Starting phenix.real_space_refine on Fri Jul 3 09:14:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ypf_73296/07_2026/9ypf_73296.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ypf_73296/07_2026/9ypf_73296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ypf_73296/07_2026/9ypf_73296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ypf_73296/07_2026/9ypf_73296.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ypf_73296/07_2026/9ypf_73296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ypf_73296/07_2026/9ypf_73296.map" } resolution = 3.5 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= 0.002 sd= 0.010 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 28 5.49 5 Mg 12 5.21 5 S 54 5.16 5 C 8233 2.51 5 N 2245 2.21 5 O 2542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13114 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2515 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "B" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1687 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "C" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2515 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "D" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1687 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "E" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2515 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "F" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1687 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "G" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 466 Classifications: {'RNA': 22} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 12} Link IDs: {'rna3p': 21} Chain breaks: 1 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.39, per 1000 atoms: 0.26 Number of scatterers: 13114 At special positions: 0 Unit cell: (122.64, 117.53, 109.5, 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 54 16.00 P 28 15.00 Mg 12 11.99 O 2542 8.00 N 2245 7.00 C 8233 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: 1.18 Conformation dependent library (CDL) restraints added in 597.4 milliseconds 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2958 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 4 sheets defined 57.7% alpha, 6.6% beta 10 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 53 through 60 removed outlier: 3.679A pdb=" N ALA A 58 " --> pdb=" O LYS A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.532A pdb=" N PHE A 100 " --> pdb=" O THR A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.584A pdb=" N GLU A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP A 121 " --> pdb=" O HIS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 138 Processing helix chain 'A' and resid 140 through 144 removed outlier: 3.645A pdb=" N TYR A 143 " --> pdb=" O GLU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 177 removed outlier: 3.573A pdb=" N SER A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 195 removed outlier: 4.395A pdb=" N ALA A 193 " --> pdb=" O ILE A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 216 through 233 removed outlier: 3.620A pdb=" N SER A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 248 removed outlier: 3.957A pdb=" N MET A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 263 through 289 removed outlier: 4.018A pdb=" N ILE A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.798A pdb=" N GLU A 302 " --> pdb=" O PHE A 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 120 removed outlier: 3.549A pdb=" N HIS B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 138 Processing helix chain 'B' and resid 157 through 177 removed outlier: 3.618A pdb=" N SER B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 192 Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 216 through 232 removed outlier: 3.605A pdb=" N VAL B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 248 removed outlier: 3.624A pdb=" N LEU B 241 " --> pdb=" O GLU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 263 through 282 removed outlier: 3.591A pdb=" N ILE B 268 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 302 removed outlier: 4.051A pdb=" N GLU B 302 " --> pdb=" O PHE B 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 96 through 100 Processing helix chain 'C' and resid 107 through 120 removed outlier: 3.539A pdb=" N TYR C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 138 removed outlier: 3.567A pdb=" N TYR C 138 " --> pdb=" O LEU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 143 removed outlier: 3.839A pdb=" N TYR C 143 " --> pdb=" O GLN C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 177 removed outlier: 3.880A pdb=" N SER C 172 " --> pdb=" O ARG C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 192 Processing helix chain 'C' and resid 194 through 200 removed outlier: 3.960A pdb=" N ARG C 198 " --> pdb=" O ILE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 215 through 232 removed outlier: 4.371A pdb=" N SER C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 Processing helix chain 'C' and resid 263 through 287 removed outlier: 3.876A pdb=" N GLU C 283 " --> pdb=" O MET C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 302 removed outlier: 3.503A pdb=" N GLU C 302 " --> pdb=" O PHE C 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 120 removed outlier: 3.543A pdb=" N HIS D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 138 Processing helix chain 'D' and resid 159 through 177 removed outlier: 5.250A pdb=" N THR D 165 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 169 " --> pdb=" O THR D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 195 through 200 Processing helix chain 'D' and resid 209 through 232 removed outlier: 8.679A pdb=" N HIS D 217 " --> pdb=" O ASN D 213 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N ILE D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL D 226 " --> pdb=" O SER D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.523A pdb=" N LEU D 241 " --> pdb=" O GLU D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 288 removed outlier: 4.066A pdb=" N LYS D 288 " --> pdb=" O LYS D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 302 Processing helix chain 'E' and resid 3 through 7 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 107 through 120 removed outlier: 3.532A pdb=" N GLN E 112 " --> pdb=" O PRO E 108 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR E 118 " --> pdb=" O GLU E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 138 Processing helix chain 'E' and resid 138 through 143 removed outlier: 3.869A pdb=" N TYR E 143 " --> pdb=" O GLN E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 177 Processing helix chain 'E' and resid 181 through 193 removed outlier: 4.366A pdb=" N ALA E 193 " --> pdb=" O ILE E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 200 removed outlier: 3.923A pdb=" N ARG E 198 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 233 removed outlier: 7.884A pdb=" N HIS E 217 " --> pdb=" O ASN E 213 " (cutoff:3.500A) removed outlier: 9.500A pdb=" N ILE E 218 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER E 219 " --> pdb=" O LEU E 215 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP E 223 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL E 225 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 248 removed outlier: 4.360A pdb=" N MET E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 256 Processing helix chain 'E' and resid 263 through 288 removed outlier: 3.598A pdb=" N MET E 281 " --> pdb=" O ALA E 277 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS E 288 " --> pdb=" O LYS E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 302 removed outlier: 3.700A pdb=" N GLU E 302 " --> pdb=" O PHE E 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 121 removed outlier: 3.689A pdb=" N HIS F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR F 118 " --> pdb=" O GLU F 114 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP F 121 " --> pdb=" O HIS F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 138 removed outlier: 3.620A pdb=" N ILE F 130 " --> pdb=" O ASN F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 143 removed outlier: 3.883A pdb=" N TYR F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 177 removed outlier: 3.701A pdb=" N MET F 166 " --> pdb=" O HIS F 162 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER F 172 " --> pdb=" O ARG F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 199 removed outlier: 4.060A pdb=" N ALA F 193 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS F 196 " --> pdb=" O HIS F 192 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL F 197 " --> pdb=" O ALA F 193 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG F 198 " --> pdb=" O ILE F 194 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU F 199 " --> pdb=" O GLY F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 215 removed outlier: 3.867A pdb=" N LEU F 214 " --> pdb=" O VAL F 210 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU F 215 " --> pdb=" O GLU F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 232 removed outlier: 3.787A pdb=" N SER F 219 " --> pdb=" O LEU F 215 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER F 222 " --> pdb=" O ILE F 218 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL F 226 " --> pdb=" O SER F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 248 removed outlier: 4.036A pdb=" N MET F 240 " --> pdb=" O GLY F 236 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE F 246 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 256 Processing helix chain 'F' and resid 263 through 287 removed outlier: 3.617A pdb=" N TYR F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET F 279 " --> pdb=" O ILE F 275 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET F 281 " --> pdb=" O ALA F 277 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE F 282 " --> pdb=" O ARG F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 302 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 6.756A pdb=" N LYS A 69 " --> pdb=" O ASN A 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 24 removed outlier: 3.741A pdb=" N LYS A 21 " --> pdb=" O HIS A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 12 through 13 removed outlier: 8.114A pdb=" N ILE C 65 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU C 88 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N HIS C 67 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE C 86 " --> pdb=" O HIS C 67 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS C 69 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N THR C 35 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ALA C 22 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N HIS C 37 " --> pdb=" O HIS C 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 44 through 47 removed outlier: 3.568A pdb=" N LYS E 21 " --> pdb=" O HIS E 37 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N GLN E 39 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N VAL E 19 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N HIS E 15 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL E 68 " --> pdb=" O HIS E 15 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE E 17 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N ILE E 65 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU E 88 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N HIS E 67 " --> pdb=" O ILE E 86 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE E 86 " --> pdb=" O HIS E 67 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LYS E 69 " --> pdb=" O ASN E 84 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1677 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4077 1.34 - 1.45: 1932 1.45 - 1.57: 7265 1.57 - 1.69: 42 1.69 - 1.81: 96 Bond restraints: 13412 Sorted by residual: bond pdb=" O3 PO4 D 401 " pdb=" P PO4 D 401 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.18e+00 bond pdb=" O3 PO4 C1002 " pdb=" P PO4 C1002 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.01e+00 bond pdb=" O3 PO4 A1003 " pdb=" P PO4 A1003 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.95e+00 bond pdb=" O3 PO4 B1003 " pdb=" P PO4 B1003 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.93e+00 bond pdb=" O4 PO4 D 401 " pdb=" P PO4 D 401 " ideal model delta sigma weight residual 1.568 1.508 0.060 2.00e-02 2.50e+03 8.91e+00 ... (remaining 13407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 17968 1.80 - 3.60: 209 3.60 - 5.40: 21 5.40 - 7.20: 8 7.20 - 9.01: 2 Bond angle restraints: 18208 Sorted by residual: angle pdb=" C GLN A 39 " pdb=" N ASP A 40 " pdb=" CA ASP A 40 " ideal model delta sigma weight residual 121.54 130.55 -9.01 1.91e+00 2.74e-01 2.22e+01 angle pdb=" C LEU F 232 " pdb=" N ASN F 233 " pdb=" CA ASN F 233 " ideal model delta sigma weight residual 122.46 127.31 -4.85 1.41e+00 5.03e-01 1.19e+01 angle pdb=" C2 C G 25 " pdb=" N1 C G 25 " pdb=" C6 C G 25 " ideal model delta sigma weight residual 120.30 118.94 1.36 4.00e-01 6.25e+00 1.15e+01 angle pdb=" N1 C G 25 " pdb=" C6 C G 25 " pdb=" C5 C G 25 " ideal model delta sigma weight residual 121.00 122.68 -1.68 5.00e-01 4.00e+00 1.12e+01 angle pdb=" C2 C G 3 " pdb=" N1 C G 3 " pdb=" C6 C G 3 " ideal model delta sigma weight residual 120.30 119.19 1.11 4.00e-01 6.25e+00 7.70e+00 ... (remaining 18203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 7161 18.00 - 36.00: 788 36.00 - 53.99: 136 53.99 - 71.99: 43 71.99 - 89.99: 23 Dihedral angle restraints: 8151 sinusoidal: 3549 harmonic: 4602 Sorted by residual: dihedral pdb=" CA MET F 279 " pdb=" C MET F 279 " pdb=" N ASN F 280 " pdb=" CA ASN F 280 " ideal model delta harmonic sigma weight residual 180.00 155.28 24.72 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA SER A 150 " pdb=" C SER A 150 " pdb=" N HIS A 151 " pdb=" CA HIS A 151 " ideal model delta harmonic sigma weight residual -180.00 -159.74 -20.26 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ALA F 156 " pdb=" C ALA F 156 " pdb=" N SER F 157 " pdb=" CA SER F 157 " ideal model delta harmonic sigma weight residual -180.00 -162.93 -17.07 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 8148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1409 0.035 - 0.070: 485 0.070 - 0.105: 104 0.105 - 0.140: 27 0.140 - 0.175: 5 Chirality restraints: 2030 Sorted by residual: chirality pdb=" C3' U G 11 " pdb=" C4' U G 11 " pdb=" O3' U G 11 " pdb=" C2' U G 11 " both_signs ideal model delta sigma weight residual False -2.48 -2.65 0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" C2' G G 16 " pdb=" C3' G G 16 " pdb=" O2' G G 16 " pdb=" C1' G G 16 " both_signs ideal model delta sigma weight residual False -2.75 -2.58 -0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" C2' U G 11 " pdb=" C3' U G 11 " pdb=" O2' U G 11 " pdb=" C1' U G 11 " both_signs ideal model delta sigma weight residual False -2.75 -2.60 -0.15 2.00e-01 2.50e+01 5.96e-01 ... (remaining 2027 not shown) Planarity restraints: 2248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G G 24 " 0.020 2.00e-02 2.50e+03 8.68e-03 2.26e+00 pdb=" N9 G G 24 " -0.021 2.00e-02 2.50e+03 pdb=" C8 G G 24 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G G 24 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G G 24 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G G 24 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G G 24 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G G 24 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G G 24 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G G 24 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G G 24 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G G 24 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 202 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO D 203 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 203 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 203 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 283 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.76e+00 pdb=" C GLU B 283 " 0.023 2.00e-02 2.50e+03 pdb=" O GLU B 283 " -0.009 2.00e-02 2.50e+03 pdb=" N LYS B 284 " -0.008 2.00e-02 2.50e+03 ... (remaining 2245 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 110 2.55 - 3.13: 10253 3.13 - 3.72: 20509 3.72 - 4.31: 28599 4.31 - 4.90: 46876 Nonbonded interactions: 106347 Sorted by model distance: nonbonded pdb=" O1 PO4 D 401 " pdb="MG MG D 403 " model vdw 1.958 2.170 nonbonded pdb=" O3 PO4 C1002 " pdb="MG MG C1003 " model vdw 1.960 2.170 nonbonded pdb=" NE2 HIS D 162 " pdb="MG MG D 403 " model vdw 1.961 2.250 nonbonded pdb="MG MG C1001 " pdb=" O1 PO4 C1002 " model vdw 1.973 2.170 nonbonded pdb=" O1 PO4 E 402 " pdb="MG MG E 403 " model vdw 1.979 2.170 ... (remaining 106342 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 1 through 1001) selection = (chain 'C' and resid 1 through 1001) selection = (chain 'E' and resid 1 through 401) } ncs_group { reference = (chain 'B' and (resid 105 through 313 or resid 1002)) selection = (chain 'D' and (resid 105 through 313 or resid 402)) selection = (chain 'F' and (resid 105 through 313 or resid 402)) } 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 group one per residue 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.810 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 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 0.061 13412 Z= 0.178 Angle : 0.505 9.005 18208 Z= 0.280 Chirality : 0.038 0.175 2030 Planarity : 0.003 0.035 2248 Dihedral : 15.730 89.988 5193 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.05 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.68 (0.21), residues: 1554 helix: 0.14 (0.18), residues: 736 sheet: -1.68 (0.48), residues: 124 loop : -0.74 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 230 TYR 0.020 0.001 TYR D 145 PHE 0.010 0.001 PHE F 155 TRP 0.005 0.001 TRP C 50 HIS 0.006 0.001 HIS F 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 (13412) covalent geometry : angle 0.50541 / 0.28 (18208) hydrogen bonds : bond 0.28076 / 18.81 ( 621) hydrogen bonds : angle 7.95869 / 5.49 ( 1723) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.542 Fit side-chains REVERT: A 217 HIS cc_start: 0.7675 (p-80) cc_final: 0.7358 (p-80) REVERT: B 276 ASP cc_start: 0.8638 (t70) cc_final: 0.8375 (t70) REVERT: D 283 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8253 (tm-30) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.0927 time to fit residues: 20.3941 Evaluate side-chains 120 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 ASN B 280 ASN C 128 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.115202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.083598 restraints weight = 26146.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.086748 restraints weight = 13737.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.087687 restraints weight = 8660.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.087809 restraints weight = 7294.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.088245 restraints weight = 7234.973| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13412 Z= 0.154 Angle : 0.567 8.852 18208 Z= 0.306 Chirality : 0.040 0.164 2030 Planarity : 0.004 0.035 2248 Dihedral : 9.944 73.646 2055 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.56 % Favored : 93.37 % Rotamer: Outliers : 0.73 % Allowed : 7.13 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.21), residues: 1554 helix: 1.03 (0.18), residues: 748 sheet: -2.15 (0.44), residues: 132 loop : -0.70 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 230 TYR 0.012 0.001 TYR D 145 PHE 0.015 0.001 PHE E 299 TRP 0.006 0.001 TRP C 50 HIS 0.011 0.001 HIS F 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (13412) covalent geometry : angle 0.56724 / 0.31 (18208) hydrogen bonds : bond 0.07199 / 4.78 ( 621) hydrogen bonds : angle 5.04422 / 3.50 ( 1723) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.517 Fit side-chains REVERT: A 34 MET cc_start: 0.8619 (tmm) cc_final: 0.8316 (tmm) REVERT: A 217 HIS cc_start: 0.7288 (p-80) cc_final: 0.6963 (p-80) REVERT: A 245 MET cc_start: 0.8960 (mmm) cc_final: 0.8338 (mpp) REVERT: A 293 GLN cc_start: 0.8655 (pm20) cc_final: 0.8325 (pm20) REVERT: F 279 MET cc_start: 0.7044 (ppp) cc_final: 0.6598 (ppp) outliers start: 10 outliers final: 7 residues processed: 142 average time/residue: 0.1008 time to fit residues: 22.4523 Evaluate side-chains 129 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 151 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 19 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 136 optimal weight: 8.9990 chunk 131 optimal weight: 20.0000 chunk 139 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 103 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 HIS ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.114446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.082720 restraints weight = 26478.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.086308 restraints weight = 13697.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.086990 restraints weight = 8406.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.086943 restraints weight = 7222.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.087397 restraints weight = 7184.579| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13412 Z= 0.173 Angle : 0.531 8.580 18208 Z= 0.285 Chirality : 0.039 0.151 2030 Planarity : 0.004 0.038 2248 Dihedral : 9.793 73.525 2055 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.11 % Favored : 93.82 % Rotamer: Outliers : 1.24 % Allowed : 9.97 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.07 (0.21), residues: 1554 helix: 1.24 (0.18), residues: 757 sheet: -2.13 (0.41), residues: 144 loop : -0.81 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 230 TYR 0.013 0.001 TYR D 145 PHE 0.022 0.001 PHE A 299 TRP 0.004 0.001 TRP C 50 HIS 0.011 0.001 HIS F 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (13412) covalent geometry : angle 0.53150 / 0.29 (18208) hydrogen bonds : bond 0.05743 / 3.80 ( 621) hydrogen bonds : angle 4.61159 / 3.22 ( 1723) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.569 Fit side-chains REVERT: A 34 MET cc_start: 0.8619 (tmm) cc_final: 0.7952 (tmm) REVERT: A 71 ASP cc_start: 0.8406 (t0) cc_final: 0.8164 (m-30) REVERT: A 217 HIS cc_start: 0.7278 (p-80) cc_final: 0.7067 (p-80) REVERT: A 245 MET cc_start: 0.8982 (mmm) cc_final: 0.8321 (mpp) REVERT: C 60 ILE cc_start: 0.8617 (mm) cc_final: 0.8380 (mt) REVERT: D 166 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8184 (mtp) REVERT: E 34 MET cc_start: 0.6737 (tpt) cc_final: 0.4941 (mmt) outliers start: 17 outliers final: 12 residues processed: 139 average time/residue: 0.0954 time to fit residues: 20.7514 Evaluate side-chains 134 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 151 HIS Chi-restraints excluded: chain F residue 192 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 144 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** 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 = 0.3714 r_free = 0.3714 target = 0.116044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.084585 restraints weight = 26079.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.088042 restraints weight = 13693.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.089035 restraints weight = 8407.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.088841 restraints weight = 7157.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.088978 restraints weight = 7452.419| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13412 Z= 0.120 Angle : 0.483 8.520 18208 Z= 0.260 Chirality : 0.038 0.135 2030 Planarity : 0.003 0.037 2248 Dihedral : 9.704 73.514 2055 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.24 % Favored : 93.69 % Rotamer: Outliers : 1.89 % Allowed : 12.37 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.29 (0.21), residues: 1554 helix: 1.51 (0.18), residues: 752 sheet: -2.12 (0.41), residues: 144 loop : -0.77 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 230 TYR 0.008 0.001 TYR D 145 PHE 0.011 0.001 PHE E 100 TRP 0.003 0.001 TRP C 50 HIS 0.014 0.001 HIS F 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (13412) covalent geometry : angle 0.48296 / 0.26 (18208) hydrogen bonds : bond 0.04596 / 3.00 ( 621) hydrogen bonds : angle 4.29681 / 3.01 ( 1723) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.493 Fit side-chains REVERT: A 34 MET cc_start: 0.8656 (tmm) cc_final: 0.8285 (tmm) REVERT: A 71 ASP cc_start: 0.8407 (t0) cc_final: 0.8107 (m-30) REVERT: A 166 MET cc_start: 0.8836 (mmm) cc_final: 0.8192 (mtt) REVERT: A 217 HIS cc_start: 0.7266 (p-80) cc_final: 0.6942 (p-80) REVERT: A 245 MET cc_start: 0.8964 (mmm) cc_final: 0.8173 (mpp) REVERT: C 60 ILE cc_start: 0.8596 (mm) cc_final: 0.8338 (mt) REVERT: E 34 MET cc_start: 0.6719 (tpt) cc_final: 0.5040 (mmt) outliers start: 26 outliers final: 16 residues processed: 147 average time/residue: 0.0885 time to fit residues: 20.2256 Evaluate side-chains 138 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 151 HIS Chi-restraints excluded: chain F residue 192 HIS Chi-restraints excluded: chain F residue 279 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 103 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 153 optimal weight: 40.0000 chunk 115 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.109073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.077569 restraints weight = 26208.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.080174 restraints weight = 15911.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.080701 restraints weight = 10451.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.080873 restraints weight = 9485.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.080974 restraints weight = 9275.816| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 13412 Z= 0.289 Angle : 0.607 8.600 18208 Z= 0.321 Chirality : 0.042 0.168 2030 Planarity : 0.004 0.036 2248 Dihedral : 9.765 73.584 2055 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.18 % Favored : 93.76 % Rotamer: Outliers : 2.04 % Allowed : 13.68 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.21), residues: 1554 helix: 1.11 (0.18), residues: 781 sheet: -2.33 (0.42), residues: 138 loop : -0.91 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 230 TYR 0.016 0.002 TYR D 145 PHE 0.015 0.002 PHE B 155 TRP 0.007 0.002 TRP A 50 HIS 0.014 0.002 HIS F 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00693 / 0.29 (13412) covalent geometry : angle 0.60738 / 0.32 (18208) hydrogen bonds : bond 0.05482 / 3.63 ( 621) hydrogen bonds : angle 4.55295 / 3.17 ( 1723) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.575 Fit side-chains REVERT: A 34 MET cc_start: 0.8698 (tmm) cc_final: 0.8316 (tmm) REVERT: A 71 ASP cc_start: 0.8389 (t0) cc_final: 0.7950 (m-30) REVERT: A 217 HIS cc_start: 0.7272 (p-80) cc_final: 0.6893 (p-80) REVERT: A 245 MET cc_start: 0.9108 (mmm) cc_final: 0.8432 (mpp) REVERT: C 60 ILE cc_start: 0.8752 (mm) cc_final: 0.8511 (mt) REVERT: D 166 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8145 (mtp) REVERT: E 34 MET cc_start: 0.6479 (tpt) cc_final: 0.4922 (mmt) outliers start: 28 outliers final: 20 residues processed: 142 average time/residue: 0.0936 time to fit residues: 20.9673 Evaluate side-chains 138 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 151 HIS Chi-restraints excluded: chain F residue 233 ASN Chi-restraints excluded: chain F residue 279 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 105 optimal weight: 30.0000 chunk 123 optimal weight: 0.6980 chunk 21 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 102 optimal weight: 30.0000 chunk 141 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** 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 = 0.3693 r_free = 0.3693 target = 0.114648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.083153 restraints weight = 26192.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.086425 restraints weight = 13752.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.087401 restraints weight = 8577.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.087325 restraints weight = 7325.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.087505 restraints weight = 7638.771| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13412 Z= 0.129 Angle : 0.495 7.617 18208 Z= 0.265 Chirality : 0.038 0.141 2030 Planarity : 0.003 0.034 2248 Dihedral : 9.696 73.560 2055 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.97 % Allowed : 13.97 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.25 (0.21), residues: 1554 helix: 1.51 (0.18), residues: 752 sheet: -2.31 (0.42), residues: 136 loop : -0.81 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 230 TYR 0.009 0.001 TYR E 177 PHE 0.014 0.001 PHE E 100 TRP 0.004 0.001 TRP C 50 HIS 0.013 0.001 HIS F 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (13412) covalent geometry : angle 0.49498 / 0.26 (18208) hydrogen bonds : bond 0.04550 / 2.97 ( 621) hydrogen bonds : angle 4.23801 / 2.97 ( 1723) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.471 Fit side-chains REVERT: A 34 MET cc_start: 0.8667 (tmm) cc_final: 0.8238 (tmm) REVERT: A 71 ASP cc_start: 0.8457 (t0) cc_final: 0.8103 (m-30) REVERT: A 217 HIS cc_start: 0.7265 (p-80) cc_final: 0.7057 (p-80) REVERT: C 60 ILE cc_start: 0.8636 (mm) cc_final: 0.8396 (mt) REVERT: E 34 MET cc_start: 0.6772 (tpt) cc_final: 0.5056 (mmt) outliers start: 27 outliers final: 19 residues processed: 148 average time/residue: 0.0836 time to fit residues: 19.4366 Evaluate side-chains 141 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 151 HIS Chi-restraints excluded: chain F residue 192 HIS Chi-restraints excluded: chain F residue 233 ASN Chi-restraints excluded: chain F residue 279 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 122 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 102 optimal weight: 40.0000 chunk 113 optimal weight: 5.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 ASN ** 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 = 0.3676 r_free = 0.3676 target = 0.113460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.081793 restraints weight = 26361.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.085340 restraints weight = 13864.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.086068 restraints weight = 8564.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.085915 restraints weight = 7382.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.086047 restraints weight = 7715.136| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13412 Z= 0.193 Angle : 0.526 8.607 18208 Z= 0.279 Chirality : 0.039 0.145 2030 Planarity : 0.003 0.034 2248 Dihedral : 9.690 73.558 2055 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.18 % Allowed : 14.63 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.21), residues: 1554 helix: 1.46 (0.18), residues: 758 sheet: -2.28 (0.41), residues: 138 loop : -0.86 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 230 TYR 0.011 0.001 TYR E 177 PHE 0.012 0.001 PHE B 155 TRP 0.005 0.001 TRP A 50 HIS 0.014 0.001 HIS F 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 (13412) covalent geometry : angle 0.52556 / 0.28 (18208) hydrogen bonds : bond 0.04679 / 3.07 ( 621) hydrogen bonds : angle 4.26305 / 2.98 ( 1723) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.461 Fit side-chains REVERT: A 34 MET cc_start: 0.8723 (tmm) cc_final: 0.8222 (tmm) REVERT: A 71 ASP cc_start: 0.8502 (t0) cc_final: 0.8129 (m-30) REVERT: A 217 HIS cc_start: 0.7262 (p-80) cc_final: 0.6874 (p-80) REVERT: A 245 MET cc_start: 0.9080 (tpp) cc_final: 0.8849 (tpp) REVERT: C 60 ILE cc_start: 0.8674 (mm) cc_final: 0.8445 (mt) REVERT: D 245 MET cc_start: 0.8974 (mmm) cc_final: 0.8561 (mtp) REVERT: E 34 MET cc_start: 0.6779 (tpt) cc_final: 0.5065 (mmt) outliers start: 30 outliers final: 26 residues processed: 145 average time/residue: 0.0927 time to fit residues: 20.9158 Evaluate side-chains 146 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 151 HIS Chi-restraints excluded: chain F residue 192 HIS Chi-restraints excluded: chain F residue 233 ASN Chi-restraints excluded: chain F residue 279 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 119 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 109 optimal weight: 40.0000 chunk 133 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.113294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.081661 restraints weight = 26180.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.085261 restraints weight = 13787.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.085725 restraints weight = 8487.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.085862 restraints weight = 7390.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.086205 restraints weight = 7356.902| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 13412 Z= 0.211 Angle : 0.546 9.722 18208 Z= 0.288 Chirality : 0.040 0.153 2030 Planarity : 0.003 0.034 2248 Dihedral : 9.700 73.564 2055 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.40 % Allowed : 14.85 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.19 (0.21), residues: 1554 helix: 1.44 (0.18), residues: 758 sheet: -2.17 (0.41), residues: 137 loop : -0.88 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 230 TYR 0.011 0.001 TYR E 177 PHE 0.012 0.001 PHE B 155 TRP 0.005 0.001 TRP A 50 HIS 0.014 0.001 HIS F 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 (13412) covalent geometry : angle 0.54631 / 0.29 (18208) hydrogen bonds : bond 0.04711 / 3.09 ( 621) hydrogen bonds : angle 4.27951 / 3.00 ( 1723) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.531 Fit side-chains REVERT: A 34 MET cc_start: 0.8684 (tmm) cc_final: 0.8162 (tmm) REVERT: A 71 ASP cc_start: 0.8519 (t0) cc_final: 0.8116 (m-30) REVERT: A 166 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8646 (mtt) REVERT: A 217 HIS cc_start: 0.7281 (p-80) cc_final: 0.6886 (p-80) REVERT: A 245 MET cc_start: 0.9134 (tpp) cc_final: 0.8837 (tpp) REVERT: C 60 ILE cc_start: 0.8695 (mm) cc_final: 0.8473 (mt) REVERT: D 245 MET cc_start: 0.8980 (mmm) cc_final: 0.8559 (mtp) REVERT: E 34 MET cc_start: 0.6832 (tpt) cc_final: 0.5088 (mmt) outliers start: 33 outliers final: 26 residues processed: 149 average time/residue: 0.0959 time to fit residues: 22.4180 Evaluate side-chains 146 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 151 HIS Chi-restraints excluded: chain F residue 233 ASN Chi-restraints excluded: chain F residue 279 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 101 optimal weight: 0.3980 chunk 152 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN B 128 GLN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.115734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.084221 restraints weight = 26266.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.087614 restraints weight = 13788.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.088603 restraints weight = 8482.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.088432 restraints weight = 7333.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.088542 restraints weight = 7560.515| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13412 Z= 0.114 Angle : 0.493 8.034 18208 Z= 0.263 Chirality : 0.037 0.136 2030 Planarity : 0.003 0.034 2248 Dihedral : 9.631 73.560 2055 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.08 % Rotamer: Outliers : 1.60 % Allowed : 15.72 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.22), residues: 1554 helix: 1.70 (0.18), residues: 749 sheet: -2.20 (0.42), residues: 135 loop : -0.80 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 230 TYR 0.009 0.001 TYR B 271 PHE 0.022 0.001 PHE E 306 TRP 0.004 0.001 TRP E 50 HIS 0.013 0.001 HIS F 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (13412) covalent geometry : angle 0.49256 / 0.26 (18208) hydrogen bonds : bond 0.04048 / 2.62 ( 621) hydrogen bonds : angle 4.05712 / 2.85 ( 1723) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 34 MET cc_start: 0.8709 (tmm) cc_final: 0.8232 (tmm) REVERT: A 71 ASP cc_start: 0.8485 (t0) cc_final: 0.8132 (m-30) REVERT: A 166 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8623 (mtt) REVERT: A 217 HIS cc_start: 0.7255 (p-80) cc_final: 0.6942 (p-80) REVERT: A 245 MET cc_start: 0.9124 (tpp) cc_final: 0.8739 (tpp) REVERT: C 60 ILE cc_start: 0.8623 (mm) cc_final: 0.8393 (mt) REVERT: E 34 MET cc_start: 0.6809 (tpt) cc_final: 0.5133 (mmt) REVERT: E 49 PHE cc_start: 0.5247 (t80) cc_final: 0.4991 (t80) REVERT: F 175 ASP cc_start: 0.8750 (t70) cc_final: 0.8542 (t0) outliers start: 22 outliers final: 20 residues processed: 149 average time/residue: 0.1024 time to fit residues: 23.4156 Evaluate side-chains 147 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 151 HIS Chi-restraints excluded: chain F residue 233 ASN Chi-restraints excluded: chain F residue 279 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 129 optimal weight: 4.9990 chunk 104 optimal weight: 30.0000 chunk 82 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 0.1980 chunk 5 optimal weight: 0.0980 chunk 9 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** 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 = 0.3693 r_free = 0.3693 target = 0.114732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.083246 restraints weight = 26274.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.086441 restraints weight = 13773.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.087283 restraints weight = 8668.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.087270 restraints weight = 7444.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.087374 restraints weight = 7760.425| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13412 Z= 0.156 Angle : 0.512 9.540 18208 Z= 0.270 Chirality : 0.038 0.145 2030 Planarity : 0.003 0.043 2248 Dihedral : 9.617 73.576 2055 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.24 % Favored : 93.69 % Rotamer: Outliers : 1.67 % Allowed : 16.01 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.36 (0.22), residues: 1554 helix: 1.61 (0.18), residues: 758 sheet: -2.24 (0.42), residues: 135 loop : -0.81 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 305 TYR 0.010 0.001 TYR E 177 PHE 0.015 0.001 PHE E 306 TRP 0.004 0.001 TRP E 50 HIS 0.014 0.001 HIS F 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (13412) covalent geometry : angle 0.51174 / 0.27 (18208) hydrogen bonds : bond 0.04183 / 2.73 ( 621) hydrogen bonds : angle 4.07762 / 2.86 ( 1723) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 34 MET cc_start: 0.8715 (tmm) cc_final: 0.8225 (tmm) REVERT: A 71 ASP cc_start: 0.8489 (t0) cc_final: 0.8121 (m-30) REVERT: A 166 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8633 (mtt) REVERT: A 217 HIS cc_start: 0.7256 (p-80) cc_final: 0.7048 (p-80) REVERT: A 245 MET cc_start: 0.9155 (tpp) cc_final: 0.8792 (tpp) REVERT: C 60 ILE cc_start: 0.8626 (mm) cc_final: 0.8401 (mt) REVERT: D 283 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8111 (tm-30) REVERT: E 34 MET cc_start: 0.6796 (tpt) cc_final: 0.5183 (mmt) REVERT: E 49 PHE cc_start: 0.5325 (t80) cc_final: 0.5089 (t80) REVERT: E 312 LEU cc_start: 0.8314 (mt) cc_final: 0.8050 (tt) REVERT: F 245 MET cc_start: 0.8831 (tpp) cc_final: 0.8603 (tpp) outliers start: 23 outliers final: 20 residues processed: 142 average time/residue: 0.0911 time to fit residues: 20.1096 Evaluate side-chains 144 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 151 HIS Chi-restraints excluded: chain F residue 233 ASN Chi-restraints excluded: chain F residue 279 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 92 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** 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 = 0.3697 r_free = 0.3697 target = 0.115005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.083579 restraints weight = 26117.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.086705 restraints weight = 13804.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.087752 restraints weight = 8696.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.087642 restraints weight = 7436.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.087759 restraints weight = 7691.174| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13412 Z= 0.141 Angle : 0.502 9.648 18208 Z= 0.265 Chirality : 0.038 0.147 2030 Planarity : 0.003 0.034 2248 Dihedral : 9.598 73.595 2055 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.60 % Allowed : 15.87 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.22), residues: 1554 helix: 1.63 (0.18), residues: 758 sheet: -2.26 (0.42), residues: 135 loop : -0.81 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 305 TYR 0.010 0.001 TYR E 177 PHE 0.014 0.001 PHE E 306 TRP 0.004 0.001 TRP E 50 HIS 0.014 0.001 HIS F 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (13412) covalent geometry : angle 0.50152 / 0.27 (18208) hydrogen bonds : bond 0.04101 / 2.68 ( 621) hydrogen bonds : angle 4.03676 / 2.84 ( 1723) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1869.20 seconds wall clock time: 33 minutes 19.88 seconds (1999.88 seconds total)