chunk 28 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 10 optimal weight: 0.0870 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 210 GLN f 149 HIS g 276 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.123482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.069581 restraints weight = 31359.474| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.14 r_work: 0.2747 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16465 Z= 0.112 Angle : 0.537 10.595 22429 Z= 0.279 Chirality : 0.043 0.254 2448 Planarity : 0.004 0.091 2747 Dihedral : 13.374 161.096 2414 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.94 % Favored : 97.00 % Rotamer: Outliers : 1.32 % Allowed : 18.50 % 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: 1.11 (0.20), residues: 1902 helix: 1.90 (0.18), residues: 894 sheet: -0.21 (0.33), residues: 249 loop : -0.28 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG d 252 TYR 0.016 0.001 TYR e 99 PHE 0.018 0.001 PHE e 133 TRP 0.047 0.001 TRP e 131 HIS 0.015 0.001 HIS f 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (16465) covalent geometry : angle 0.53663 / 0.28 (22429) hydrogen bonds : bond 0.03244 / 3.53 ( 710) hydrogen bonds : angle 3.93099 / 4.03 ( 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 183 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.9050 (m) cc_final: 0.8800 (t) REVERT: a 252 ARG cc_start: 0.8702 (tpp-160) cc_final: 0.8439 (tpp80) REVERT: b 162 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8603 (tt0) REVERT: b 251 THR cc_start: 0.9171 (m) cc_final: 0.8906 (p) REVERT: c 64 LYS cc_start: 0.8796 (tppt) cc_final: 0.8525 (tppt) REVERT: c 154 TYR cc_start: 0.9066 (p90) cc_final: 0.8638 (p90) REVERT: c 156 CYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8796 (m) REVERT: d 39 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8427 (mt-10) REVERT: d 64 LYS cc_start: 0.8897 (tppp) cc_final: 0.8600 (tppt) REVERT: d 137 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8569 (p) REVERT: d 149 HIS cc_start: 0.9083 (m-70) cc_final: 0.8556 (m90) REVERT: d 182 MET cc_start: 0.8701 (ttp) cc_final: 0.7633 (pmm) REVERT: d 244 ARG cc_start: 0.8195 (mmt-90) cc_final: 0.7900 (mmm160) REVERT: d 252 ARG cc_start: 0.8955 (tpp80) cc_final: 0.8750 (tpp-160) REVERT: d 254 LEU cc_start: 0.8675 (tm) cc_final: 0.8320 (mm) REVERT: d 271 ARG cc_start: 0.8760 (tpt90) cc_final: 0.8494 (tpt90) REVERT: e 33 ASP cc_start: 0.8814 (t0) cc_final: 0.8588 (t0) REVERT: e 116 PHE cc_start: 0.9651 (m-80) cc_final: 0.9424 (m-80) REVERT: e 132 LEU cc_start: 0.9230 (mm) cc_final: 0.8711 (tt) REVERT: e 176 TRP cc_start: 0.8419 (t60) cc_final: 0.8182 (t60) REVERT: e 177 TRP cc_start: 0.8776 (t-100) cc_final: 0.8375 (t-100) REVERT: e 250 LEU cc_start: 0.9229 (mt) cc_final: 0.8988 (tt) REVERT: f 173 MET cc_start: 0.8452 (mmm) cc_final: 0.7860 (mtp) REVERT: f 245 MET cc_start: 0.7870 (ttm) cc_final: 0.7421 (tmm) REVERT: f 250 LEU cc_start: 0.8563 (tp) cc_final: 0.8322 (tp) REVERT: g 97 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8222 (mtt-85) REVERT: g 149 HIS cc_start: 0.8304 (m90) cc_final: 0.7871 (m90) REVERT: g 159 TRP cc_start: 0.8570 (m100) cc_final: 0.8129 (m100) REVERT: g 176 TRP cc_start: 0.8211 (t60) cc_final: 0.7814 (t-100) REVERT: g 182 MET cc_start: 0.8459 (ttm) cc_final: 0.8117 (tmm) outliers start: 22 outliers final: 12 residues processed: 179 average time/residue: 0.6577 time to fit residues: 130.1673 Evaluate side-chains 174 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 189 SER Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 39 GLU Chi-restraints excluded: chain d residue 132 LEU Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 251 THR Chi-restraints excluded: chain e residue 15 VAL 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 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: 0.8980 chunk 15 optimal weight: 0.7980 chunk 178 optimal weight: 8.9990 chunk 2 optimal weight: 0.0980 chunk 184 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 159 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 210 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.123314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.069868 restraints weight = 31523.729| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.08 r_work: 0.2762 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16465 Z= 0.123 Angle : 0.555 17.646 22429 Z= 0.285 Chirality : 0.043 0.240 2448 Planarity : 0.004 0.091 2747 Dihedral : 13.304 160.090 2414 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.89 % Favored : 97.06 % Rotamer: Outliers : 1.20 % Allowed : 18.32 % Favored : 80.48 % 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: 892 sheet: -0.17 (0.34), residues: 249 loop : -0.26 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG d 252 TYR 0.018 0.001 TYR e 99 PHE 0.014 0.001 PHE e 246 TRP 0.041 0.001 TRP d 272 HIS 0.007 0.001 HIS b 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (16465) covalent geometry : angle 0.55505 / 0.29 (22429) hydrogen bonds : bond 0.03258 / 3.57 ( 710) hydrogen bonds : angle 3.93859 / 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 180 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.9047 (m) cc_final: 0.8826 (t) REVERT: a 252 ARG cc_start: 0.8704 (tpp-160) cc_final: 0.8433 (tpp80) REVERT: b 162 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8558 (tt0) REVERT: b 251 THR cc_start: 0.9166 (m) cc_final: 0.8908 (p) REVERT: c 64 LYS cc_start: 0.8798 (tppt) cc_final: 0.8522 (tppt) REVERT: c 154 TYR cc_start: 0.9083 (p90) cc_final: 0.8750 (p90) REVERT: c 156 CYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8873 (m) REVERT: d 39 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8436 (mt-10) REVERT: d 64 LYS cc_start: 0.8918 (tppp) cc_final: 0.8614 (tppt) REVERT: d 137 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8499 (p) REVERT: d 149 HIS cc_start: 0.9102 (m-70) cc_final: 0.8558 (m90) REVERT: d 182 MET cc_start: 0.8713 (ttp) cc_final: 0.7636 (pmm) REVERT: d 244 ARG cc_start: 0.8206 (mmt-90) cc_final: 0.7903 (mmm160) REVERT: d 253 ARG cc_start: 0.8687 (tpm170) cc_final: 0.8408 (tpp-160) REVERT: d 254 LEU cc_start: 0.8673 (tm) cc_final: 0.8296 (mm) REVERT: d 271 ARG cc_start: 0.8760 (tpt90) cc_final: 0.8526 (tpt90) REVERT: e 33 ASP cc_start: 0.8773 (t0) cc_final: 0.8531 (t0) REVERT: e 132 LEU cc_start: 0.9214 (mm) cc_final: 0.8601 (tt) REVERT: e 176 TRP cc_start: 0.8404 (t60) cc_final: 0.8151 (t60) REVERT: e 177 TRP cc_start: 0.8786 (t-100) cc_final: 0.8397 (t-100) REVERT: f 173 MET cc_start: 0.8441 (mmm) cc_final: 0.7845 (mtp) REVERT: f 245 MET cc_start: 0.7870 (ttm) cc_final: 0.7428 (tmm) REVERT: f 250 LEU cc_start: 0.8608 (tp) cc_final: 0.8360 (tp) REVERT: g 97 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8219 (mtt-85) REVERT: g 149 HIS cc_start: 0.8337 (m90) cc_final: 0.7908 (m90) REVERT: g 159 TRP cc_start: 0.8571 (m100) cc_final: 0.8117 (m100) REVERT: g 176 TRP cc_start: 0.8225 (t60) cc_final: 0.7811 (t-100) REVERT: g 182 MET cc_start: 0.8467 (ttm) cc_final: 0.8122 (tmm) REVERT: g 224 MET cc_start: 0.7735 (mmm) cc_final: 0.7314 (mpm) REVERT: g 245 MET cc_start: 0.8130 (mtt) cc_final: 0.7829 (mpt) outliers start: 20 outliers final: 11 residues processed: 178 average time/residue: 0.6792 time to fit residues: 133.3573 Evaluate side-chains 169 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 189 SER Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 39 GLU Chi-restraints excluded: chain d residue 132 LEU Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain e residue 15 VAL 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 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: 6.9990 chunk 33 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 163 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 210 GLN f 149 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.122230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.068501 restraints weight = 31333.019| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.07 r_work: 0.2764 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16465 Z= 0.149 Angle : 0.571 17.115 22429 Z= 0.293 Chirality : 0.043 0.214 2448 Planarity : 0.004 0.090 2747 Dihedral : 13.286 161.507 2414 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.84 % Favored : 97.11 % Rotamer: Outliers : 1.14 % Allowed : 18.86 % Favored : 80.00 % 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: 1.19 (0.20), residues: 1902 helix: 1.98 (0.18), residues: 890 sheet: -0.14 (0.34), residues: 251 loop : -0.26 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG g 200 TYR 0.027 0.001 TYR a 99 PHE 0.016 0.001 PHE e 133 TRP 0.048 0.001 TRP d 272 HIS 0.022 0.001 HIS f 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (16465) covalent geometry : angle 0.57085 / 0.29 (22429) hydrogen bonds : bond 0.03405 / 3.73 ( 710) hydrogen bonds : angle 3.95452 / 4.06 ( 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 182 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 SER cc_start: 0.9055 (m) cc_final: 0.8842 (t) REVERT: a 224 MET cc_start: 0.9316 (mmm) cc_final: 0.8861 (tpt) REVERT: a 252 ARG cc_start: 0.8704 (tpp-160) cc_final: 0.8432 (tpp80) REVERT: a 255 ASP cc_start: 0.7789 (m-30) cc_final: 0.7540 (p0) REVERT: b 185 LYS cc_start: 0.9346 (mmmt) cc_final: 0.8967 (tptt) REVERT: b 251 THR cc_start: 0.9153 (m) cc_final: 0.8895 (p) REVERT: c 64 LYS cc_start: 0.8798 (tppt) cc_final: 0.8528 (tppt) REVERT: c 154 TYR cc_start: 0.9090 (p90) cc_final: 0.8743 (p90) REVERT: c 156 CYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8931 (m) REVERT: d 39 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8442 (mt-10) REVERT: d 64 LYS cc_start: 0.8948 (tppp) cc_final: 0.8650 (tppt) REVERT: d 137 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8366 (p) REVERT: d 149 HIS cc_start: 0.9116 (m-70) cc_final: 0.8568 (m90) REVERT: d 182 MET cc_start: 0.8720 (ttp) cc_final: 0.7648 (pmm) REVERT: d 244 ARG cc_start: 0.8226 (mmt-90) cc_final: 0.7927 (mmm160) REVERT: d 254 LEU cc_start: 0.8665 (tm) cc_final: 0.8179 (mm) REVERT: e 33 ASP cc_start: 0.8818 (t0) cc_final: 0.8583 (t0) REVERT: e 40 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8820 (tmtm) REVERT: e 132 LEU cc_start: 0.9232 (mm) cc_final: 0.8701 (tt) REVERT: e 175 ILE cc_start: 0.9248 (mt) cc_final: 0.9038 (mm) REVERT: e 176 TRP cc_start: 0.8408 (t60) cc_final: 0.8177 (t60) REVERT: e 177 TRP cc_start: 0.8786 (t-100) cc_final: 0.8384 (t-100) REVERT: e 250 LEU cc_start: 0.9210 (mt) cc_final: 0.8972 (tt) REVERT: f 173 MET cc_start: 0.8503 (mmm) cc_final: 0.7918 (mtp) REVERT: f 245 MET cc_start: 0.7896 (ttm) cc_final: 0.7431 (tmm) REVERT: f 250 LEU cc_start: 0.8601 (tp) cc_final: 0.8349 (tp) REVERT: g 97 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8245 (mtt-85) REVERT: g 149 HIS cc_start: 0.8346 (m90) cc_final: 0.7932 (m90) REVERT: g 159 TRP cc_start: 0.8583 (m100) cc_final: 0.8129 (m100) REVERT: g 176 TRP cc_start: 0.8223 (t60) cc_final: 0.7812 (t-100) REVERT: g 182 MET cc_start: 0.8519 (ttm) cc_final: 0.8224 (tmm) REVERT: g 285 TYR cc_start: 0.8868 (m-80) cc_final: 0.8611 (m-10) outliers start: 19 outliers final: 12 residues processed: 181 average time/residue: 0.6982 time to fit residues: 139.0726 Evaluate side-chains 172 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 189 SER Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 39 GLU Chi-restraints excluded: chain d residue 132 LEU Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 171 ASP Chi-restraints excluded: chain e residue 15 VAL 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 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: 0.9980 chunk 39 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 181 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 70 optimal weight: 0.0670 chunk 124 optimal weight: 0.0060 overall best weight: 0.4734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 256 HIS ** d 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.122936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.069390 restraints weight = 31237.479| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.07 r_work: 0.2785 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16465 Z= 0.118 Angle : 0.579 18.423 22429 Z= 0.297 Chirality : 0.043 0.238 2448 Planarity : 0.004 0.090 2747 Dihedral : 13.243 162.727 2414 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.05 % Favored : 96.90 % Rotamer: Outliers : 1.32 % Allowed : 18.80 % Favored : 79.88 % 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: 1.19 (0.20), residues: 1902 helix: 1.98 (0.18), residues: 892 sheet: -0.15 (0.34), residues: 250 loop : -0.26 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG d 252 TYR 0.018 0.001 TYR e 99 PHE 0.016 0.001 PHE e 133 TRP 0.047 0.001 TRP d 272 HIS 0.008 0.001 HIS b 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (16465) covalent geometry : angle 0.57925 / 0.30 (22429) hydrogen bonds : bond 0.03244 / 3.54 ( 710) hydrogen bonds : angle 3.94426 / 4.04 ( 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 187 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 252 ARG cc_start: 0.8706 (tpp-160) cc_final: 0.8433 (tpp80) REVERT: a 255 ASP cc_start: 0.7787 (m-30) cc_final: 0.7541 (p0) REVERT: b 185 LYS cc_start: 0.9360 (mmmt) cc_final: 0.8970 (tptt) REVERT: b 251 THR cc_start: 0.9149 (m) cc_final: 0.8898 (p) REVERT: c 64 LYS cc_start: 0.8784 (tppt) cc_final: 0.8516 (tppt) REVERT: c 154 TYR cc_start: 0.9075 (p90) cc_final: 0.8732 (p90) REVERT: c 156 CYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8927 (m) REVERT: d 39 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8434 (mt-10) REVERT: d 64 LYS cc_start: 0.8944 (tppp) cc_final: 0.8651 (tppt) REVERT: d 137 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8405 (p) REVERT: d 149 HIS cc_start: 0.9105 (m-70) cc_final: 0.8534 (m90) REVERT: d 182 MET cc_start: 0.8717 (ttp) cc_final: 0.7642 (pmm) REVERT: d 244 ARG cc_start: 0.8201 (mmt-90) cc_final: 0.7908 (mmm160) REVERT: d 254 LEU cc_start: 0.8620 (tm) cc_final: 0.8274 (mm) REVERT: e 33 ASP cc_start: 0.8790 (t0) cc_final: 0.8555 (t0) REVERT: e 132 LEU cc_start: 0.9230 (mm) cc_final: 0.8696 (tt) REVERT: e 175 ILE cc_start: 0.9245 (mt) cc_final: 0.9043 (mm) REVERT: e 176 TRP cc_start: 0.8403 (t60) cc_final: 0.8166 (t60) REVERT: e 177 TRP cc_start: 0.8801 (t-100) cc_final: 0.8424 (t-100) REVERT: e 250 LEU cc_start: 0.9229 (mt) cc_final: 0.8991 (tt) REVERT: f 173 MET cc_start: 0.8491 (mmm) cc_final: 0.7912 (mtp) REVERT: f 245 MET cc_start: 0.7773 (ttm) cc_final: 0.7323 (tmm) REVERT: f 250 LEU cc_start: 0.8631 (tp) cc_final: 0.8391 (tp) REVERT: g 97 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8245 (mtt-85) REVERT: g 149 HIS cc_start: 0.8339 (m90) cc_final: 0.7914 (m90) REVERT: g 159 TRP cc_start: 0.8586 (m100) cc_final: 0.8123 (m100) REVERT: g 176 TRP cc_start: 0.8222 (t60) cc_final: 0.7845 (t-100) REVERT: g 182 MET cc_start: 0.8493 (ttm) cc_final: 0.8191 (tmm) REVERT: g 200 ARG cc_start: 0.8876 (mmp-170) cc_final: 0.8654 (mmp80) REVERT: g 224 MET cc_start: 0.7695 (mmm) cc_final: 0.7338 (mpm) REVERT: g 245 MET cc_start: 0.8161 (mtt) cc_final: 0.7845 (mpp) REVERT: g 285 TYR cc_start: 0.8847 (m-80) cc_final: 0.8592 (m-10) outliers start: 22 outliers final: 12 residues processed: 183 average time/residue: 0.5602 time to fit residues: 113.4568 Evaluate side-chains 171 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 189 SER Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 39 GLU Chi-restraints excluded: chain d residue 132 LEU Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain e residue 15 VAL 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 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 100 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 124 optimal weight: 0.0980 chunk 84 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 256 HIS ** d 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.123018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.069680 restraints weight = 31177.577| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.04 r_work: 0.2788 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16465 Z= 0.119 Angle : 0.574 17.682 22429 Z= 0.293 Chirality : 0.043 0.205 2448 Planarity : 0.004 0.087 2747 Dihedral : 13.173 161.781 2414 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.05 % Favored : 96.90 % Rotamer: Outliers : 0.96 % Allowed : 19.46 % Favored : 79.58 % 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: 1.21 (0.20), residues: 1902 helix: 2.02 (0.18), residues: 889 sheet: -0.07 (0.34), residues: 250 loop : -0.30 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG d 252 TYR 0.021 0.001 TYR g 99 PHE 0.033 0.001 PHE g 269 TRP 0.065 0.001 TRP d 272 HIS 0.008 0.001 HIS b 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (16465) covalent geometry : angle 0.57376 / 0.29 (22429) hydrogen bonds : bond 0.03229 / 3.54 ( 710) hydrogen bonds : angle 3.94608 / 4.04 ( 2033) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5626.23 seconds wall clock time: 96 minutes 58.36 seconds (5818.36 seconds total)