Starting phenix.real_space_refine on Wed Mar 4 14:48:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yk1_33883/03_2026/7yk1_33883.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yk1_33883/03_2026/7yk1_33883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yk1_33883/03_2026/7yk1_33883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yk1_33883/03_2026/7yk1_33883.map" model { file = "/net/cci-nas-00/data/ceres_data/7yk1_33883/03_2026/7yk1_33883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yk1_33883/03_2026/7yk1_33883.cif" } resolution = 3.08 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= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 6 5.21 5 S 90 5.16 5 C 8934 2.51 5 N 2496 2.21 5 O 2808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14364 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2334 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 8, 'TRANS': 297} Chain breaks: 1 Chain: "B" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2334 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 8, 'TRANS': 297} Chain breaks: 1 Chain: "C" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2334 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 8, 'TRANS': 297} Chain breaks: 1 Chain: "D" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2334 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 8, 'TRANS': 297} Chain breaks: 1 Chain: "E" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2334 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 8, 'TRANS': 297} Chain breaks: 1 Chain: "F" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2334 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 8, 'TRANS': 297} Chain breaks: 1 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 1, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 1, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 1, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 1, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 1, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 1, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.59, per 1000 atoms: 0.25 Number of scatterers: 14364 At special positions: 0 Unit cell: (124.02, 130.38, 77.38, 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 90 16.00 P 30 15.00 Mg 6 11.99 O 2808 8.00 N 2496 7.00 C 8934 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 494.6 milliseconds 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3468 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 25 sheets defined 42.3% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 removed outlier: 3.805A pdb=" N SER A 16 " --> pdb=" O HIS A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 80 Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.540A pdb=" N GLY A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 138 removed outlier: 3.675A pdb=" N PHE A 138 " --> pdb=" O GLN A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 174 through 184 Processing helix chain 'A' and resid 227 through 239 removed outlier: 5.649A pdb=" N ALA A 233 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 263 Processing helix chain 'A' and resid 292 through 306 Processing helix chain 'A' and resid 308 through 315 removed outlier: 3.533A pdb=" N TYR A 311 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS A 315 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 24 removed outlier: 3.810A pdb=" N SER B 16 " --> pdb=" O HIS B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 80 Processing helix chain 'B' and resid 107 through 120 removed outlier: 3.535A pdb=" N GLY B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 138 removed outlier: 3.688A pdb=" N PHE B 138 " --> pdb=" O GLN B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 159 Processing helix chain 'B' and resid 161 through 164 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 229 through 239 Processing helix chain 'B' and resid 257 through 263 Processing helix chain 'B' and resid 292 through 306 Processing helix chain 'B' and resid 308 through 315 removed outlier: 3.860A pdb=" N HIS B 315 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 24 removed outlier: 3.785A pdb=" N SER C 16 " --> pdb=" O HIS C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 80 Processing helix chain 'C' and resid 107 through 120 removed outlier: 3.552A pdb=" N GLY C 120 " --> pdb=" O LEU C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 138 removed outlier: 3.654A pdb=" N PHE C 138 " --> pdb=" O GLN C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 159 Processing helix chain 'C' and resid 161 through 164 Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 174 through 186 Processing helix chain 'C' and resid 229 through 239 Processing helix chain 'C' and resid 257 through 263 Processing helix chain 'C' and resid 292 through 306 Processing helix chain 'C' and resid 308 through 315 removed outlier: 3.512A pdb=" N TYR C 311 " --> pdb=" O SER C 308 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS C 315 " --> pdb=" O LEU C 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 23 removed outlier: 3.712A pdb=" N SER D 16 " --> pdb=" O HIS D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 80 Processing helix chain 'D' and resid 107 through 120 removed outlier: 3.638A pdb=" N GLY D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 138 removed outlier: 3.553A pdb=" N PHE D 138 " --> pdb=" O GLN D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 159 Processing helix chain 'D' and resid 160 through 164 removed outlier: 4.502A pdb=" N LYS D 163 " --> pdb=" O ALA D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 174 through 186 removed outlier: 3.532A pdb=" N VAL D 178 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 239 Processing helix chain 'D' and resid 257 through 263 Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 292 through 306 Processing helix chain 'D' and resid 308 through 315 removed outlier: 3.573A pdb=" N TYR D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS D 315 " --> pdb=" O LEU D 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 24 removed outlier: 3.585A pdb=" N SER E 16 " --> pdb=" O HIS E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 80 Processing helix chain 'E' and resid 107 through 120 Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 147 through 159 Processing helix chain 'E' and resid 161 through 164 Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 174 through 186 Processing helix chain 'E' and resid 229 through 239 Processing helix chain 'E' and resid 257 through 263 Processing helix chain 'E' and resid 277 through 283 removed outlier: 3.526A pdb=" N HIS E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 306 Processing helix chain 'E' and resid 308 through 315 removed outlier: 3.504A pdb=" N TYR E 311 " --> pdb=" O SER E 308 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS E 315 " --> pdb=" O LEU E 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 24 removed outlier: 3.823A pdb=" N SER F 16 " --> pdb=" O HIS F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 80 Processing helix chain 'F' and resid 107 through 120 removed outlier: 3.638A pdb=" N GLY F 120 " --> pdb=" O LEU F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 138 removed outlier: 3.554A pdb=" N PHE F 138 " --> pdb=" O GLN F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 159 Processing helix chain 'F' and resid 160 through 164 removed outlier: 4.590A pdb=" N LYS F 163 " --> pdb=" O ALA F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 173 No H-bonds generated for 'chain 'F' and resid 171 through 173' Processing helix chain 'F' and resid 174 through 186 Processing helix chain 'F' and resid 229 through 239 Processing helix chain 'F' and resid 257 through 263 Processing helix chain 'F' and resid 279 through 283 Processing helix chain 'F' and resid 292 through 306 Processing helix chain 'F' and resid 308 through 315 removed outlier: 3.532A pdb=" N TYR F 311 " --> pdb=" O SER F 308 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS F 315 " --> pdb=" O LEU F 312 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.613A pdb=" N VAL A 53 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL A 88 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS A 123 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET A 127 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE A 124 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU A 145 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR A 126 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 188 through 189 removed outlier: 3.565A pdb=" N ILE A 167 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL A 244 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 269 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA A 246 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N VAL A 271 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N GLN A 288 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL A 269 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE A 290 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 271 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 193 Processing sheet with id=AA5, first strand: chain 'A' and resid 222 through 223 Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.617A pdb=" N VAL B 53 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL B 88 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE B 55 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS B 123 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET B 127 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE B 124 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU B 145 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N THR B 126 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 34 Processing sheet with id=AA8, first strand: chain 'B' and resid 206 through 208 removed outlier: 6.603A pdb=" N ILE B 167 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE B 192 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER B 169 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL B 244 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 269 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA B 246 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL B 271 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLN B 288 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL B 269 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE B 290 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 271 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 222 through 223 Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.691A pdb=" N VAL C 53 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL C 88 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE C 55 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS C 123 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N MET C 127 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE C 124 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU C 145 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR C 126 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 34 Processing sheet with id=AB3, first strand: chain 'C' and resid 206 through 208 removed outlier: 6.419A pdb=" N ILE C 167 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE C 192 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N SER C 169 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL C 244 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL C 269 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA C 246 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL C 271 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 222 through 223 Processing sheet with id=AB5, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.569A pdb=" N VAL D 53 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL D 88 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE D 55 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS D 123 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET D 127 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE D 124 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU D 145 " --> pdb=" O ILE D 124 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR D 126 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 30 through 34 Processing sheet with id=AB7, first strand: chain 'D' and resid 206 through 208 removed outlier: 6.496A pdb=" N ILE D 167 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ILE D 192 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N SER D 169 " --> pdb=" O ILE D 192 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL D 244 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL D 269 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA D 246 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL D 271 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N GLN D 288 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL D 269 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE D 290 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL D 271 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 222 through 223 Processing sheet with id=AB9, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.688A pdb=" N VAL E 53 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL E 88 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE E 55 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS E 123 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N MET E 127 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE E 124 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU E 145 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR E 126 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 30 through 34 Processing sheet with id=AC2, first strand: chain 'E' and resid 206 through 208 removed outlier: 6.430A pdb=" N ILE E 167 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE E 192 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N SER E 169 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL E 244 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL E 269 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA E 246 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N VAL E 271 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 222 through 223 Processing sheet with id=AC4, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.558A pdb=" N VAL F 53 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL F 88 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE F 55 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS F 123 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET F 127 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE F 124 " --> pdb=" O ASP F 143 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU F 145 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR F 126 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 30 through 34 Processing sheet with id=AC6, first strand: chain 'F' and resid 206 through 208 removed outlier: 6.476A pdb=" N ILE F 167 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE F 192 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N SER F 169 " --> pdb=" O ILE F 192 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL F 244 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL F 269 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA F 246 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL F 271 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 222 through 223 617 hydrogen bonds defined for protein. 1674 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 1.85 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: 4723 1.34 - 1.46: 1766 1.46 - 1.57: 7917 1.57 - 1.69: 36 1.69 - 1.81: 138 Bond restraints: 14580 Sorted by residual: bond pdb=" O3 PO4 A 401 " pdb=" P PO4 A 401 " ideal model delta sigma weight residual 1.569 1.504 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" O3 PO4 F 403 " pdb=" P PO4 F 403 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 1.01e+01 bond pdb=" O4 PO4 B 401 " pdb=" P PO4 B 401 " ideal model delta sigma weight residual 1.568 1.505 0.063 2.00e-02 2.50e+03 9.98e+00 bond pdb=" O3 PO4 C 403 " pdb=" P PO4 C 403 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 9.92e+00 bond pdb=" O3 PO4 D 402 " pdb=" P PO4 D 402 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.68e+00 ... (remaining 14575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 19104 1.45 - 2.91: 453 2.91 - 4.36: 139 4.36 - 5.81: 100 5.81 - 7.27: 10 Bond angle restraints: 19806 Sorted by residual: angle pdb=" N VAL D 48 " pdb=" CA VAL D 48 " pdb=" C VAL D 48 " ideal model delta sigma weight residual 112.29 108.63 3.66 9.40e-01 1.13e+00 1.51e+01 angle pdb=" C ILE D 229 " pdb=" N CYS D 230 " pdb=" CA CYS D 230 " ideal model delta sigma weight residual 121.54 128.14 -6.60 1.91e+00 2.74e-01 1.19e+01 angle pdb=" N THR D 228 " pdb=" CA THR D 228 " pdb=" C THR D 228 " ideal model delta sigma weight residual 110.80 103.53 7.27 2.13e+00 2.20e-01 1.16e+01 angle pdb=" C ASP F 210 " pdb=" N VAL F 211 " pdb=" CA VAL F 211 " ideal model delta sigma weight residual 121.97 126.92 -4.95 1.80e+00 3.09e-01 7.58e+00 angle pdb=" N THR F 228 " pdb=" CA THR F 228 " pdb=" C THR F 228 " ideal model delta sigma weight residual 110.19 106.88 3.31 1.24e+00 6.50e-01 7.13e+00 ... (remaining 19801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.40: 8437 34.40 - 68.80: 289 68.80 - 103.20: 63 103.20 - 137.60: 13 137.60 - 172.01: 12 Dihedral angle restraints: 8814 sinusoidal: 3492 harmonic: 5322 Sorted by residual: dihedral pdb=" C2' ADP D 401 " pdb=" C1' ADP D 401 " pdb=" N9 ADP D 401 " pdb=" C4 ADP D 401 " ideal model delta sinusoidal sigma weight residual 91.55 -96.45 -172.01 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C2' ADP F 402 " pdb=" C1' ADP F 402 " pdb=" N9 ADP F 402 " pdb=" C4 ADP F 402 " ideal model delta sinusoidal sigma weight residual 91.55 -96.46 -172.00 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C2' ADP C 402 " pdb=" C1' ADP C 402 " pdb=" N9 ADP C 402 " pdb=" C4 ADP C 402 " ideal model delta sinusoidal sigma weight residual 91.55 -100.95 -167.50 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 8811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1265 0.031 - 0.062: 664 0.062 - 0.093: 235 0.093 - 0.124: 169 0.124 - 0.155: 19 Chirality restraints: 2352 Sorted by residual: chirality pdb=" CB VAL F 211 " pdb=" CA VAL F 211 " pdb=" CG1 VAL F 211 " pdb=" CG2 VAL F 211 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA ILE C 290 " pdb=" N ILE C 290 " pdb=" C ILE C 290 " pdb=" CB ILE C 290 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CB ILE C 229 " pdb=" CA ILE C 229 " pdb=" CG1 ILE C 229 " pdb=" CG2 ILE C 229 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 2349 not shown) Planarity restraints: 2472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 213 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C ASP E 213 " -0.025 2.00e-02 2.50e+03 pdb=" O ASP E 213 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG E 214 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 12 " -0.001 2.00e-02 2.50e+03 1.07e-02 1.72e+00 pdb=" CG HIS F 12 " 0.016 2.00e-02 2.50e+03 pdb=" ND1 HIS F 12 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS F 12 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS F 12 " 0.011 2.00e-02 2.50e+03 pdb=" NE2 HIS F 12 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 12 " 0.002 2.00e-02 2.50e+03 1.01e-02 1.54e+00 pdb=" CG HIS C 12 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS C 12 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 HIS C 12 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS C 12 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 HIS C 12 " 0.003 2.00e-02 2.50e+03 ... (remaining 2469 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 162 2.60 - 3.18: 11659 3.18 - 3.75: 21679 3.75 - 4.33: 32617 4.33 - 4.90: 53304 Nonbonded interactions: 119421 Sorted by model distance: nonbonded pdb=" O1A ADP B 404 " pdb="MG MG E 404 " model vdw 2.029 2.170 nonbonded pdb=" O2A ADP A 403 " pdb="MG MG C 404 " model vdw 2.038 2.170 nonbonded pdb="MG MG A 402 " pdb=" O1A ADP C 401 " model vdw 2.090 2.170 nonbonded pdb="MG MG B 402 " pdb=" O2A ADP E 402 " model vdw 2.093 2.170 nonbonded pdb=" O THR B 249 " pdb=" OG1 THR B 272 " model vdw 2.138 3.040 ... (remaining 119416 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 316) selection = (chain 'B' and resid 2 through 316) selection = (chain 'C' and resid 2 through 316) selection = (chain 'D' and resid 2 through 316) selection = (chain 'E' and resid 2 through 316) selection = (chain 'F' and resid 2 through 316) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.160 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 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 : 0.006 0.065 14586 Z= 0.251 Angle : 0.690 7.265 19806 Z= 0.325 Chirality : 0.047 0.155 2352 Planarity : 0.004 0.028 2472 Dihedral : 20.078 172.005 5346 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.77 % Allowed : 5.24 % Favored : 93.98 % Rotamer: Outliers : 0.26 % Allowed : 17.64 % Favored : 82.11 % 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: -1.48 (0.19), residues: 1812 helix: -0.60 (0.19), residues: 690 sheet: -0.65 (0.23), residues: 534 loop : -1.50 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 184 TYR 0.011 0.002 TYR B 54 PHE 0.013 0.002 PHE A 313 TRP 0.005 0.001 TRP E 154 HIS 0.016 0.002 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00587 (14580) covalent geometry : angle 0.69006 (19806) hydrogen bonds : bond 0.22542 ( 617) hydrogen bonds : angle 6.81448 ( 1674) Misc. bond : bond 0.00073 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 190 time to evaluate : 0.449 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 191 average time/residue: 0.1174 time to fit residues: 33.3606 Evaluate side-chains 188 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 184 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 206 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.116940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.101328 restraints weight = 15139.931| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 0.95 r_work: 0.2769 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14586 Z= 0.156 Angle : 0.671 6.935 19806 Z= 0.314 Chirality : 0.047 0.148 2352 Planarity : 0.004 0.027 2472 Dihedral : 16.201 172.526 2071 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.02 % Favored : 93.27 % Rotamer: Outliers : 2.33 % Allowed : 16.67 % Favored : 81.01 % 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: -0.41 (0.20), residues: 1812 helix: 0.83 (0.20), residues: 660 sheet: -0.71 (0.23), residues: 534 loop : -0.90 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 184 TYR 0.007 0.001 TYR D 54 PHE 0.008 0.001 PHE A 313 TRP 0.006 0.001 TRP C 154 HIS 0.005 0.001 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00369 (14580) covalent geometry : angle 0.67109 (19806) hydrogen bonds : bond 0.04099 ( 617) hydrogen bonds : angle 4.43308 ( 1674) Misc. bond : bond 0.00059 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 0.568 Fit side-chains outliers start: 36 outliers final: 25 residues processed: 222 average time/residue: 0.1467 time to fit residues: 46.1707 Evaluate side-chains 214 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 164 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 74 optimal weight: 0.0470 chunk 167 optimal weight: 8.9990 chunk 119 optimal weight: 0.0980 chunk 24 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 4 optimal weight: 0.0030 chunk 35 optimal weight: 4.9990 overall best weight: 1.2090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.118563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.103901 restraints weight = 15196.583| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 0.89 r_work: 0.2789 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14586 Z= 0.112 Angle : 0.636 6.995 19806 Z= 0.291 Chirality : 0.045 0.174 2352 Planarity : 0.003 0.027 2472 Dihedral : 15.162 174.428 2066 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.72 % Allowed : 4.58 % Favored : 94.70 % Rotamer: Outliers : 2.65 % Allowed : 16.34 % Favored : 81.01 % 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: -0.05 (0.20), residues: 1812 helix: 1.41 (0.20), residues: 660 sheet: -0.58 (0.24), residues: 522 loop : -1.00 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 184 TYR 0.006 0.001 TYR E 311 PHE 0.007 0.001 PHE C 138 TRP 0.006 0.001 TRP C 154 HIS 0.005 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00254 (14580) covalent geometry : angle 0.63554 (19806) hydrogen bonds : bond 0.03161 ( 617) hydrogen bonds : angle 4.10900 ( 1674) Misc. bond : bond 0.00049 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 220 time to evaluate : 0.616 Fit side-chains REVERT: A 26 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: B 33 LYS cc_start: 0.8194 (ptpt) cc_final: 0.7768 (ptmt) REVERT: C 32 THR cc_start: 0.8760 (m) cc_final: 0.8552 (p) REVERT: D 12 HIS cc_start: 0.8484 (OUTLIER) cc_final: 0.8258 (t-90) REVERT: F 176 LYS cc_start: 0.8303 (mmmm) cc_final: 0.8100 (mmmm) outliers start: 41 outliers final: 23 residues processed: 245 average time/residue: 0.1391 time to fit residues: 49.0640 Evaluate side-chains 233 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 228 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 158 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 288 GLN F 288 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.115342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.2906 r_free = 0.2906 target = 0.100220 restraints weight = 15259.725| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.01 r_work: 0.2771 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14586 Z= 0.212 Angle : 0.710 7.258 19806 Z= 0.330 Chirality : 0.049 0.163 2352 Planarity : 0.004 0.026 2472 Dihedral : 15.078 171.639 2066 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.07 % Favored : 93.10 % Rotamer: Outliers : 3.04 % Allowed : 16.60 % Favored : 80.36 % 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 (0.20), residues: 1812 helix: 1.34 (0.21), residues: 660 sheet: -0.79 (0.23), residues: 534 loop : -1.11 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 84 TYR 0.008 0.001 TYR E 311 PHE 0.012 0.002 PHE A 313 TRP 0.007 0.002 TRP C 154 HIS 0.007 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00518 (14580) covalent geometry : angle 0.70993 (19806) hydrogen bonds : bond 0.04008 ( 617) hydrogen bonds : angle 4.24304 ( 1674) Misc. bond : bond 0.00127 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 0.563 Fit side-chains REVERT: A 26 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: B 26 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: F 12 HIS cc_start: 0.8605 (OUTLIER) cc_final: 0.8294 (t-90) REVERT: F 29 LYS cc_start: 0.9082 (mttp) cc_final: 0.8804 (mttm) REVERT: F 176 LYS cc_start: 0.8356 (mmmm) cc_final: 0.8129 (mmmm) outliers start: 47 outliers final: 31 residues processed: 218 average time/residue: 0.1349 time to fit residues: 42.9739 Evaluate side-chains 222 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 206 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 48 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 92 optimal weight: 0.0040 chunk 120 optimal weight: 8.9990 chunk 162 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 157 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 overall best weight: 2.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.117574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.109260 restraints weight = 15206.267| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 0.38 r_work: 0.2853 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14586 Z= 0.152 Angle : 0.665 6.858 19806 Z= 0.305 Chirality : 0.047 0.166 2352 Planarity : 0.003 0.027 2472 Dihedral : 14.711 176.057 2066 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.72 % Allowed : 4.86 % Favored : 94.43 % Rotamer: Outliers : 2.97 % Allowed : 17.18 % Favored : 79.84 % 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: -0.13 (0.20), residues: 1812 helix: 1.53 (0.21), residues: 660 sheet: -0.76 (0.23), residues: 534 loop : -1.14 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 177 TYR 0.006 0.001 TYR E 311 PHE 0.008 0.001 PHE C 138 TRP 0.005 0.001 TRP C 154 HIS 0.005 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00363 (14580) covalent geometry : angle 0.66500 (19806) hydrogen bonds : bond 0.03329 ( 617) hydrogen bonds : angle 4.14485 ( 1674) Misc. bond : bond 0.00104 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 196 time to evaluate : 0.571 Fit side-chains REVERT: A 26 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: B 26 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: D 12 HIS cc_start: 0.8603 (OUTLIER) cc_final: 0.8359 (t-90) REVERT: D 25 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8451 (pp) REVERT: F 12 HIS cc_start: 0.8612 (OUTLIER) cc_final: 0.8332 (t-90) REVERT: F 25 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8485 (pp) REVERT: F 29 LYS cc_start: 0.9019 (mttp) cc_final: 0.8763 (mttm) REVERT: F 176 LYS cc_start: 0.8360 (mmmm) cc_final: 0.8130 (mmmm) outliers start: 46 outliers final: 31 residues processed: 224 average time/residue: 0.1325 time to fit residues: 43.1400 Evaluate side-chains 227 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 281 MET Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 208 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 53 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 170 optimal weight: 10.0000 chunk 126 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.120224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.111713 restraints weight = 15212.329| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 0.39 r_work: 0.2900 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14586 Z= 0.100 Angle : 0.628 6.977 19806 Z= 0.285 Chirality : 0.045 0.158 2352 Planarity : 0.003 0.027 2472 Dihedral : 14.333 174.908 2066 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.72 % Allowed : 4.91 % Favored : 94.37 % Rotamer: Outliers : 2.65 % Allowed : 18.02 % Favored : 79.33 % 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: 0.17 (0.20), residues: 1812 helix: 1.81 (0.21), residues: 660 sheet: -0.53 (0.24), residues: 522 loop : -1.08 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 177 TYR 0.005 0.001 TYR E 311 PHE 0.007 0.001 PHE E 138 TRP 0.004 0.001 TRP F 162 HIS 0.005 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00224 (14580) covalent geometry : angle 0.62761 (19806) hydrogen bonds : bond 0.02636 ( 617) hydrogen bonds : angle 3.97397 ( 1674) Misc. bond : bond 0.00054 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 0.553 Fit side-chains REVERT: A 26 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7643 (mp0) REVERT: B 26 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: B 195 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7600 (mt-10) REVERT: D 12 HIS cc_start: 0.8517 (OUTLIER) cc_final: 0.8279 (t-90) REVERT: D 25 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8475 (pp) REVERT: D 29 LYS cc_start: 0.9038 (mttp) cc_final: 0.8783 (mttm) REVERT: E 69 GLU cc_start: 0.8355 (tt0) cc_final: 0.8064 (tt0) REVERT: F 12 HIS cc_start: 0.8605 (OUTLIER) cc_final: 0.8318 (t-90) REVERT: F 25 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8467 (pp) REVERT: F 29 LYS cc_start: 0.9002 (mttp) cc_final: 0.8739 (mttm) REVERT: F 184 ARG cc_start: 0.8127 (tpp-160) cc_final: 0.7832 (ttm-80) outliers start: 41 outliers final: 27 residues processed: 241 average time/residue: 0.1316 time to fit residues: 45.6708 Evaluate side-chains 234 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 281 MET Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 208 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 13 optimal weight: 0.6980 chunk 56 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 160 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 21 optimal weight: 0.4980 chunk 63 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.116518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.102365 restraints weight = 15192.003| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 0.85 r_work: 0.2804 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14586 Z= 0.153 Angle : 0.667 7.527 19806 Z= 0.306 Chirality : 0.047 0.138 2352 Planarity : 0.003 0.025 2472 Dihedral : 14.555 178.457 2064 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.02 % Favored : 93.27 % Rotamer: Outliers : 2.52 % Allowed : 18.02 % Favored : 79.46 % 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 (0.20), residues: 1812 helix: 1.72 (0.21), residues: 660 sheet: -0.64 (0.23), residues: 534 loop : -1.08 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 177 TYR 0.006 0.001 TYR E 311 PHE 0.009 0.001 PHE C 138 TRP 0.005 0.001 TRP C 154 HIS 0.005 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00368 (14580) covalent geometry : angle 0.66749 (19806) hydrogen bonds : bond 0.03293 ( 617) hydrogen bonds : angle 4.07101 ( 1674) Misc. bond : bond 0.00106 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 0.543 Fit side-chains REVERT: A 26 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: A 33 LYS cc_start: 0.8154 (ptpt) cc_final: 0.7738 (ptmt) REVERT: A 157 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7666 (mm-30) REVERT: B 26 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: B 157 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7678 (mm-30) REVERT: D 12 HIS cc_start: 0.8525 (OUTLIER) cc_final: 0.8238 (t-90) REVERT: D 25 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8412 (pp) REVERT: F 12 HIS cc_start: 0.8594 (OUTLIER) cc_final: 0.8277 (t-90) REVERT: F 25 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8428 (pp) REVERT: F 29 LYS cc_start: 0.9031 (mttp) cc_final: 0.8751 (mttm) REVERT: F 222 MET cc_start: 0.8383 (ptp) cc_final: 0.8169 (ptp) outliers start: 39 outliers final: 30 residues processed: 222 average time/residue: 0.1282 time to fit residues: 41.7654 Evaluate side-chains 235 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 281 MET Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 208 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 114 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 123 optimal weight: 0.0040 chunk 75 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.119021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.110921 restraints weight = 15148.405| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 0.37 r_work: 0.2866 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14586 Z= 0.117 Angle : 0.640 6.814 19806 Z= 0.291 Chirality : 0.046 0.132 2352 Planarity : 0.003 0.026 2472 Dihedral : 14.261 174.344 2064 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.72 % Allowed : 4.97 % Favored : 94.32 % Rotamer: Outliers : 2.58 % Allowed : 18.28 % Favored : 79.13 % 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: 1812 helix: 1.85 (0.21), residues: 660 sheet: -0.56 (0.24), residues: 534 loop : -1.06 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 177 TYR 0.005 0.001 TYR E 311 PHE 0.008 0.001 PHE C 138 TRP 0.004 0.001 TRP C 154 HIS 0.005 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00271 (14580) covalent geometry : angle 0.63974 (19806) hydrogen bonds : bond 0.02817 ( 617) hydrogen bonds : angle 3.99226 ( 1674) Misc. bond : bond 0.00084 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 205 time to evaluate : 0.679 Fit side-chains REVERT: A 26 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: B 26 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8115 (mp0) REVERT: B 157 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7773 (mm-30) REVERT: D 12 HIS cc_start: 0.8688 (OUTLIER) cc_final: 0.8399 (t-90) REVERT: D 25 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8489 (pp) REVERT: F 12 HIS cc_start: 0.8690 (OUTLIER) cc_final: 0.8382 (t-90) REVERT: F 25 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8483 (pp) REVERT: F 29 LYS cc_start: 0.9110 (mttp) cc_final: 0.8872 (mttm) REVERT: F 184 ARG cc_start: 0.8388 (tpp-160) cc_final: 0.8112 (ttm-80) outliers start: 40 outliers final: 27 residues processed: 227 average time/residue: 0.1327 time to fit residues: 43.8436 Evaluate side-chains 234 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 281 MET Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 208 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 19 optimal weight: 9.9990 chunk 93 optimal weight: 0.0770 chunk 115 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 overall best weight: 2.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.116154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.107527 restraints weight = 15275.861| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 0.39 r_work: 0.2857 rms_B_bonded: 0.93 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 1.70 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14586 Z= 0.170 Angle : 0.682 7.398 19806 Z= 0.314 Chirality : 0.047 0.139 2352 Planarity : 0.003 0.025 2472 Dihedral : 14.218 172.250 2064 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.24 % Favored : 93.05 % Rotamer: Outliers : 2.39 % Allowed : 18.48 % Favored : 79.13 % 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: 0.00 (0.20), residues: 1812 helix: 1.66 (0.21), residues: 660 sheet: -0.66 (0.23), residues: 534 loop : -1.12 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 177 TYR 0.007 0.001 TYR E 311 PHE 0.009 0.001 PHE A 313 TRP 0.006 0.001 TRP C 154 HIS 0.006 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00412 (14580) covalent geometry : angle 0.68166 (19806) hydrogen bonds : bond 0.03445 ( 617) hydrogen bonds : angle 4.10636 ( 1674) Misc. bond : bond 0.00121 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 0.472 Fit side-chains REVERT: A 26 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7565 (mp0) REVERT: A 33 LYS cc_start: 0.8099 (ptpt) cc_final: 0.7771 (ptmt) REVERT: B 26 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: D 12 HIS cc_start: 0.8512 (OUTLIER) cc_final: 0.8212 (t-90) REVERT: D 25 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8434 (pp) REVERT: F 25 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8451 (pp) REVERT: F 29 LYS cc_start: 0.8949 (mttp) cc_final: 0.8679 (mttm) REVERT: F 176 LYS cc_start: 0.8307 (mmmm) cc_final: 0.8095 (mmmm) outliers start: 37 outliers final: 28 residues processed: 220 average time/residue: 0.1271 time to fit residues: 40.3764 Evaluate side-chains 232 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 281 MET Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 208 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 150 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 92 optimal weight: 0.0010 chunk 173 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 143 optimal weight: 0.1980 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.120472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.111773 restraints weight = 15104.988| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 0.40 r_work: 0.2905 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14586 Z= 0.099 Angle : 0.627 7.120 19806 Z= 0.284 Chirality : 0.045 0.130 2352 Planarity : 0.003 0.027 2472 Dihedral : 13.860 175.539 2064 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.72 % Allowed : 4.47 % Favored : 94.81 % Rotamer: Outliers : 2.07 % Allowed : 19.06 % Favored : 78.88 % 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: 0.26 (0.21), residues: 1812 helix: 1.94 (0.21), residues: 660 sheet: -0.49 (0.25), residues: 498 loop : -1.08 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 177 TYR 0.004 0.001 TYR D 54 PHE 0.007 0.001 PHE E 138 TRP 0.004 0.001 TRP D 162 HIS 0.005 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00225 (14580) covalent geometry : angle 0.62674 (19806) hydrogen bonds : bond 0.02508 ( 617) hydrogen bonds : angle 3.93180 ( 1674) Misc. bond : bond 0.00059 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 224 time to evaluate : 0.475 Fit side-chains REVERT: A 26 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: B 26 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: B 195 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7617 (mt-10) REVERT: C 32 THR cc_start: 0.8575 (p) cc_final: 0.8366 (m) REVERT: D 12 HIS cc_start: 0.8508 (OUTLIER) cc_final: 0.8258 (t-90) REVERT: D 25 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8483 (pp) REVERT: F 12 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.8049 (t70) REVERT: F 25 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8459 (pp) REVERT: F 29 LYS cc_start: 0.8982 (mttp) cc_final: 0.8718 (mttm) REVERT: F 184 ARG cc_start: 0.8141 (tpp-160) cc_final: 0.7886 (ttm-80) outliers start: 32 outliers final: 25 residues processed: 240 average time/residue: 0.1253 time to fit residues: 43.3821 Evaluate side-chains 243 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 281 MET Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 208 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 143 optimal weight: 8.9990 chunk 154 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 171 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.117640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.108933 restraints weight = 15182.234| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 0.39 r_work: 0.2818 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14586 Z= 0.144 Angle : 0.663 6.981 19806 Z= 0.303 Chirality : 0.046 0.142 2352 Planarity : 0.003 0.026 2472 Dihedral : 13.914 173.828 2064 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.72 % Allowed : 5.96 % Favored : 93.32 % Rotamer: Outliers : 2.33 % Allowed : 18.73 % Favored : 78.94 % 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: 0.17 (0.21), residues: 1812 helix: 1.82 (0.21), residues: 660 sheet: -0.59 (0.24), residues: 534 loop : -1.04 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 177 TYR 0.006 0.001 TYR E 311 PHE 0.008 0.001 PHE B 313 TRP 0.005 0.001 TRP C 154 HIS 0.005 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00342 (14580) covalent geometry : angle 0.66266 (19806) hydrogen bonds : bond 0.03159 ( 617) hydrogen bonds : angle 4.02586 ( 1674) Misc. bond : bond 0.00098 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3374.04 seconds wall clock time: 58 minutes 34.19 seconds (3514.19 seconds total)