Starting phenix.real_space_refine on Thu Jun 12 21:57:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yk1_33883/06_2025/7yk1_33883.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yk1_33883/06_2025/7yk1_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_33883/06_2025/7yk1_33883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yk1_33883/06_2025/7yk1_33883.map" model { file = "/net/cci-nas-00/data/ceres_data/7yk1_33883/06_2025/7yk1_33883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yk1_33883/06_2025/7yk1_33883.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.73, per 1000 atoms: 0.68 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: 3.59 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 2.06 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: 4.62 Time building geometry restraints manager: 4.24 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: 0.02 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: 1.010 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: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 36.320 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.060 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.960 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.001 TRP E 154 HIS 0.016 0.002 HIS F 12 PHE 0.013 0.002 PHE A 313 TYR 0.011 0.002 TYR B 54 ARG 0.004 0.000 ARG F 184 Details of bonding type rmsd hydrogen bonds : bond 0.22542 ( 617) hydrogen bonds : angle 6.81448 ( 1674) covalent geometry : bond 0.00587 (14580) covalent geometry : angle 0.69006 (19806) 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 : 1.750 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 191 average time/residue: 0.2604 time to fit residues: 73.6802 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 : 1.620 ------------------------------------------------------------------------------- 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 151 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3130 r_free = 0.3130 target = 0.116482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.101950 restraints weight = 15137.531| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 0.90 r_work: 0.2787 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 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 0.037 14586 Z= 0.167 Angle : 0.678 6.906 19806 Z= 0.318 Chirality : 0.047 0.149 2352 Planarity : 0.004 0.028 2472 Dihedral : 16.238 172.157 2071 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.02 % Favored : 93.27 % Rotamer: Outliers : 2.45 % Allowed : 16.47 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.20), residues: 1812 helix: 0.80 (0.20), residues: 660 sheet: -0.73 (0.23), residues: 534 loop : -0.93 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 154 HIS 0.006 0.001 HIS F 12 PHE 0.008 0.001 PHE A 313 TYR 0.008 0.001 TYR D 54 ARG 0.004 0.000 ARG F 184 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 617) hydrogen bonds : angle 4.44830 ( 1674) covalent geometry : bond 0.00397 (14580) covalent geometry : angle 0.67784 (19806) Misc. bond : bond 0.00066 ( 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 241 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 2.091 Fit side-chains REVERT: A 33 LYS cc_start: 0.8267 (ptpt) cc_final: 0.7797 (ptmt) REVERT: F 176 LYS cc_start: 0.8227 (mmmm) cc_final: 0.7881 (mmmm) outliers start: 38 outliers final: 25 residues processed: 226 average time/residue: 0.2981 time to fit residues: 95.6205 Evaluate side-chains 218 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 1.551 ------------------------------------------------------------------------------- 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 4 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 106 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 288 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.117774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.101561 restraints weight = 15129.739| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 0.96 r_work: 0.2761 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1197 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= 0.131 Angle : 0.649 6.930 19806 Z= 0.298 Chirality : 0.046 0.183 2352 Planarity : 0.003 0.028 2472 Dihedral : 15.228 173.405 2066 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.72 % Allowed : 4.64 % Favored : 94.65 % Rotamer: Outliers : 2.78 % Allowed : 16.73 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.20), residues: 1812 helix: 1.35 (0.20), residues: 660 sheet: -0.64 (0.23), residues: 522 loop : -1.08 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 154 HIS 0.005 0.001 HIS E 12 PHE 0.008 0.001 PHE A 138 TYR 0.006 0.001 TYR E 311 ARG 0.003 0.000 ARG F 184 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 617) hydrogen bonds : angle 4.15436 ( 1674) covalent geometry : bond 0.00305 (14580) covalent geometry : angle 0.64885 (19806) Misc. bond : bond 0.00063 ( 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 259 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 216 time to evaluate : 1.574 Fit side-chains REVERT: A 26 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: B 33 LYS cc_start: 0.8227 (ptpt) cc_final: 0.7790 (ptmt) REVERT: D 12 HIS cc_start: 0.8540 (OUTLIER) cc_final: 0.8312 (t-90) REVERT: F 12 HIS cc_start: 0.8595 (OUTLIER) cc_final: 0.8336 (t-90) REVERT: F 176 LYS cc_start: 0.8353 (mmmm) cc_final: 0.8144 (mmmm) outliers start: 43 outliers final: 29 residues processed: 244 average time/residue: 0.2831 time to fit residues: 98.7416 Evaluate side-chains 237 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 1.573 ------------------------------------------------------------------------------- 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 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 206 VAL 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 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 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 164 ASN Chi-restraints excluded: chain E residue 178 VAL 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 164 ASN Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 206 VAL 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 107 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 24 optimal weight: 0.0370 chunk 127 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 overall best weight: 2.5264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 288 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.116072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.2917 r_free = 0.2917 target = 0.100888 restraints weight = 15186.471| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 0.96 r_work: 0.2790 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1183 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= 0.169 Angle : 0.683 7.064 19806 Z= 0.315 Chirality : 0.047 0.156 2352 Planarity : 0.003 0.028 2472 Dihedral : 14.818 171.958 2066 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.13 % Favored : 93.16 % Rotamer: Outliers : 2.97 % Allowed : 17.12 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.20), residues: 1812 helix: 1.42 (0.20), residues: 660 sheet: -0.78 (0.23), residues: 534 loop : -1.11 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 154 HIS 0.006 0.001 HIS C 12 PHE 0.010 0.001 PHE B 313 TYR 0.007 0.001 TYR E 311 ARG 0.002 0.000 ARG F 184 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 617) hydrogen bonds : angle 4.17583 ( 1674) covalent geometry : bond 0.00407 (14580) covalent geometry : angle 0.68322 (19806) Misc. bond : bond 0.00104 ( 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 245 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 199 time to evaluate : 1.676 Fit side-chains REVERT: A 26 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: B 26 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: F 29 LYS cc_start: 0.9091 (mttp) cc_final: 0.8817 (mttm) REVERT: F 176 LYS cc_start: 0.8330 (mmmm) cc_final: 0.8110 (mmmm) outliers start: 46 outliers final: 32 residues processed: 228 average time/residue: 0.3806 time to fit residues: 127.6945 Evaluate side-chains 232 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 198 time to evaluate : 2.865 ------------------------------------------------------------------------------- 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 C residue 12 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 43 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 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 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 F residue 43 GLU Chi-restraints excluded: chain F residue 164 ASN 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 46 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 169 optimal weight: 0.0570 chunk 103 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- 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 = 0.3188 r_free = 0.3188 target = 0.121201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.112617 restraints weight = 15138.340| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 0.38 r_work: 0.2873 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14586 Z= 0.101 Angle : 0.626 6.804 19806 Z= 0.283 Chirality : 0.045 0.152 2352 Planarity : 0.003 0.028 2472 Dihedral : 14.363 176.314 2066 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.72 % Allowed : 4.58 % Favored : 94.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.20), residues: 1812 helix: 1.78 (0.20), residues: 660 sheet: -0.55 (0.24), residues: 522 loop : -1.08 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 154 HIS 0.005 0.001 HIS C 12 PHE 0.007 0.001 PHE D 138 TYR 0.005 0.001 TYR E 311 ARG 0.001 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.02645 ( 617) hydrogen bonds : angle 3.99522 ( 1674) covalent geometry : bond 0.00228 (14580) covalent geometry : angle 0.62620 (19806) Misc. bond : bond 0.00055 ( 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 262 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 223 time to evaluate : 1.542 Fit side-chains REVERT: A 26 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: B 26 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8149 (mp0) REVERT: B 195 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7607 (mt-10) REVERT: D 12 HIS cc_start: 0.8585 (OUTLIER) cc_final: 0.8365 (t70) REVERT: D 25 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8540 (pp) REVERT: F 12 HIS cc_start: 0.8662 (OUTLIER) cc_final: 0.8337 (t70) REVERT: F 25 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8591 (pp) REVERT: F 29 LYS cc_start: 0.9134 (mttp) cc_final: 0.8900 (mttm) outliers start: 39 outliers final: 22 residues processed: 246 average time/residue: 0.2792 time to fit residues: 98.3530 Evaluate side-chains 239 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 1.507 ------------------------------------------------------------------------------- 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 228 THR Chi-restraints excluded: chain B residue 234 ASP 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 104 ARG 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 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 27 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3134 r_free = 0.3134 target = 0.117055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.108229 restraints weight = 15359.062| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 0.39 r_work: 0.2818 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14586 Z= 0.172 Angle : 0.679 6.789 19806 Z= 0.312 Chirality : 0.047 0.169 2352 Planarity : 0.003 0.028 2472 Dihedral : 14.591 172.384 2064 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.07 % Favored : 93.21 % Rotamer: Outliers : 2.71 % Allowed : 17.89 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.20), residues: 1812 helix: 1.65 (0.21), residues: 660 sheet: -0.70 (0.23), residues: 534 loop : -1.09 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 154 HIS 0.006 0.001 HIS C 12 PHE 0.010 0.001 PHE C 313 TYR 0.007 0.001 TYR C 311 ARG 0.002 0.000 ARG C 301 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 617) hydrogen bonds : angle 4.11359 ( 1674) covalent geometry : bond 0.00415 (14580) covalent geometry : angle 0.67856 (19806) Misc. bond : bond 0.00115 ( 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 244 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 1.706 Fit side-chains REVERT: A 26 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8136 (mp0) REVERT: B 26 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8150 (mp0) REVERT: D 12 HIS cc_start: 0.8680 (OUTLIER) cc_final: 0.8342 (t-90) REVERT: D 25 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8483 (pp) REVERT: D 29 LYS cc_start: 0.9180 (mttt) cc_final: 0.8910 (mttm) REVERT: F 12 HIS cc_start: 0.8755 (OUTLIER) cc_final: 0.8374 (t-90) REVERT: F 25 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8519 (pp) REVERT: F 29 LYS cc_start: 0.9118 (mttp) cc_final: 0.8876 (mttm) REVERT: F 176 LYS cc_start: 0.8485 (mmmm) cc_final: 0.8260 (mmmm) outliers start: 42 outliers final: 31 residues processed: 226 average time/residue: 0.2699 time to fit residues: 88.9140 Evaluate side-chains 239 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 202 time to evaluate : 1.746 ------------------------------------------------------------------------------- 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 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 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 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 5 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 177 optimal weight: 0.3980 chunk 82 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 = 0.116221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.107225 restraints weight = 15363.336| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 0.40 r_work: 0.2861 rms_B_bonded: 0.97 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 1.77 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1335 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= 0.163 Angle : 0.674 7.594 19806 Z= 0.310 Chirality : 0.047 0.147 2352 Planarity : 0.003 0.028 2472 Dihedral : 14.621 177.587 2064 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.72 % Allowed : 5.35 % Favored : 93.93 % Rotamer: Outliers : 2.71 % Allowed : 18.22 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 1812 helix: 1.65 (0.21), residues: 660 sheet: -0.72 (0.23), residues: 534 loop : -1.15 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 154 HIS 0.005 0.001 HIS E 12 PHE 0.009 0.001 PHE C 313 TYR 0.007 0.001 TYR E 311 ARG 0.001 0.000 ARG C 301 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 617) hydrogen bonds : angle 4.11930 ( 1674) covalent geometry : bond 0.00393 (14580) covalent geometry : angle 0.67390 (19806) Misc. bond : bond 0.00120 ( 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 248 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 206 time to evaluate : 1.515 Fit side-chains REVERT: A 26 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: A 33 LYS cc_start: 0.8121 (ptpt) cc_final: 0.7758 (ptmt) REVERT: B 26 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: B 157 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7617 (mm-30) REVERT: D 12 HIS cc_start: 0.8504 (OUTLIER) cc_final: 0.8167 (t-90) REVERT: D 25 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8436 (pp) REVERT: D 29 LYS cc_start: 0.9006 (mttt) cc_final: 0.8744 (mttm) REVERT: F 12 HIS cc_start: 0.8587 (OUTLIER) cc_final: 0.8223 (t-90) REVERT: F 25 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8469 (pp) REVERT: F 29 LYS cc_start: 0.8973 (mttp) cc_final: 0.8707 (mttm) REVERT: F 176 LYS cc_start: 0.8316 (mmmm) cc_final: 0.8088 (mmmm) outliers start: 42 outliers final: 32 residues processed: 228 average time/residue: 0.2747 time to fit residues: 90.4672 Evaluate side-chains 236 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 198 time to evaluate : 1.578 ------------------------------------------------------------------------------- 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 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 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 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 100 optimal weight: 0.1980 chunk 59 optimal weight: 6.9990 chunk 163 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3187 r_free = 0.3187 target = 0.120993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.112515 restraints weight = 15158.613| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 0.39 r_work: 0.2914 rms_B_bonded: 0.95 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14586 Z= 0.095 Angle : 0.621 6.794 19806 Z= 0.280 Chirality : 0.045 0.130 2352 Planarity : 0.003 0.028 2472 Dihedral : 14.175 175.523 2064 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.72 % Allowed : 4.86 % Favored : 94.43 % Rotamer: Outliers : 2.58 % Allowed : 18.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.21), residues: 1812 helix: 1.96 (0.21), residues: 660 sheet: -0.50 (0.25), residues: 498 loop : -1.10 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 162 HIS 0.005 0.001 HIS E 12 PHE 0.006 0.001 PHE E 138 TYR 0.004 0.001 TYR E 311 ARG 0.001 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.02459 ( 617) hydrogen bonds : angle 3.92146 ( 1674) covalent geometry : bond 0.00212 (14580) covalent geometry : angle 0.62095 (19806) Misc. bond : bond 0.00063 ( 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 271 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 231 time to evaluate : 1.705 Fit side-chains REVERT: A 26 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: B 26 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: B 157 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7574 (mm-30) REVERT: B 195 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7602 (mt-10) REVERT: D 12 HIS cc_start: 0.8463 (OUTLIER) cc_final: 0.8234 (t70) REVERT: D 25 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8484 (pp) REVERT: D 29 LYS cc_start: 0.8991 (mttt) cc_final: 0.8733 (mttm) REVERT: D 101 ASP cc_start: 0.8228 (p0) cc_final: 0.7974 (p0) REVERT: F 12 HIS cc_start: 0.8571 (OUTLIER) cc_final: 0.8316 (t70) REVERT: F 25 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8493 (pp) REVERT: F 29 LYS cc_start: 0.8979 (mttp) cc_final: 0.8721 (mttm) REVERT: F 184 ARG cc_start: 0.8174 (tpp-160) cc_final: 0.7893 (ttm-80) REVERT: F 222 MET cc_start: 0.8448 (ptp) cc_final: 0.8172 (ptp) outliers start: 40 outliers final: 26 residues processed: 252 average time/residue: 0.3032 time to fit residues: 109.4868 Evaluate side-chains 252 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 1.943 ------------------------------------------------------------------------------- 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 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 154 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 33 optimal weight: 0.0370 chunk 60 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 overall best weight: 2.1062 ------------------------------------------------------------------------------- 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 = 0.3145 r_free = 0.3145 target = 0.117754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.109698 restraints weight = 15140.397| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 0.37 r_work: 0.2861 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14586 Z= 0.149 Angle : 0.665 7.125 19806 Z= 0.305 Chirality : 0.047 0.146 2352 Planarity : 0.003 0.027 2472 Dihedral : 14.185 173.412 2064 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.72 % Allowed : 5.91 % Favored : 93.38 % Rotamer: Outliers : 2.45 % Allowed : 18.80 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.21), residues: 1812 helix: 1.81 (0.21), residues: 660 sheet: -0.60 (0.24), residues: 534 loop : -1.06 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 154 HIS 0.005 0.001 HIS C 12 PHE 0.009 0.001 PHE E 138 TYR 0.010 0.001 TYR A 54 ARG 0.002 0.000 ARG C 22 Details of bonding type rmsd hydrogen bonds : bond 0.03224 ( 617) hydrogen bonds : angle 4.04780 ( 1674) covalent geometry : bond 0.00355 (14580) covalent geometry : angle 0.66526 (19806) Misc. bond : bond 0.00104 ( 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 250 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 1.672 Fit side-chains REVERT: A 26 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: B 26 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: D 12 HIS cc_start: 0.8548 (OUTLIER) cc_final: 0.8228 (t-90) REVERT: D 25 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8448 (pp) REVERT: D 29 LYS cc_start: 0.9026 (mttt) cc_final: 0.8756 (mttm) REVERT: F 12 HIS cc_start: 0.8624 (OUTLIER) cc_final: 0.8297 (t-90) REVERT: F 25 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8468 (pp) REVERT: F 29 LYS cc_start: 0.9020 (mttp) cc_final: 0.8766 (mttm) REVERT: F 184 ARG cc_start: 0.8247 (tpp-160) cc_final: 0.7920 (ttm-80) outliers start: 38 outliers final: 28 residues processed: 231 average time/residue: 0.2775 time to fit residues: 93.8421 Evaluate side-chains 240 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 1.782 ------------------------------------------------------------------------------- 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 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 13 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 166 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 173 optimal weight: 8.9990 chunk 158 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.3194 r_free = 0.3194 target = 0.121395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.113025 restraints weight = 15018.055| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 0.38 r_work: 0.2940 rms_B_bonded: 0.84 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 1.45 restraints_weight: 0.2500 r_work: 0.2609 rms_B_bonded: 4.59 restraints_weight: 0.1250 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14586 Z= 0.093 Angle : 0.622 7.215 19806 Z= 0.281 Chirality : 0.045 0.133 2352 Planarity : 0.003 0.028 2472 Dihedral : 13.846 176.955 2064 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.72 % Allowed : 4.30 % Favored : 94.98 % Rotamer: Outliers : 2.07 % Allowed : 19.12 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.21), residues: 1812 helix: 2.04 (0.21), residues: 660 sheet: -0.41 (0.25), residues: 522 loop : -1.05 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 162 HIS 0.005 0.001 HIS E 12 PHE 0.007 0.001 PHE E 138 TYR 0.006 0.001 TYR A 54 ARG 0.002 0.000 ARG C 22 Details of bonding type rmsd hydrogen bonds : bond 0.02378 ( 617) hydrogen bonds : angle 3.88313 ( 1674) covalent geometry : bond 0.00206 (14580) covalent geometry : angle 0.62171 (19806) Misc. bond : bond 0.00062 ( 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 255 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 1.551 Fit side-chains REVERT: A 26 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8191 (mp0) REVERT: B 26 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8240 (mp0) REVERT: D 12 HIS cc_start: 0.8536 (OUTLIER) cc_final: 0.8299 (t70) REVERT: D 25 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8498 (pp) REVERT: D 29 LYS cc_start: 0.9128 (mttt) cc_final: 0.8806 (mttm) REVERT: D 101 ASP cc_start: 0.8519 (p0) cc_final: 0.8288 (p0) REVERT: F 12 HIS cc_start: 0.8635 (OUTLIER) cc_final: 0.8355 (t70) REVERT: F 25 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8487 (pp) REVERT: F 29 LYS cc_start: 0.9110 (mttp) cc_final: 0.8840 (mttm) REVERT: F 184 ARG cc_start: 0.8377 (tpp-160) cc_final: 0.8117 (ttm-80) REVERT: F 222 MET cc_start: 0.8725 (ptp) cc_final: 0.8370 (ptp) outliers start: 32 outliers final: 24 residues processed: 240 average time/residue: 0.2740 time to fit residues: 94.9007 Evaluate side-chains 246 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 1.566 ------------------------------------------------------------------------------- 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 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 178 VAL Chi-restraints excluded: chain E residue 228 THR 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 31 optimal weight: 8.9990 chunk 52 optimal weight: 0.0670 chunk 175 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 147 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 overall best weight: 1.4524 ------------------------------------------------------------------------------- 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 = 0.3160 r_free = 0.3160 target = 0.118797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.110415 restraints weight = 15230.302| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 0.38 r_work: 0.2890 rms_B_bonded: 0.96 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1628 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= 0.119 Angle : 0.642 6.886 19806 Z= 0.292 Chirality : 0.046 0.147 2352 Planarity : 0.003 0.027 2472 Dihedral : 13.860 176.150 2064 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.72 % Allowed : 5.30 % Favored : 93.98 % Rotamer: Outliers : 2.33 % Allowed : 18.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1812 helix: 2.01 (0.21), residues: 660 sheet: -0.42 (0.24), residues: 522 loop : -1.03 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 154 HIS 0.005 0.001 HIS C 12 PHE 0.008 0.001 PHE E 138 TYR 0.006 0.001 TYR E 54 ARG 0.002 0.000 ARG C 22 Details of bonding type rmsd hydrogen bonds : bond 0.02848 ( 617) hydrogen bonds : angle 3.93297 ( 1674) covalent geometry : bond 0.00279 (14580) covalent geometry : angle 0.64231 (19806) Misc. bond : bond 0.00079 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7405.04 seconds wall clock time: 130 minutes 51.71 seconds (7851.71 seconds total)