Starting phenix.real_space_refine on Tue Dec 31 00:34:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yk1_33883/12_2024/7yk1_33883.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yk1_33883/12_2024/7yk1_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_33883/12_2024/7yk1_33883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yk1_33883/12_2024/7yk1_33883.map" model { file = "/net/cci-nas-00/data/ceres_data/7yk1_33883/12_2024/7yk1_33883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yk1_33883/12_2024/7yk1_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-5532/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: 8.84, per 1000 atoms: 0.62 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: 3.79 Conformation dependent library (CDL) restraints added in 1.8 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: 2.14 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: 4.61 Time building geometry restraints manager: 4.30 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: 0.00 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 34.510 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.050 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.330 ------------------------------------------------------------------------------- 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 14580 Z= 0.397 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 *********************** 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 : 1.640 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 191 average time/residue: 0.2830 time to fit residues: 79.4861 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 : 1.864 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 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 14580 Z= 0.266 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 *********************** 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 : 1.628 Fit side-chains REVERT: A 33 LYS cc_start: 0.8352 (ptpt) cc_final: 0.8010 (ptmt) REVERT: C 32 THR cc_start: 0.8739 (p) cc_final: 0.8522 (m) REVERT: F 176 LYS cc_start: 0.8223 (mmmm) cc_final: 0.7867 (mmmm) outliers start: 38 outliers final: 25 residues processed: 226 average time/residue: 0.3110 time to fit residues: 99.2109 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 : 1.522 ------------------------------------------------------------------------------- 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 90 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 chunk 162 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14580 Z= 0.273 Angle : 0.678 7.139 19806 Z= 0.315 Chirality : 0.047 0.189 2352 Planarity : 0.003 0.029 2472 Dihedral : 15.419 171.716 2066 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.72 % Allowed : 5.35 % Favored : 93.93 % Rotamer: Outliers : 3.04 % Allowed : 16.47 % 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: -0.33 (0.20), residues: 1812 helix: 1.22 (0.20), residues: 660 sheet: -0.81 (0.23), residues: 534 loop : -1.10 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 154 HIS 0.006 0.001 HIS E 12 PHE 0.010 0.001 PHE B 313 TYR 0.007 0.001 TYR E 311 ARG 0.003 0.000 ARG F 184 *********************** 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: 47 poor density : 212 time to evaluate : 1.570 Fit side-chains REVERT: A 26 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: A 176 LYS cc_start: 0.8154 (mmmm) cc_final: 0.7946 (mtpp) REVERT: B 33 LYS cc_start: 0.8323 (ptpt) cc_final: 0.8013 (ptmt) REVERT: C 32 THR cc_start: 0.8769 (p) cc_final: 0.8454 (m) REVERT: D 12 HIS cc_start: 0.8611 (OUTLIER) cc_final: 0.8390 (t-90) REVERT: F 12 HIS cc_start: 0.8644 (OUTLIER) cc_final: 0.8376 (t-90) REVERT: F 176 LYS cc_start: 0.8335 (mmmm) cc_final: 0.8127 (mmmm) outliers start: 47 outliers final: 31 residues processed: 242 average time/residue: 0.2905 time to fit residues: 100.6834 Evaluate side-chains 231 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 1.744 ------------------------------------------------------------------------------- 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 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 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 43 GLU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 206 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 173 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14580 Z= 0.239 Angle : 0.664 6.941 19806 Z= 0.305 Chirality : 0.047 0.152 2352 Planarity : 0.003 0.029 2472 Dihedral : 14.747 173.940 2066 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.72 % Allowed : 5.24 % Favored : 94.04 % 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: -0.19 (0.20), residues: 1812 helix: 1.47 (0.20), residues: 660 sheet: -0.80 (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 0.006 0.001 HIS C 12 PHE 0.008 0.001 PHE A 313 TYR 0.007 0.001 TYR E 311 ARG 0.002 0.000 ARG F 184 *********************** 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 244 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 198 time to evaluate : 1.764 Fit side-chains REVERT: A 26 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: A 176 LYS cc_start: 0.8150 (mmmm) cc_final: 0.7933 (mtpp) REVERT: B 26 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: D 25 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8566 (pp) REVERT: F 18 ARG cc_start: 0.8821 (mtp85) cc_final: 0.8605 (mtp85) outliers start: 46 outliers final: 31 residues processed: 228 average time/residue: 0.3038 time to fit residues: 98.5286 Evaluate side-chains 234 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 1.617 ------------------------------------------------------------------------------- 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 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 25 LEU 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 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 144 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 2 optimal weight: 0.0570 chunk 129 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14580 Z= 0.156 Angle : 0.628 6.724 19806 Z= 0.284 Chirality : 0.045 0.157 2352 Planarity : 0.003 0.028 2472 Dihedral : 14.245 174.857 2066 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.72 % Allowed : 4.69 % Favored : 94.59 % Rotamer: Outliers : 2.33 % Allowed : 18.28 % 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: 0.13 (0.20), residues: 1812 helix: 1.80 (0.20), residues: 660 sheet: -0.57 (0.24), residues: 522 loop : -1.10 (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 E 138 TYR 0.005 0.001 TYR E 311 ARG 0.002 0.000 ARG F 184 *********************** 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 259 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 223 time to evaluate : 1.648 Fit side-chains REVERT: A 26 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: B 26 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: B 195 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7541 (mt-10) REVERT: D 18 ARG cc_start: 0.8791 (mtp85) cc_final: 0.8474 (mtp85) REVERT: E 69 GLU cc_start: 0.8613 (tt0) cc_final: 0.8327 (tt0) REVERT: F 12 HIS cc_start: 0.8628 (OUTLIER) cc_final: 0.8381 (t70) REVERT: F 29 LYS cc_start: 0.9007 (mttp) cc_final: 0.8729 (mttm) outliers start: 36 outliers final: 23 residues processed: 242 average time/residue: 0.3019 time to fit residues: 103.5041 Evaluate side-chains 235 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 1.629 ------------------------------------------------------------------------------- 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 210 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 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 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 58 optimal weight: 0.0670 chunk 156 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14580 Z= 0.230 Angle : 0.659 6.646 19806 Z= 0.301 Chirality : 0.047 0.163 2352 Planarity : 0.003 0.027 2472 Dihedral : 14.404 173.260 2064 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.72 % Allowed : 5.74 % Favored : 93.54 % Rotamer: Outliers : 2.45 % Allowed : 18.09 % 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: 0.10 (0.20), residues: 1812 helix: 1.78 (0.21), residues: 660 sheet: -0.60 (0.24), residues: 522 loop : -1.12 (0.24), residues: 630 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 0.006 0.001 TYR C 311 ARG 0.002 0.000 ARG C 22 *********************** 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: 38 poor density : 206 time to evaluate : 1.548 Fit side-chains REVERT: A 26 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: A 157 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7457 (mm-30) REVERT: B 26 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7690 (mp0) REVERT: B 157 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7534 (mm-30) REVERT: D 12 HIS cc_start: 0.8584 (OUTLIER) cc_final: 0.7765 (t70) REVERT: D 25 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8558 (pp) REVERT: D 29 LYS cc_start: 0.9004 (mttt) cc_final: 0.8788 (mttm) REVERT: F 12 HIS cc_start: 0.8712 (OUTLIER) cc_final: 0.8386 (t70) REVERT: F 25 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8573 (pp) REVERT: F 29 LYS cc_start: 0.9010 (mttp) cc_final: 0.8715 (mttm) outliers start: 38 outliers final: 27 residues processed: 228 average time/residue: 0.3007 time to fit residues: 98.6721 Evaluate side-chains 235 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 1.668 ------------------------------------------------------------------------------- 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 176 LYS 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 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 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 167 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14580 Z= 0.209 Angle : 0.651 7.172 19806 Z= 0.297 Chirality : 0.046 0.139 2352 Planarity : 0.003 0.028 2472 Dihedral : 14.429 177.855 2064 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.72 % Allowed : 4.69 % Favored : 94.59 % Rotamer: Outliers : 2.78 % Allowed : 18.15 % 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: 0.14 (0.20), residues: 1812 helix: 1.83 (0.21), residues: 660 sheet: -0.56 (0.24), residues: 522 loop : -1.13 (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 E 12 PHE 0.008 0.001 PHE E 138 TYR 0.006 0.001 TYR E 311 ARG 0.002 0.000 ARG C 22 *********************** 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 257 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 214 time to evaluate : 1.456 Fit side-chains REVERT: A 26 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: B 26 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: B 157 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7499 (mm-30) REVERT: B 195 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7589 (mt-10) REVERT: D 12 HIS cc_start: 0.8650 (OUTLIER) cc_final: 0.7900 (t70) REVERT: D 25 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8557 (pp) REVERT: D 29 LYS cc_start: 0.9009 (mttt) cc_final: 0.8794 (mttm) REVERT: F 12 HIS cc_start: 0.8731 (OUTLIER) cc_final: 0.8436 (t70) REVERT: F 25 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8569 (pp) REVERT: F 29 LYS cc_start: 0.9004 (mttp) cc_final: 0.8727 (mttm) outliers start: 43 outliers final: 30 residues processed: 238 average time/residue: 0.2905 time to fit residues: 98.9704 Evaluate side-chains 244 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 1.916 ------------------------------------------------------------------------------- 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 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 104 ARG Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 281 MET Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 208 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 136 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14580 Z= 0.260 Angle : 0.673 7.382 19806 Z= 0.309 Chirality : 0.047 0.140 2352 Planarity : 0.003 0.028 2472 Dihedral : 14.347 172.299 2064 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.13 % Favored : 93.16 % Rotamer: Outliers : 2.71 % Allowed : 18.41 % 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: 0.03 (0.20), residues: 1812 helix: 1.71 (0.21), residues: 660 sheet: -0.67 (0.23), residues: 534 loop : -1.11 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 154 HIS 0.006 0.001 HIS C 12 PHE 0.009 0.001 PHE C 313 TYR 0.006 0.001 TYR C 311 ARG 0.001 0.000 ARG C 22 *********************** 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 249 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 207 time to evaluate : 1.742 Fit side-chains REVERT: A 26 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: B 26 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: D 12 HIS cc_start: 0.8665 (OUTLIER) cc_final: 0.7971 (t70) REVERT: D 25 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8563 (pp) REVERT: D 29 LYS cc_start: 0.9023 (mttt) cc_final: 0.8822 (mttm) REVERT: F 12 HIS cc_start: 0.8709 (OUTLIER) cc_final: 0.8369 (t-90) REVERT: F 25 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8534 (pp) outliers start: 42 outliers final: 30 residues processed: 230 average time/residue: 0.3049 time to fit residues: 101.6810 Evaluate side-chains 236 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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 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 104 ARG Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 281 MET Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 208 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 151 optimal weight: 7.9990 chunk 161 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14580 Z= 0.206 Angle : 0.651 6.916 19806 Z= 0.297 Chirality : 0.046 0.142 2352 Planarity : 0.003 0.028 2472 Dihedral : 14.105 173.250 2064 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.72 % Allowed : 4.80 % Favored : 94.48 % Rotamer: Outliers : 2.65 % Allowed : 18.22 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.11 (0.21), residues: 1812 helix: 1.80 (0.21), residues: 660 sheet: -0.64 (0.24), residues: 534 loop : -1.09 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 154 HIS 0.005 0.001 HIS E 12 PHE 0.008 0.001 PHE B 138 TYR 0.006 0.001 TYR E 311 ARG 0.001 0.000 ARG C 22 *********************** 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: 41 poor density : 209 time to evaluate : 1.612 Fit side-chains REVERT: A 26 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: B 26 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: D 12 HIS cc_start: 0.8630 (OUTLIER) cc_final: 0.7745 (t70) REVERT: D 25 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8579 (pp) REVERT: F 12 HIS cc_start: 0.8683 (OUTLIER) cc_final: 0.8382 (t70) REVERT: F 25 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8529 (pp) REVERT: F 29 LYS cc_start: 0.9004 (mttp) cc_final: 0.8710 (mttm) REVERT: F 184 ARG cc_start: 0.8027 (tpp-160) cc_final: 0.7684 (ttm-80) outliers start: 41 outliers final: 31 residues processed: 230 average time/residue: 0.2961 time to fit residues: 97.6758 Evaluate side-chains 248 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 211 time to evaluate : 1.823 ------------------------------------------------------------------------------- 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 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 C residue 281 MET Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 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 170 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14580 Z= 0.199 Angle : 0.649 6.880 19806 Z= 0.296 Chirality : 0.046 0.144 2352 Planarity : 0.003 0.028 2472 Dihedral : 13.923 173.762 2064 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.72 % Allowed : 5.46 % Favored : 93.82 % Rotamer: Outliers : 2.39 % Allowed : 18.54 % 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: 0.13 (0.21), residues: 1812 helix: 1.83 (0.20), residues: 660 sheet: -0.62 (0.24), residues: 534 loop : -1.08 (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 0.008 0.001 PHE E 138 TYR 0.006 0.001 TYR C 311 ARG 0.001 0.000 ARG C 22 ********************** 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 254 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 217 time to evaluate : 1.763 Fit side-chains REVERT: A 26 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: B 26 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: D 12 HIS cc_start: 0.8623 (OUTLIER) cc_final: 0.7831 (t70) REVERT: D 25 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8554 (pp) REVERT: E 22 ARG cc_start: 0.8843 (mtt180) cc_final: 0.8616 (mtt180) REVERT: F 12 HIS cc_start: 0.8736 (OUTLIER) cc_final: 0.8442 (t70) REVERT: F 25 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8489 (pp) REVERT: F 29 LYS cc_start: 0.9008 (mttp) cc_final: 0.8729 (mttm) REVERT: F 184 ARG cc_start: 0.8009 (tpp-160) cc_final: 0.7680 (ttm-80) outliers start: 37 outliers final: 30 residues processed: 235 average time/residue: 0.2927 time to fit residues: 98.8362 Evaluate side-chains 252 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 1.760 ------------------------------------------------------------------------------- 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 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 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 152 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 0.0870 chunk 143 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 125 optimal weight: 7.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 = 0.3186 r_free = 0.3186 target = 0.120717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 116)---------------| | r_work = 0.3001 r_free = 0.3001 target = 0.106377 restraints weight = 15003.799| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 0.93 r_work: 0.2820 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14580 Z= 0.144 Angle : 0.623 7.097 19806 Z= 0.281 Chirality : 0.045 0.141 2352 Planarity : 0.003 0.028 2472 Dihedral : 13.663 176.688 2064 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.72 % Allowed : 4.42 % Favored : 94.87 % Rotamer: Outliers : 2.13 % Allowed : 18.86 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.33 (0.21), residues: 1812 helix: 2.02 (0.20), residues: 660 sheet: -0.46 (0.25), residues: 498 loop : -1.07 (0.24), residues: 654 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 0.004 0.001 TYR C 311 ARG 0.002 0.000 ARG C 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2856.12 seconds wall clock time: 53 minutes 30.49 seconds (3210.49 seconds total)