Starting phenix.real_space_refine on Thu Feb 5 18:50:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h95_51953/02_2026/9h95_51953.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h95_51953/02_2026/9h95_51953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9h95_51953/02_2026/9h95_51953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h95_51953/02_2026/9h95_51953.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h95_51953/02_2026/9h95_51953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h95_51953/02_2026/9h95_51953.map" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 12796 2.51 5 N 3087 2.21 5 O 3234 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19201 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2647 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 8, 'TRANS': 323} Chain: "B" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2647 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 8, 'TRANS': 323} Chain: "C" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2647 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 8, 'TRANS': 323} Chain: "D" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2647 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 8, 'TRANS': 323} Chain: "E" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2647 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 8, 'TRANS': 323} Chain: "F" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2647 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 8, 'TRANS': 323} Chain: "G" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2647 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 8, 'TRANS': 323} Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 96 Unusual residues: {'D12': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 96 Unusual residues: {'D12': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 96 Unusual residues: {'D12': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 96 Unusual residues: {'D12': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 96 Unusual residues: {'D12': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 96 Unusual residues: {'D12': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "G" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 96 Unusual residues: {'D12': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 4.40, per 1000 atoms: 0.23 Number of scatterers: 19201 At special positions: 0 Unit cell: (120.142, 119.196, 141.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3234 8.00 N 3087 7.00 C 12796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 808.9 milliseconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4326 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 15 sheets defined 62.3% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 9 through 32 Processing helix chain 'A' and resid 39 through 69 removed outlier: 3.535A pdb=" N HIS A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 108 Processing helix chain 'A' and resid 111 through 134 Processing helix chain 'A' and resid 142 through 160 Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.639A pdb=" N ALA A 248 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA A 249 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 264 Processing helix chain 'A' and resid 298 through 320 removed outlier: 3.511A pdb=" N HIS A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 8 Processing helix chain 'B' and resid 9 through 32 Processing helix chain 'B' and resid 39 through 69 removed outlier: 3.535A pdb=" N HIS B 43 " --> pdb=" O GLY B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 108 Processing helix chain 'B' and resid 111 through 134 Processing helix chain 'B' and resid 142 through 160 Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 219 through 223 Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 244 through 249 removed outlier: 3.638A pdb=" N ALA B 248 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA B 249 " --> pdb=" O GLU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 264 Processing helix chain 'B' and resid 298 through 320 removed outlier: 3.512A pdb=" N HIS B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 9 through 32 Processing helix chain 'C' and resid 39 through 69 removed outlier: 3.535A pdb=" N HIS C 43 " --> pdb=" O GLY C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 108 Processing helix chain 'C' and resid 111 through 134 Processing helix chain 'C' and resid 142 through 160 Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 219 through 223 Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 244 through 249 removed outlier: 3.639A pdb=" N ALA C 248 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA C 249 " --> pdb=" O GLU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 264 Processing helix chain 'C' and resid 298 through 320 removed outlier: 3.511A pdb=" N HIS C 320 " --> pdb=" O ILE C 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 8 Processing helix chain 'D' and resid 9 through 32 Processing helix chain 'D' and resid 39 through 69 removed outlier: 3.535A pdb=" N HIS D 43 " --> pdb=" O GLY D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 108 Processing helix chain 'D' and resid 111 through 134 Processing helix chain 'D' and resid 142 through 160 Processing helix chain 'D' and resid 160 through 176 Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 229 through 232 Processing helix chain 'D' and resid 244 through 249 removed outlier: 3.639A pdb=" N ALA D 248 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA D 249 " --> pdb=" O GLU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 264 Processing helix chain 'D' and resid 298 through 320 removed outlier: 3.512A pdb=" N HIS D 320 " --> pdb=" O ILE D 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 9 through 32 Processing helix chain 'E' and resid 39 through 69 removed outlier: 3.535A pdb=" N HIS E 43 " --> pdb=" O GLY E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 108 Processing helix chain 'E' and resid 111 through 134 Processing helix chain 'E' and resid 142 through 160 Processing helix chain 'E' and resid 160 through 176 Processing helix chain 'E' and resid 219 through 223 Processing helix chain 'E' and resid 229 through 232 Processing helix chain 'E' and resid 244 through 249 removed outlier: 3.638A pdb=" N ALA E 248 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA E 249 " --> pdb=" O GLU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 264 Processing helix chain 'E' and resid 298 through 320 removed outlier: 3.511A pdb=" N HIS E 320 " --> pdb=" O ILE E 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 8 Processing helix chain 'F' and resid 9 through 32 Processing helix chain 'F' and resid 39 through 69 removed outlier: 3.535A pdb=" N HIS F 43 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 108 Processing helix chain 'F' and resid 111 through 134 Processing helix chain 'F' and resid 142 through 160 Processing helix chain 'F' and resid 160 through 176 Processing helix chain 'F' and resid 219 through 223 Processing helix chain 'F' and resid 229 through 232 Processing helix chain 'F' and resid 244 through 249 removed outlier: 3.639A pdb=" N ALA F 248 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA F 249 " --> pdb=" O GLU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 264 Processing helix chain 'F' and resid 298 through 320 removed outlier: 3.511A pdb=" N HIS F 320 " --> pdb=" O ILE F 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 8 Processing helix chain 'G' and resid 9 through 32 Processing helix chain 'G' and resid 39 through 69 removed outlier: 3.535A pdb=" N HIS G 43 " --> pdb=" O GLY G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 108 Processing helix chain 'G' and resid 111 through 134 Processing helix chain 'G' and resid 142 through 160 Processing helix chain 'G' and resid 160 through 176 Processing helix chain 'G' and resid 219 through 223 Processing helix chain 'G' and resid 229 through 232 Processing helix chain 'G' and resid 244 through 249 removed outlier: 3.639A pdb=" N ALA G 248 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA G 249 " --> pdb=" O GLU G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 264 Processing helix chain 'G' and resid 298 through 320 removed outlier: 3.512A pdb=" N HIS G 320 " --> pdb=" O ILE G 316 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 185 removed outlier: 6.620A pdb=" N LYS A 205 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE A 199 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ILE A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 7.321A pdb=" N ILE B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE B 199 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS B 205 " --> pdb=" O ALA B 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 243 removed outlier: 3.842A pdb=" N ARG A 235 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN A 287 " --> pdb=" O ASN A 279 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 334 removed outlier: 3.813A pdb=" N MET B 333 " --> pdb=" O ASP A 334 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET C 333 " --> pdb=" O ASP B 334 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET D 333 " --> pdb=" O ASP C 334 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET E 333 " --> pdb=" O ASP D 334 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET F 333 " --> pdb=" O ASP E 334 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET G 333 " --> pdb=" O ASP F 334 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLN A 329 " --> pdb=" O TYR G 332 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ASP G 334 " --> pdb=" O GLN A 329 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU A 331 " --> pdb=" O ASP G 334 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 226 through 227 removed outlier: 7.322A pdb=" N ILE C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE C 199 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS C 205 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 235 through 243 removed outlier: 3.843A pdb=" N ARG B 235 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN B 287 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 226 through 227 removed outlier: 7.321A pdb=" N ILE D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE D 199 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS D 205 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 235 through 243 removed outlier: 3.841A pdb=" N ARG C 235 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN C 287 " --> pdb=" O ASN C 279 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 226 through 227 removed outlier: 7.321A pdb=" N ILE E 203 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE E 199 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS E 205 " --> pdb=" O ALA E 197 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 235 through 243 removed outlier: 3.842A pdb=" N ARG D 235 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN D 287 " --> pdb=" O ASN D 279 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 226 through 227 removed outlier: 7.321A pdb=" N ILE F 203 " --> pdb=" O ILE F 199 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE F 199 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS F 205 " --> pdb=" O ALA F 197 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 235 through 243 removed outlier: 3.842A pdb=" N ARG E 235 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASN E 287 " --> pdb=" O ASN E 279 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 226 through 227 removed outlier: 7.322A pdb=" N ILE G 203 " --> pdb=" O ILE G 199 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE G 199 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS G 205 " --> pdb=" O ALA G 197 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 235 through 243 removed outlier: 3.842A pdb=" N ARG F 235 " --> pdb=" O THR F 294 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN F 287 " --> pdb=" O ASN F 279 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 235 through 243 removed outlier: 3.842A pdb=" N ARG G 235 " --> pdb=" O THR G 294 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN G 287 " --> pdb=" O ASN G 279 " (cutoff:3.500A) 1312 hydrogen bonds defined for protein. 3705 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: 3.23 Time building geometry restraints manager: 2.16 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: 5803 1.34 - 1.46: 4536 1.46 - 1.58: 9051 1.58 - 1.70: 0 1.70 - 1.82: 147 Bond restraints: 19537 Sorted by residual: bond pdb=" CG GLU D 136 " pdb=" CD GLU D 136 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.30e-01 bond pdb=" CB GLU A 136 " pdb=" CG GLU A 136 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.99e-01 bond pdb=" CG GLU B 136 " pdb=" CD GLU B 136 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 6.86e-01 bond pdb=" CG GLU C 136 " pdb=" CD GLU C 136 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.59e-01 bond pdb=" CB GLU D 136 " pdb=" CG GLU D 136 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.54e-01 ... (remaining 19532 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 25827 1.85 - 3.69: 262 3.69 - 5.54: 63 5.54 - 7.38: 14 7.38 - 9.23: 14 Bond angle restraints: 26180 Sorted by residual: angle pdb=" CB MET C 118 " pdb=" CG MET C 118 " pdb=" SD MET C 118 " ideal model delta sigma weight residual 112.70 121.93 -9.23 3.00e+00 1.11e-01 9.47e+00 angle pdb=" CB MET G 118 " pdb=" CG MET G 118 " pdb=" SD MET G 118 " ideal model delta sigma weight residual 112.70 121.92 -9.22 3.00e+00 1.11e-01 9.45e+00 angle pdb=" CB MET A 118 " pdb=" CG MET A 118 " pdb=" SD MET A 118 " ideal model delta sigma weight residual 112.70 121.91 -9.21 3.00e+00 1.11e-01 9.43e+00 angle pdb=" CB MET F 118 " pdb=" CG MET F 118 " pdb=" SD MET F 118 " ideal model delta sigma weight residual 112.70 121.90 -9.20 3.00e+00 1.11e-01 9.41e+00 angle pdb=" CB MET B 118 " pdb=" CG MET B 118 " pdb=" SD MET B 118 " ideal model delta sigma weight residual 112.70 121.90 -9.20 3.00e+00 1.11e-01 9.41e+00 ... (remaining 26175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 10172 17.72 - 35.43: 1070 35.43 - 53.15: 350 53.15 - 70.87: 42 70.87 - 88.59: 14 Dihedral angle restraints: 11648 sinusoidal: 4928 harmonic: 6720 Sorted by residual: dihedral pdb=" CA PHE B 278 " pdb=" C PHE B 278 " pdb=" N ASN B 279 " pdb=" CA ASN B 279 " ideal model delta harmonic sigma weight residual 180.00 -161.45 -18.55 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA PHE E 278 " pdb=" C PHE E 278 " pdb=" N ASN E 279 " pdb=" CA ASN E 279 " ideal model delta harmonic sigma weight residual -180.00 -161.45 -18.55 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA PHE C 278 " pdb=" C PHE C 278 " pdb=" N ASN C 279 " pdb=" CA ASN C 279 " ideal model delta harmonic sigma weight residual 180.00 -161.46 -18.54 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 11645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1766 0.027 - 0.053: 674 0.053 - 0.080: 364 0.080 - 0.106: 127 0.106 - 0.133: 58 Chirality restraints: 2989 Sorted by residual: chirality pdb=" CG LEU B 13 " pdb=" CB LEU B 13 " pdb=" CD1 LEU B 13 " pdb=" CD2 LEU B 13 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA VAL D 276 " pdb=" N VAL D 276 " pdb=" C VAL D 276 " pdb=" CB VAL D 276 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CG LEU F 13 " pdb=" CB LEU F 13 " pdb=" CD1 LEU F 13 " pdb=" CD2 LEU F 13 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 2986 not shown) Planarity restraints: 3171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 29 " -0.014 2.00e-02 2.50e+03 1.25e-02 3.90e+00 pdb=" CG TRP C 29 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP C 29 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP C 29 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 29 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 29 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 29 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 29 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 29 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 29 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 29 " 0.013 2.00e-02 2.50e+03 1.24e-02 3.84e+00 pdb=" CG TRP D 29 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP D 29 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP D 29 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 29 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 29 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 29 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 29 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 29 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 29 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 29 " 0.014 2.00e-02 2.50e+03 1.24e-02 3.83e+00 pdb=" CG TRP F 29 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP F 29 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP F 29 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 29 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 29 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 29 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 29 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 29 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP F 29 " 0.000 2.00e-02 2.50e+03 ... (remaining 3168 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 5881 2.84 - 3.35: 17613 3.35 - 3.87: 31118 3.87 - 4.38: 34301 4.38 - 4.90: 59956 Nonbonded interactions: 148869 Sorted by model distance: nonbonded pdb=" NZ LYS G 69 " pdb=" O LYS G 71 " model vdw 2.319 3.120 nonbonded pdb=" NZ LYS C 69 " pdb=" O LYS C 71 " model vdw 2.320 3.120 nonbonded pdb=" NZ LYS D 69 " pdb=" O LYS D 71 " model vdw 2.320 3.120 nonbonded pdb=" NZ LYS A 69 " pdb=" O LYS A 71 " model vdw 2.320 3.120 nonbonded pdb=" NZ LYS E 69 " pdb=" O LYS E 71 " model vdw 2.320 3.120 ... (remaining 148864 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 1.110 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: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.890 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 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 : 0.003 0.025 19537 Z= 0.150 Angle : 0.562 9.231 26180 Z= 0.279 Chirality : 0.040 0.133 2989 Planarity : 0.003 0.022 3171 Dihedral : 16.017 88.586 7322 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.74 % Allowed : 25.69 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.18), residues: 2310 helix: 2.93 (0.14), residues: 1351 sheet: -0.53 (0.31), residues: 259 loop : -1.33 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 116 TYR 0.010 0.001 TYR C 291 PHE 0.023 0.001 PHE C 138 TRP 0.034 0.002 TRP C 29 HIS 0.001 0.000 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00348 (19537) covalent geometry : angle 0.56207 (26180) hydrogen bonds : bond 0.14456 ( 1312) hydrogen bonds : angle 4.80054 ( 3705) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 201 time to evaluate : 0.715 Fit side-chains REVERT: A 68 TYR cc_start: 0.8117 (t80) cc_final: 0.7692 (t80) REVERT: B 65 ILE cc_start: 0.8610 (mm) cc_final: 0.8316 (tp) REVERT: B 68 TYR cc_start: 0.8177 (t80) cc_final: 0.7825 (t80) REVERT: C 65 ILE cc_start: 0.8695 (mm) cc_final: 0.8458 (tp) REVERT: C 68 TYR cc_start: 0.8121 (t80) cc_final: 0.7718 (t80) REVERT: D 65 ILE cc_start: 0.8704 (mm) cc_final: 0.8494 (tp) REVERT: D 68 TYR cc_start: 0.8082 (t80) cc_final: 0.7625 (t80) REVERT: D 118 MET cc_start: 0.8981 (tpp) cc_final: 0.8409 (tpt) REVERT: D 140 MET cc_start: 0.5203 (OUTLIER) cc_final: 0.4899 (pp-130) REVERT: E 68 TYR cc_start: 0.8082 (t80) cc_final: 0.7658 (t80) REVERT: F 68 TYR cc_start: 0.8110 (t80) cc_final: 0.7676 (t80) REVERT: F 116 ARG cc_start: 0.8568 (mmm-85) cc_final: 0.8008 (mmm-85) REVERT: F 140 MET cc_start: 0.4945 (OUTLIER) cc_final: 0.4615 (pp-130) REVERT: G 68 TYR cc_start: 0.8179 (t80) cc_final: 0.7709 (t80) REVERT: G 118 MET cc_start: 0.8739 (tpp) cc_final: 0.8235 (tpt) outliers start: 35 outliers final: 11 residues processed: 229 average time/residue: 0.5671 time to fit residues: 147.9196 Evaluate side-chains 190 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 140 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 60.0000 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 20.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN B 272 GLN C 272 GLN E 272 GLN F 272 GLN G 272 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.115907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.059867 restraints weight = 35216.285| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 2.10 r_work: 0.2604 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 19537 Z= 0.139 Angle : 0.515 7.616 26180 Z= 0.265 Chirality : 0.041 0.147 2989 Planarity : 0.003 0.027 3171 Dihedral : 4.828 43.646 3046 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.51 % Allowed : 21.68 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.18), residues: 2310 helix: 3.21 (0.14), residues: 1330 sheet: 0.30 (0.33), residues: 224 loop : -1.11 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 116 TYR 0.015 0.001 TYR E 291 PHE 0.021 0.002 PHE A 138 TRP 0.018 0.001 TRP F 29 HIS 0.001 0.000 HIS G 265 Details of bonding type rmsd covalent geometry : bond 0.00318 (19537) covalent geometry : angle 0.51483 (26180) hydrogen bonds : bond 0.04267 ( 1312) hydrogen bonds : angle 3.59505 ( 3705) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 178 time to evaluate : 0.827 Fit side-chains REVERT: A 65 ILE cc_start: 0.8637 (mm) cc_final: 0.8377 (tp) REVERT: A 68 TYR cc_start: 0.8061 (t80) cc_final: 0.7662 (t80) REVERT: A 98 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7828 (mp) REVERT: B 65 ILE cc_start: 0.8532 (mm) cc_final: 0.8302 (tp) REVERT: B 68 TYR cc_start: 0.8072 (t80) cc_final: 0.7673 (t80) REVERT: B 98 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7725 (mp) REVERT: C 68 TYR cc_start: 0.7929 (t80) cc_final: 0.7540 (t80) REVERT: C 98 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7867 (mp) REVERT: D 68 TYR cc_start: 0.8006 (t80) cc_final: 0.7521 (t80) REVERT: D 118 MET cc_start: 0.8807 (tpp) cc_final: 0.8336 (tpt) REVERT: D 140 MET cc_start: 0.5464 (OUTLIER) cc_final: 0.5075 (pp-130) REVERT: D 172 MET cc_start: 0.8655 (tmm) cc_final: 0.8455 (tmm) REVERT: E 118 MET cc_start: 0.8757 (tpt) cc_final: 0.8501 (tpt) REVERT: E 140 MET cc_start: 0.5115 (OUTLIER) cc_final: 0.4865 (pp-130) REVERT: F 28 PHE cc_start: 0.9120 (t80) cc_final: 0.8733 (t80) REVERT: F 98 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7742 (mp) REVERT: F 140 MET cc_start: 0.5036 (OUTLIER) cc_final: 0.4518 (pp-130) REVERT: G 65 ILE cc_start: 0.8635 (mm) cc_final: 0.8364 (tp) REVERT: G 98 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7654 (mp) outliers start: 91 outliers final: 40 residues processed: 254 average time/residue: 0.4206 time to fit residues: 126.2325 Evaluate side-chains 219 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 223 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 159 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 120 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 101 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 220 optimal weight: 0.7980 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS B 137 HIS D 272 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.115930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.059709 restraints weight = 35458.147| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.11 r_work: 0.2601 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2500 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19537 Z= 0.137 Angle : 0.524 8.534 26180 Z= 0.267 Chirality : 0.041 0.168 2989 Planarity : 0.003 0.030 3171 Dihedral : 4.533 31.073 3033 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 4.51 % Allowed : 22.27 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.18), residues: 2310 helix: 3.29 (0.13), residues: 1330 sheet: -0.33 (0.32), residues: 259 loop : -0.90 (0.21), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 116 TYR 0.018 0.001 TYR E 291 PHE 0.023 0.001 PHE B 138 TRP 0.019 0.001 TRP A 29 HIS 0.001 0.000 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00316 (19537) covalent geometry : angle 0.52432 (26180) hydrogen bonds : bond 0.04160 ( 1312) hydrogen bonds : angle 3.52429 ( 3705) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 186 time to evaluate : 0.664 Fit side-chains REVERT: A 65 ILE cc_start: 0.8542 (mm) cc_final: 0.8268 (tp) REVERT: A 68 TYR cc_start: 0.8043 (t80) cc_final: 0.7654 (t80) REVERT: A 98 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7839 (mp) REVERT: B 65 ILE cc_start: 0.8568 (mm) cc_final: 0.8350 (tp) REVERT: B 68 TYR cc_start: 0.8071 (t80) cc_final: 0.7682 (t80) REVERT: B 98 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7744 (mp) REVERT: B 137 HIS cc_start: 0.8755 (OUTLIER) cc_final: 0.8498 (m170) REVERT: B 140 MET cc_start: 0.5640 (OUTLIER) cc_final: 0.5334 (pp-130) REVERT: C 68 TYR cc_start: 0.7903 (t80) cc_final: 0.7452 (t80) REVERT: C 98 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7864 (mp) REVERT: C 140 MET cc_start: 0.5887 (OUTLIER) cc_final: 0.5423 (pp-130) REVERT: D 98 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7824 (mp) REVERT: D 140 MET cc_start: 0.5604 (OUTLIER) cc_final: 0.5190 (pp-130) REVERT: E 68 TYR cc_start: 0.7917 (m-80) cc_final: 0.7695 (m-80) REVERT: E 98 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7765 (mp) REVERT: E 140 MET cc_start: 0.5117 (OUTLIER) cc_final: 0.4908 (pp-130) REVERT: F 98 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7735 (mp) REVERT: F 140 MET cc_start: 0.5109 (OUTLIER) cc_final: 0.4294 (pp-130) REVERT: G 65 ILE cc_start: 0.8648 (mm) cc_final: 0.8382 (tp) REVERT: G 98 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7680 (mp) REVERT: G 140 MET cc_start: 0.5143 (OUTLIER) cc_final: 0.4698 (pp-130) REVERT: G 333 MET cc_start: 0.8926 (tpp) cc_final: 0.8600 (mmm) outliers start: 91 outliers final: 41 residues processed: 252 average time/residue: 0.4368 time to fit residues: 128.6765 Evaluate side-chains 229 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 174 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 223 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 12 optimal weight: 5.9990 chunk 172 optimal weight: 30.0000 chunk 102 optimal weight: 50.0000 chunk 80 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 73 optimal weight: 30.0000 chunk 157 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 199 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 222 optimal weight: 4.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.114276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.057823 restraints weight = 35342.860| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 2.10 r_work: 0.2557 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2455 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 19537 Z= 0.240 Angle : 0.576 8.279 26180 Z= 0.299 Chirality : 0.044 0.181 2989 Planarity : 0.004 0.035 3171 Dihedral : 5.163 32.762 3033 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.02 % Allowed : 23.16 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.17), residues: 2310 helix: 3.12 (0.13), residues: 1330 sheet: -0.38 (0.32), residues: 259 loop : -1.03 (0.20), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 110 TYR 0.021 0.001 TYR E 291 PHE 0.023 0.002 PHE G 138 TRP 0.021 0.002 TRP B 29 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00579 (19537) covalent geometry : angle 0.57589 (26180) hydrogen bonds : bond 0.05274 ( 1312) hydrogen bonds : angle 3.75247 ( 3705) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 174 time to evaluate : 0.781 Fit side-chains REVERT: A 65 ILE cc_start: 0.8554 (mm) cc_final: 0.8305 (tp) REVERT: A 68 TYR cc_start: 0.8047 (t80) cc_final: 0.7603 (t80) REVERT: A 98 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7940 (mp) REVERT: B 65 ILE cc_start: 0.8504 (mm) cc_final: 0.8279 (tp) REVERT: B 68 TYR cc_start: 0.8056 (t80) cc_final: 0.7654 (t80) REVERT: B 98 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7866 (mp) REVERT: B 140 MET cc_start: 0.6088 (OUTLIER) cc_final: 0.5487 (pp-130) REVERT: C 68 TYR cc_start: 0.7853 (t80) cc_final: 0.7412 (t80) REVERT: C 98 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7918 (mp) REVERT: C 140 MET cc_start: 0.6223 (OUTLIER) cc_final: 0.5833 (pp-130) REVERT: D 98 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7960 (mp) REVERT: D 140 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.5443 (pp-130) REVERT: E 68 TYR cc_start: 0.8176 (m-80) cc_final: 0.7947 (m-80) REVERT: E 98 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7822 (mp) REVERT: F 98 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7866 (mp) REVERT: F 140 MET cc_start: 0.5565 (OUTLIER) cc_final: 0.4906 (pp-130) REVERT: G 65 ILE cc_start: 0.8694 (mm) cc_final: 0.8455 (tp) REVERT: G 98 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7892 (mp) REVERT: G 140 MET cc_start: 0.5717 (OUTLIER) cc_final: 0.5278 (pp-130) REVERT: G 333 MET cc_start: 0.8865 (tpp) cc_final: 0.8586 (mpp) outliers start: 81 outliers final: 42 residues processed: 237 average time/residue: 0.4613 time to fit residues: 127.6096 Evaluate side-chains 226 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 172 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 223 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 184 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 223 optimal weight: 0.9980 chunk 67 optimal weight: 30.0000 chunk 45 optimal weight: 5.9990 chunk 112 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN G 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.116708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.060975 restraints weight = 35389.257| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.09 r_work: 0.2630 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19537 Z= 0.105 Angle : 0.526 10.031 26180 Z= 0.261 Chirality : 0.041 0.202 2989 Planarity : 0.003 0.036 3171 Dihedral : 4.437 30.002 3033 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.41 % Allowed : 22.62 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.18), residues: 2310 helix: 3.56 (0.13), residues: 1288 sheet: -0.17 (0.32), residues: 273 loop : -0.80 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 110 TYR 0.016 0.001 TYR E 291 PHE 0.027 0.001 PHE B 138 TRP 0.023 0.001 TRP B 29 HIS 0.001 0.000 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00227 (19537) covalent geometry : angle 0.52563 (26180) hydrogen bonds : bond 0.03579 ( 1312) hydrogen bonds : angle 3.42547 ( 3705) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 177 time to evaluate : 0.766 Fit side-chains REVERT: A 65 ILE cc_start: 0.8585 (mm) cc_final: 0.8322 (tp) REVERT: A 68 TYR cc_start: 0.7934 (t80) cc_final: 0.7559 (t80) REVERT: A 98 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7809 (mp) REVERT: B 65 ILE cc_start: 0.8497 (mm) cc_final: 0.8278 (tp) REVERT: B 68 TYR cc_start: 0.7924 (t80) cc_final: 0.7578 (t80) REVERT: B 98 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7867 (mp) REVERT: B 140 MET cc_start: 0.5840 (OUTLIER) cc_final: 0.5289 (pp-130) REVERT: C 68 TYR cc_start: 0.7907 (t80) cc_final: 0.7491 (t80) REVERT: C 98 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7786 (mp) REVERT: C 140 MET cc_start: 0.6113 (OUTLIER) cc_final: 0.5664 (pp-130) REVERT: D 98 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7821 (mp) REVERT: D 140 MET cc_start: 0.5897 (OUTLIER) cc_final: 0.5265 (pp-130) REVERT: E 68 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: E 118 MET cc_start: 0.8836 (tpt) cc_final: 0.8562 (tpt) REVERT: F 98 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7740 (mp) REVERT: F 140 MET cc_start: 0.5438 (OUTLIER) cc_final: 0.4519 (pp-130) REVERT: G 65 ILE cc_start: 0.8685 (mm) cc_final: 0.8454 (tp) REVERT: G 98 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7765 (mp) REVERT: G 140 MET cc_start: 0.5459 (OUTLIER) cc_final: 0.5012 (pp-130) REVERT: G 333 MET cc_start: 0.8713 (tpp) cc_final: 0.8509 (mmm) outliers start: 89 outliers final: 33 residues processed: 249 average time/residue: 0.4747 time to fit residues: 138.0587 Evaluate side-chains 218 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 223 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 203 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 219 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 166 optimal weight: 30.0000 chunk 46 optimal weight: 0.8980 chunk 135 optimal weight: 40.0000 chunk 90 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN B 137 HIS G 105 GLN G 137 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.116281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.060176 restraints weight = 35069.587| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.10 r_work: 0.2611 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19537 Z= 0.126 Angle : 0.543 8.560 26180 Z= 0.270 Chirality : 0.042 0.210 2989 Planarity : 0.003 0.029 3171 Dihedral : 4.488 31.503 3033 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.82 % Allowed : 23.36 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.18), residues: 2310 helix: 3.37 (0.13), residues: 1330 sheet: -0.27 (0.33), residues: 259 loop : -0.97 (0.21), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 110 TYR 0.018 0.001 TYR E 291 PHE 0.026 0.001 PHE D 138 TRP 0.026 0.001 TRP B 29 HIS 0.001 0.000 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00288 (19537) covalent geometry : angle 0.54321 (26180) hydrogen bonds : bond 0.03909 ( 1312) hydrogen bonds : angle 3.47263 ( 3705) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 175 time to evaluate : 0.726 Fit side-chains REVERT: A 65 ILE cc_start: 0.8570 (mm) cc_final: 0.8333 (tp) REVERT: A 98 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7813 (mp) REVERT: A 140 MET cc_start: 0.5712 (OUTLIER) cc_final: 0.5231 (pp-130) REVERT: B 68 TYR cc_start: 0.8040 (t80) cc_final: 0.7676 (t80) REVERT: B 98 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7846 (mp) REVERT: B 137 HIS cc_start: 0.8652 (OUTLIER) cc_final: 0.8411 (m-70) REVERT: B 140 MET cc_start: 0.5906 (OUTLIER) cc_final: 0.5335 (pp-130) REVERT: C 68 TYR cc_start: 0.7896 (t80) cc_final: 0.7496 (t80) REVERT: C 98 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7803 (mp) REVERT: C 140 MET cc_start: 0.6185 (OUTLIER) cc_final: 0.5684 (pp-130) REVERT: D 98 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7824 (mp) REVERT: D 140 MET cc_start: 0.6178 (OUTLIER) cc_final: 0.5494 (pp-130) REVERT: E 68 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.7808 (m-80) REVERT: E 98 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7799 (mp) REVERT: F 98 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7760 (mp) REVERT: F 140 MET cc_start: 0.5672 (OUTLIER) cc_final: 0.4846 (pp-130) REVERT: G 65 ILE cc_start: 0.8685 (mm) cc_final: 0.8454 (tp) REVERT: G 98 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7762 (mp) REVERT: G 140 MET cc_start: 0.5637 (OUTLIER) cc_final: 0.5061 (pp-130) REVERT: G 333 MET cc_start: 0.8671 (mpp) cc_final: 0.8423 (mmm) outliers start: 77 outliers final: 33 residues processed: 241 average time/residue: 0.3955 time to fit residues: 111.4380 Evaluate side-chains 219 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 223 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 143 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 228 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 chunk 193 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 206 optimal weight: 8.9990 chunk 168 optimal weight: 40.0000 chunk 35 optimal weight: 20.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN B 137 HIS G 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.115543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.059595 restraints weight = 35222.467| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.09 r_work: 0.2594 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2494 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 19537 Z= 0.154 Angle : 0.565 9.236 26180 Z= 0.281 Chirality : 0.043 0.221 2989 Planarity : 0.003 0.030 3171 Dihedral : 4.637 32.337 3033 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.72 % Allowed : 23.51 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.49 (0.18), residues: 2310 helix: 3.35 (0.13), residues: 1330 sheet: -0.30 (0.33), residues: 259 loop : -1.01 (0.21), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 110 TYR 0.018 0.001 TYR E 291 PHE 0.026 0.001 PHE A 138 TRP 0.029 0.002 TRP B 29 HIS 0.005 0.000 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00362 (19537) covalent geometry : angle 0.56492 (26180) hydrogen bonds : bond 0.04227 ( 1312) hydrogen bonds : angle 3.55360 ( 3705) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 176 time to evaluate : 0.608 Fit side-chains REVERT: A 65 ILE cc_start: 0.8593 (mm) cc_final: 0.8354 (tp) REVERT: A 98 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7904 (mp) REVERT: A 140 MET cc_start: 0.5903 (OUTLIER) cc_final: 0.5512 (pp-130) REVERT: B 68 TYR cc_start: 0.7942 (t80) cc_final: 0.7461 (t80) REVERT: B 98 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7855 (mp) REVERT: B 140 MET cc_start: 0.5904 (OUTLIER) cc_final: 0.5354 (pp-130) REVERT: B 318 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8873 (mt0) REVERT: C 68 TYR cc_start: 0.7904 (t80) cc_final: 0.7477 (t80) REVERT: C 98 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7810 (mp) REVERT: C 140 MET cc_start: 0.6258 (OUTLIER) cc_final: 0.5731 (pp-130) REVERT: D 98 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7841 (mp) REVERT: D 140 MET cc_start: 0.6164 (OUTLIER) cc_final: 0.5485 (pp-130) REVERT: D 158 MET cc_start: 0.8884 (mtp) cc_final: 0.8640 (mtm) REVERT: E 68 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7818 (m-80) REVERT: E 98 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7819 (mp) REVERT: F 68 TYR cc_start: 0.7959 (m-80) cc_final: 0.7753 (m-80) REVERT: F 98 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7770 (mp) REVERT: F 140 MET cc_start: 0.5879 (OUTLIER) cc_final: 0.4925 (pp-130) REVERT: G 65 ILE cc_start: 0.8687 (mm) cc_final: 0.8458 (tp) REVERT: G 68 TYR cc_start: 0.8092 (m-80) cc_final: 0.7876 (m-80) REVERT: G 98 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7824 (mp) REVERT: G 140 MET cc_start: 0.5778 (OUTLIER) cc_final: 0.5209 (pp-130) outliers start: 75 outliers final: 39 residues processed: 235 average time/residue: 0.4242 time to fit residues: 115.6959 Evaluate side-chains 220 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 166 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 318 GLN Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 232 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 76 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 139 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 69 optimal weight: 30.0000 chunk 57 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 102 optimal weight: 40.0000 chunk 43 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN G 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.116550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.060775 restraints weight = 35284.270| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.10 r_work: 0.2624 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19537 Z= 0.117 Angle : 0.566 9.888 26180 Z= 0.276 Chirality : 0.042 0.234 2989 Planarity : 0.003 0.070 3171 Dihedral : 4.407 33.989 3033 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.27 % Allowed : 23.96 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.74 (0.18), residues: 2310 helix: 3.61 (0.13), residues: 1288 sheet: -0.15 (0.32), residues: 273 loop : -0.79 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 110 TYR 0.017 0.001 TYR E 291 PHE 0.028 0.001 PHE D 138 TRP 0.035 0.001 TRP B 29 HIS 0.001 0.000 HIS G 137 Details of bonding type rmsd covalent geometry : bond 0.00262 (19537) covalent geometry : angle 0.56611 (26180) hydrogen bonds : bond 0.03671 ( 1312) hydrogen bonds : angle 3.43506 ( 3705) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 170 time to evaluate : 0.710 Fit side-chains REVERT: A 65 ILE cc_start: 0.8567 (mm) cc_final: 0.8336 (tp) REVERT: A 98 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7781 (mp) REVERT: A 140 MET cc_start: 0.5834 (OUTLIER) cc_final: 0.5420 (pp-130) REVERT: B 68 TYR cc_start: 0.7912 (t80) cc_final: 0.7457 (t80) REVERT: B 98 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7856 (mp) REVERT: B 140 MET cc_start: 0.5969 (OUTLIER) cc_final: 0.5400 (pp-130) REVERT: B 318 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8802 (mt0) REVERT: C 68 TYR cc_start: 0.7886 (t80) cc_final: 0.7470 (t80) REVERT: C 98 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7801 (mp) REVERT: C 140 MET cc_start: 0.6139 (OUTLIER) cc_final: 0.5698 (pp-130) REVERT: D 98 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7807 (mp) REVERT: D 140 MET cc_start: 0.6219 (OUTLIER) cc_final: 0.5490 (pp-130) REVERT: D 158 MET cc_start: 0.8810 (mtp) cc_final: 0.8578 (mtm) REVERT: E 68 TYR cc_start: 0.8180 (OUTLIER) cc_final: 0.7931 (m-80) REVERT: E 98 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7803 (mp) REVERT: E 118 MET cc_start: 0.8818 (tpt) cc_final: 0.8584 (tpt) REVERT: F 68 TYR cc_start: 0.8059 (m-80) cc_final: 0.7846 (m-80) REVERT: F 98 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7717 (mp) REVERT: F 140 MET cc_start: 0.6039 (OUTLIER) cc_final: 0.5007 (pp-130) REVERT: F 318 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8763 (mt0) REVERT: G 65 ILE cc_start: 0.8688 (mm) cc_final: 0.8469 (tp) REVERT: G 68 TYR cc_start: 0.7946 (m-80) cc_final: 0.7734 (m-80) REVERT: G 98 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7773 (mp) REVERT: G 140 MET cc_start: 0.5804 (OUTLIER) cc_final: 0.5068 (pp-130) outliers start: 66 outliers final: 36 residues processed: 224 average time/residue: 0.5012 time to fit residues: 130.3344 Evaluate side-chains 219 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 167 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 318 GLN Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 318 GLN Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 232 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 103 optimal weight: 20.0000 chunk 188 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 174 optimal weight: 8.9990 chunk 169 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 318 GLN G 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.114216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.058034 restraints weight = 35114.232| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 2.07 r_work: 0.2547 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2442 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 19537 Z= 0.244 Angle : 0.629 10.930 26180 Z= 0.315 Chirality : 0.045 0.229 2989 Planarity : 0.004 0.046 3171 Dihedral : 5.123 34.508 3033 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.27 % Allowed : 24.21 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.17), residues: 2310 helix: 3.22 (0.14), residues: 1330 sheet: -0.36 (0.32), residues: 259 loop : -1.05 (0.20), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 110 TYR 0.021 0.001 TYR E 291 PHE 0.026 0.002 PHE B 138 TRP 0.031 0.002 TRP A 29 HIS 0.002 0.001 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00589 (19537) covalent geometry : angle 0.62882 (26180) hydrogen bonds : bond 0.05101 ( 1312) hydrogen bonds : angle 3.73887 ( 3705) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 166 time to evaluate : 0.898 Fit side-chains REVERT: A 65 ILE cc_start: 0.8548 (mm) cc_final: 0.8322 (tp) REVERT: A 98 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7909 (mp) REVERT: A 140 MET cc_start: 0.6250 (ppp) cc_final: 0.5857 (pp-130) REVERT: B 68 TYR cc_start: 0.7899 (t80) cc_final: 0.7430 (t80) REVERT: B 98 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7814 (mp) REVERT: B 140 MET cc_start: 0.6231 (OUTLIER) cc_final: 0.5675 (pp-130) REVERT: C 68 TYR cc_start: 0.7848 (t80) cc_final: 0.7415 (t80) REVERT: C 98 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7876 (mp) REVERT: C 140 MET cc_start: 0.6493 (OUTLIER) cc_final: 0.6042 (pp-130) REVERT: D 98 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7881 (mp) REVERT: D 140 MET cc_start: 0.6520 (OUTLIER) cc_final: 0.5819 (pp-130) REVERT: D 158 MET cc_start: 0.8897 (mtp) cc_final: 0.8662 (mtm) REVERT: E 68 TYR cc_start: 0.8147 (m-80) cc_final: 0.7946 (m-80) REVERT: E 98 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7789 (mp) REVERT: F 98 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7816 (mp) REVERT: F 140 MET cc_start: 0.6374 (OUTLIER) cc_final: 0.5378 (pp-130) REVERT: G 65 ILE cc_start: 0.8625 (mm) cc_final: 0.8397 (tp) REVERT: G 98 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7815 (mp) REVERT: G 140 MET cc_start: 0.6208 (OUTLIER) cc_final: 0.5503 (pp-130) outliers start: 66 outliers final: 40 residues processed: 223 average time/residue: 0.4777 time to fit residues: 124.8064 Evaluate side-chains 215 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 163 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 232 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 103 optimal weight: 5.9990 chunk 33 optimal weight: 50.0000 chunk 192 optimal weight: 1.9990 chunk 146 optimal weight: 8.9990 chunk 210 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 219 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 157 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN G 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.114617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.058675 restraints weight = 35259.311| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 2.05 r_work: 0.2559 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2455 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 19537 Z= 0.198 Angle : 0.620 11.416 26180 Z= 0.308 Chirality : 0.044 0.232 2989 Planarity : 0.003 0.050 3171 Dihedral : 5.015 35.355 3033 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.63 % Allowed : 25.10 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.18), residues: 2310 helix: 3.01 (0.14), residues: 1358 sheet: -0.37 (0.32), residues: 259 loop : -1.37 (0.20), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 110 TYR 0.019 0.001 TYR E 291 PHE 0.027 0.002 PHE C 138 TRP 0.043 0.002 TRP B 29 HIS 0.001 0.000 HIS G 137 Details of bonding type rmsd covalent geometry : bond 0.00476 (19537) covalent geometry : angle 0.61994 (26180) hydrogen bonds : bond 0.04698 ( 1312) hydrogen bonds : angle 3.70660 ( 3705) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 163 time to evaluate : 0.497 Fit side-chains REVERT: A 65 ILE cc_start: 0.8594 (mm) cc_final: 0.8370 (tp) REVERT: A 98 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7837 (mp) REVERT: A 140 MET cc_start: 0.6243 (ppp) cc_final: 0.5477 (pp-130) REVERT: B 68 TYR cc_start: 0.7798 (t80) cc_final: 0.7324 (t80) REVERT: B 98 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7822 (mp) REVERT: B 140 MET cc_start: 0.6224 (OUTLIER) cc_final: 0.5697 (pp-130) REVERT: C 68 TYR cc_start: 0.7827 (t80) cc_final: 0.7422 (t80) REVERT: C 98 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7790 (mp) REVERT: C 140 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.6061 (pp-130) REVERT: D 98 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7849 (mp) REVERT: D 140 MET cc_start: 0.6618 (OUTLIER) cc_final: 0.5892 (pp-130) REVERT: D 158 MET cc_start: 0.8856 (mtp) cc_final: 0.8627 (mtm) REVERT: E 68 TYR cc_start: 0.8138 (m-80) cc_final: 0.7905 (m-80) REVERT: E 98 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7775 (mp) REVERT: F 68 TYR cc_start: 0.7926 (m-80) cc_final: 0.7617 (m-10) REVERT: F 98 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7802 (mp) REVERT: F 140 MET cc_start: 0.6386 (OUTLIER) cc_final: 0.5471 (pp-130) REVERT: G 65 ILE cc_start: 0.8577 (mm) cc_final: 0.8350 (tp) REVERT: G 68 TYR cc_start: 0.7931 (m-80) cc_final: 0.7680 (m-80) REVERT: G 98 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7820 (mp) REVERT: G 140 MET cc_start: 0.6389 (OUTLIER) cc_final: 0.5707 (pp-130) REVERT: G 333 MET cc_start: 0.8896 (tpp) cc_final: 0.8640 (mmm) outliers start: 53 outliers final: 37 residues processed: 208 average time/residue: 0.4313 time to fit residues: 104.8616 Evaluate side-chains 211 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 162 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 232 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 18 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 199 optimal weight: 30.0000 chunk 94 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 30.0000 chunk 54 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 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.114872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.058700 restraints weight = 35223.888| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 2.08 r_work: 0.2561 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 19537 Z= 0.189 Angle : 0.788 59.103 26180 Z= 0.429 Chirality : 0.045 0.760 2989 Planarity : 0.003 0.046 3171 Dihedral : 5.016 35.421 3033 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.78 % Allowed : 24.80 % Favored : 72.42 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.18), residues: 2310 helix: 3.01 (0.14), residues: 1358 sheet: -0.37 (0.32), residues: 259 loop : -1.36 (0.20), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 110 TYR 0.019 0.001 TYR E 291 PHE 0.013 0.002 PHE C 138 TRP 0.036 0.002 TRP B 29 HIS 0.001 0.000 HIS G 137 Details of bonding type rmsd covalent geometry : bond 0.00436 (19537) covalent geometry : angle 0.78792 (26180) hydrogen bonds : bond 0.04654 ( 1312) hydrogen bonds : angle 3.70691 ( 3705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11888.57 seconds wall clock time: 201 minutes 53.70 seconds (12113.70 seconds total)