Starting phenix.real_space_refine on Thu Feb 5 21:46:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h2p_51813/02_2026/9h2p_51813_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h2p_51813/02_2026/9h2p_51813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9h2p_51813/02_2026/9h2p_51813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h2p_51813/02_2026/9h2p_51813.map" model { file = "/net/cci-nas-00/data/ceres_data/9h2p_51813/02_2026/9h2p_51813_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h2p_51813/02_2026/9h2p_51813_trim.cif" } resolution = 2.3 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 12586 2.51 5 N 3080 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 21 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: 18984 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2640 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 8, 'TRANS': 323} Chain: "B" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2640 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 8, 'TRANS': 323} Chain: "C" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2640 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 8, 'TRANS': 323} Chain: "D" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2640 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 8, 'TRANS': 323} Chain: "E" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2640 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 8, 'TRANS': 323} Chain: "F" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2640 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 8, 'TRANS': 323} Chain: "G" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2640 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 8, 'TRANS': 323} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'D12': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'D12': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'D12': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'D12': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'D12': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'D12': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'D12': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 3.68, per 1000 atoms: 0.19 Number of scatterers: 18984 At special positions: 0 Unit cell: (119.196, 121.088, 135.278, 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 3080 7.00 C 12586 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: 1.53 Conformation dependent library (CDL) restraints added in 779.4 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: 77 helices and 15 sheets defined 59.3% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 7 through 30 removed outlier: 3.862A pdb=" N LEU A 11 " --> pdb=" O THR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 69 Processing helix chain 'A' and resid 76 through 109 Processing helix chain 'A' and resid 111 through 134 Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 150 through 177 removed outlier: 3.569A pdb=" N ALA A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 222 Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.597A pdb=" N ALA A 248 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 4.874A 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 Processing helix chain 'B' and resid 7 through 30 removed outlier: 3.862A pdb=" N LEU B 11 " --> pdb=" O THR B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 69 Processing helix chain 'B' and resid 76 through 109 Processing helix chain 'B' and resid 111 through 134 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 150 through 177 removed outlier: 3.568A pdb=" N ALA B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 222 Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 244 through 249 removed outlier: 3.598A pdb=" N ALA B 248 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 4.874A 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 Processing helix chain 'C' and resid 7 through 30 removed outlier: 3.862A pdb=" N LEU C 11 " --> pdb=" O THR C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 69 Processing helix chain 'C' and resid 76 through 109 Processing helix chain 'C' and resid 111 through 134 Processing helix chain 'C' and resid 142 through 147 Processing helix chain 'C' and resid 150 through 177 removed outlier: 3.568A pdb=" N ALA C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 222 Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 244 through 249 removed outlier: 3.597A pdb=" N ALA C 248 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 4.874A 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 Processing helix chain 'D' and resid 7 through 30 removed outlier: 3.862A pdb=" N LEU D 11 " --> pdb=" O THR D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 69 Processing helix chain 'D' and resid 76 through 109 Processing helix chain 'D' and resid 111 through 134 Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 150 through 177 removed outlier: 3.568A pdb=" N ALA D 159 " --> pdb=" O ALA D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 222 Processing helix chain 'D' and resid 229 through 232 Processing helix chain 'D' and resid 244 through 249 removed outlier: 3.597A pdb=" N ALA D 248 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 4.874A 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 Processing helix chain 'E' and resid 7 through 30 removed outlier: 3.862A pdb=" N LEU E 11 " --> pdb=" O THR E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 69 Processing helix chain 'E' and resid 76 through 109 Processing helix chain 'E' and resid 111 through 134 Processing helix chain 'E' and resid 142 through 147 Processing helix chain 'E' and resid 150 through 177 removed outlier: 3.569A pdb=" N ALA E 159 " --> pdb=" O ALA E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 222 Processing helix chain 'E' and resid 229 through 232 Processing helix chain 'E' and resid 244 through 249 removed outlier: 3.597A pdb=" N ALA E 248 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 4.873A 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 Processing helix chain 'F' and resid 7 through 30 removed outlier: 3.862A pdb=" N LEU F 11 " --> pdb=" O THR F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 69 Processing helix chain 'F' and resid 76 through 109 Processing helix chain 'F' and resid 111 through 134 Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 150 through 177 removed outlier: 3.568A pdb=" N ALA F 159 " --> pdb=" O ALA F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 222 Processing helix chain 'F' and resid 229 through 232 Processing helix chain 'F' and resid 244 through 249 removed outlier: 3.597A pdb=" N ALA F 248 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 4.873A 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 Processing helix chain 'G' and resid 7 through 30 removed outlier: 3.862A pdb=" N LEU G 11 " --> pdb=" O THR G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 69 Processing helix chain 'G' and resid 76 through 109 Processing helix chain 'G' and resid 111 through 134 Processing helix chain 'G' and resid 142 through 147 Processing helix chain 'G' and resid 150 through 177 removed outlier: 3.569A pdb=" N ALA G 159 " --> pdb=" O ALA G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 222 Processing helix chain 'G' and resid 229 through 232 Processing helix chain 'G' and resid 244 through 249 removed outlier: 3.596A pdb=" N ALA G 248 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 4.874A 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 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 185 removed outlier: 6.760A pdb=" N LYS A 205 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE A 199 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.944A 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: 6.943A pdb=" N ILE B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE B 199 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.760A 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: 3.791A pdb=" N ARG A 235 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASN A 287 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR A 277 " --> pdb=" O MET A 289 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 334 removed outlier: 3.734A pdb=" N MET B 333 " --> pdb=" O ASP A 334 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET C 333 " --> pdb=" O ASP B 334 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET D 333 " --> pdb=" O ASP C 334 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET E 333 " --> pdb=" O ASP D 334 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET F 333 " --> pdb=" O ASP E 334 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET G 333 " --> pdb=" O ASP F 334 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN A 329 " --> pdb=" O TYR G 332 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ASP G 334 " --> pdb=" O GLN A 329 " (cutoff:3.500A) removed outlier: 6.738A 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: 6.944A pdb=" N ILE C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE C 199 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.760A 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: 3.792A pdb=" N ARG B 235 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASN B 287 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR B 277 " --> pdb=" O MET B 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 226 through 227 removed outlier: 6.944A pdb=" N ILE D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE D 199 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.761A 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: 3.792A pdb=" N ARG C 235 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASN C 287 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR C 277 " --> pdb=" O MET C 289 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 226 through 227 removed outlier: 6.944A pdb=" N ILE E 203 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE E 199 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 6.760A 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: 3.791A pdb=" N ARG D 235 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASN D 287 " --> pdb=" O ASN D 279 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR D 277 " --> pdb=" O MET D 289 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 226 through 227 removed outlier: 6.944A pdb=" N ILE F 203 " --> pdb=" O ILE F 199 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE F 199 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 6.761A 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: 3.791A pdb=" N ARG E 235 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ASN E 287 " --> pdb=" O ASN E 279 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR E 277 " --> pdb=" O MET E 289 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 226 through 227 removed outlier: 6.944A pdb=" N ILE G 203 " --> pdb=" O ILE G 199 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE G 199 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.761A 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: 3.792A pdb=" N ARG F 235 " --> pdb=" O THR F 294 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASN F 287 " --> pdb=" O ASN F 279 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR F 277 " --> pdb=" O MET F 289 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 235 through 243 removed outlier: 3.791A pdb=" N ARG G 235 " --> pdb=" O THR G 294 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASN G 287 " --> pdb=" O ASN G 279 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR G 277 " --> pdb=" O MET G 289 " (cutoff:3.500A) 1256 hydrogen bonds defined for protein. 3621 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: 2.58 Time building geometry restraints manager: 2.01 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: 3558 1.46 - 1.58: 9826 1.58 - 1.69: 0 1.69 - 1.81: 147 Bond restraints: 19334 Sorted by residual: bond pdb=" N THR C 7 " pdb=" CA THR C 7 " ideal model delta sigma weight residual 1.457 1.470 -0.012 1.29e-02 6.01e+03 9.31e-01 bond pdb=" N THR F 7 " pdb=" CA THR F 7 " ideal model delta sigma weight residual 1.457 1.470 -0.012 1.29e-02 6.01e+03 9.18e-01 bond pdb=" N THR G 7 " pdb=" CA THR G 7 " ideal model delta sigma weight residual 1.457 1.470 -0.012 1.29e-02 6.01e+03 8.92e-01 bond pdb=" N THR E 7 " pdb=" CA THR E 7 " ideal model delta sigma weight residual 1.457 1.470 -0.012 1.29e-02 6.01e+03 8.90e-01 bond pdb=" N THR D 7 " pdb=" CA THR D 7 " ideal model delta sigma weight residual 1.457 1.470 -0.012 1.29e-02 6.01e+03 8.86e-01 ... (remaining 19329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 25330 1.00 - 2.00: 495 2.00 - 3.00: 130 3.00 - 4.00: 22 4.00 - 5.00: 7 Bond angle restraints: 25984 Sorted by residual: angle pdb=" C THR A 7 " pdb=" CA THR A 7 " pdb=" CB THR A 7 " ideal model delta sigma weight residual 110.42 115.42 -5.00 1.99e+00 2.53e-01 6.31e+00 angle pdb=" C THR D 7 " pdb=" CA THR D 7 " pdb=" CB THR D 7 " ideal model delta sigma weight residual 110.42 115.40 -4.98 1.99e+00 2.53e-01 6.28e+00 angle pdb=" C THR E 7 " pdb=" CA THR E 7 " pdb=" CB THR E 7 " ideal model delta sigma weight residual 110.42 115.38 -4.96 1.99e+00 2.53e-01 6.21e+00 angle pdb=" C THR G 7 " pdb=" CA THR G 7 " pdb=" CB THR G 7 " ideal model delta sigma weight residual 110.42 115.38 -4.96 1.99e+00 2.53e-01 6.20e+00 angle pdb=" C THR C 7 " pdb=" CA THR C 7 " pdb=" CB THR C 7 " ideal model delta sigma weight residual 110.42 115.37 -4.95 1.99e+00 2.53e-01 6.18e+00 ... (remaining 25979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.51: 10028 16.51 - 33.03: 997 33.03 - 49.54: 364 49.54 - 66.05: 70 66.05 - 82.57: 21 Dihedral angle restraints: 11480 sinusoidal: 4760 harmonic: 6720 Sorted by residual: dihedral pdb=" CG ARG E 177 " pdb=" CD ARG E 177 " pdb=" NE ARG E 177 " pdb=" CZ ARG E 177 " ideal model delta sinusoidal sigma weight residual 90.00 42.47 47.53 2 1.50e+01 4.44e-03 1.16e+01 dihedral pdb=" CG ARG G 177 " pdb=" CD ARG G 177 " pdb=" NE ARG G 177 " pdb=" CZ ARG G 177 " ideal model delta sinusoidal sigma weight residual 90.00 42.49 47.51 2 1.50e+01 4.44e-03 1.16e+01 dihedral pdb=" CG ARG D 177 " pdb=" CD ARG D 177 " pdb=" NE ARG D 177 " pdb=" CZ ARG D 177 " ideal model delta sinusoidal sigma weight residual 90.00 42.51 47.49 2 1.50e+01 4.44e-03 1.16e+01 ... (remaining 11477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2075 0.028 - 0.056: 489 0.056 - 0.084: 278 0.084 - 0.112: 100 0.112 - 0.140: 40 Chirality restraints: 2982 Sorted by residual: chirality pdb=" CA ILE E 224 " pdb=" N ILE E 224 " pdb=" C ILE E 224 " pdb=" CB ILE E 224 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA ILE A 224 " pdb=" N ILE A 224 " pdb=" C ILE A 224 " pdb=" CB ILE A 224 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA ILE G 224 " pdb=" N ILE G 224 " pdb=" C ILE G 224 " pdb=" CB ILE G 224 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 2979 not shown) Planarity restraints: 3171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 191 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C ASN E 191 " 0.028 2.00e-02 2.50e+03 pdb=" O ASN E 191 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE E 192 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 191 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C ASN A 191 " 0.028 2.00e-02 2.50e+03 pdb=" O ASN A 191 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE A 192 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 191 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C ASN B 191 " 0.028 2.00e-02 2.50e+03 pdb=" O ASN B 191 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE B 192 " -0.009 2.00e-02 2.50e+03 ... (remaining 3168 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1621 2.74 - 3.28: 19067 3.28 - 3.82: 30930 3.82 - 4.36: 35209 4.36 - 4.90: 62296 Nonbonded interactions: 149123 Sorted by model distance: nonbonded pdb=" O PHE C 6 " pdb=" OG1 THR C 7 " model vdw 2.200 3.040 nonbonded pdb=" O PHE F 6 " pdb=" OG1 THR F 7 " model vdw 2.200 3.040 nonbonded pdb=" O PHE B 6 " pdb=" OG1 THR B 7 " model vdw 2.200 3.040 nonbonded pdb=" O PHE A 6 " pdb=" OG1 THR A 7 " model vdw 2.201 3.040 nonbonded pdb=" O PHE E 6 " pdb=" OG1 THR E 7 " model vdw 2.201 3.040 ... (remaining 149118 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.010 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 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 : 0.002 0.014 19334 Z= 0.091 Angle : 0.380 4.999 25984 Z= 0.222 Chirality : 0.037 0.140 2982 Planarity : 0.002 0.020 3171 Dihedral : 15.342 82.565 7154 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 21.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.35 % Allowed : 16.78 % Favored : 82.87 % 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: 2.69 (0.18), residues: 2310 helix: 3.91 (0.14), residues: 1309 sheet: -0.79 (0.30), residues: 315 loop : -1.40 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 177 TYR 0.007 0.001 TYR A 291 PHE 0.006 0.001 PHE C 209 TRP 0.003 0.000 TRP B 184 HIS 0.002 0.001 HIS G 320 Details of bonding type rmsd covalent geometry : bond 0.00177 (19334) covalent geometry : angle 0.37965 (25984) hydrogen bonds : bond 0.11880 ( 1256) hydrogen bonds : angle 4.75432 ( 3621) *********************** 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 209 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 202 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: B 96 LEU cc_start: 0.9164 (tp) cc_final: 0.8956 (pp) REVERT: B 104 GLN cc_start: 0.7655 (tt0) cc_final: 0.6992 (tp40) REVERT: B 256 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8464 (mt-10) REVERT: C 104 GLN cc_start: 0.7623 (tt0) cc_final: 0.7175 (tp40) REVERT: D 104 GLN cc_start: 0.7666 (tt0) cc_final: 0.7237 (tp40) REVERT: D 146 LEU cc_start: 0.8665 (mm) cc_final: 0.8465 (mm) REVERT: E 104 GLN cc_start: 0.7625 (tt0) cc_final: 0.7377 (tp40) REVERT: G 96 LEU cc_start: 0.9161 (tp) cc_final: 0.8957 (pp) outliers start: 7 outliers final: 1 residues processed: 202 average time/residue: 0.6575 time to fit residues: 147.3462 Evaluate side-chains 175 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 60.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 30.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.157974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.073327 restraints weight = 26830.130| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.42 r_work: 0.2671 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19334 Z= 0.162 Angle : 0.545 6.683 25984 Z= 0.284 Chirality : 0.044 0.166 2982 Planarity : 0.003 0.018 3171 Dihedral : 4.996 59.067 2900 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.10 % Allowed : 15.63 % Favored : 82.27 % 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: 1.98 (0.18), residues: 2310 helix: 3.15 (0.14), residues: 1323 sheet: -0.30 (0.31), residues: 280 loop : -1.78 (0.20), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 177 TYR 0.016 0.001 TYR F 291 PHE 0.011 0.001 PHE C 28 TRP 0.005 0.001 TRP D 29 HIS 0.003 0.001 HIS G 320 Details of bonding type rmsd covalent geometry : bond 0.00382 (19334) covalent geometry : angle 0.54463 (25984) hydrogen bonds : bond 0.04170 ( 1256) hydrogen bonds : angle 4.00323 ( 3621) *********************** 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 202 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 0.752 Fit side-chains REVERT: A 11 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6631 (mp) REVERT: B 11 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6586 (mp) REVERT: B 42 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8506 (m-10) REVERT: C 11 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6843 (mp) REVERT: D 11 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7001 (mp) REVERT: D 256 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8286 (mt-10) REVERT: E 11 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6876 (mp) REVERT: E 198 GLU cc_start: 0.8694 (pt0) cc_final: 0.8486 (pt0) REVERT: E 256 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8264 (mt-10) REVERT: F 11 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6757 (mp) REVERT: G 11 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6505 (mp) outliers start: 42 outliers final: 3 residues processed: 173 average time/residue: 0.6797 time to fit residues: 131.9095 Evaluate side-chains 162 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain G residue 11 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 34 optimal weight: 40.0000 chunk 89 optimal weight: 0.9980 chunk 174 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 26 optimal weight: 0.0570 chunk 138 optimal weight: 10.0000 chunk 154 optimal weight: 0.0970 chunk 19 optimal weight: 3.9990 chunk 146 optimal weight: 0.0020 chunk 161 optimal weight: 3.9990 overall best weight: 0.4304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.161737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.080492 restraints weight = 26792.639| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.35 r_work: 0.2833 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 19334 Z= 0.092 Angle : 0.482 7.124 25984 Z= 0.243 Chirality : 0.041 0.140 2982 Planarity : 0.002 0.020 3171 Dihedral : 4.328 57.154 2898 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.75 % Allowed : 17.13 % Favored : 81.12 % 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: 2.06 (0.18), residues: 2310 helix: 3.13 (0.14), residues: 1330 sheet: 0.60 (0.36), residues: 224 loop : -1.86 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 177 TYR 0.013 0.001 TYR A 291 PHE 0.025 0.001 PHE C 148 TRP 0.004 0.000 TRP B 29 HIS 0.001 0.001 HIS E 43 Details of bonding type rmsd covalent geometry : bond 0.00186 (19334) covalent geometry : angle 0.48163 (25984) hydrogen bonds : bond 0.02856 ( 1256) hydrogen bonds : angle 3.64006 ( 3621) *********************** 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 180 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.677 Fit side-chains REVERT: A 11 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6542 (mp) REVERT: B 11 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6493 (mp) REVERT: D 256 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8334 (mt-10) REVERT: E 198 GLU cc_start: 0.8823 (pt0) cc_final: 0.8613 (pt0) REVERT: E 256 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8282 (mt-10) REVERT: F 11 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6648 (mp) REVERT: G 11 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6389 (mp) REVERT: G 261 MET cc_start: 0.8426 (tmm) cc_final: 0.8207 (tmm) outliers start: 35 outliers final: 5 residues processed: 164 average time/residue: 0.6382 time to fit residues: 118.1106 Evaluate side-chains 154 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain G residue 11 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 171 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 190 optimal weight: 0.6980 chunk 60 optimal weight: 0.3980 chunk 110 optimal weight: 20.0000 chunk 124 optimal weight: 0.9990 chunk 95 optimal weight: 0.0370 chunk 170 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 overall best weight: 1.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.159530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.077411 restraints weight = 26665.739| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.37 r_work: 0.2771 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19334 Z= 0.119 Angle : 0.498 6.863 25984 Z= 0.252 Chirality : 0.042 0.147 2982 Planarity : 0.002 0.021 3171 Dihedral : 4.643 54.636 2898 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.75 % Allowed : 16.98 % Favored : 81.27 % 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: 1.97 (0.17), residues: 2310 helix: 3.09 (0.14), residues: 1330 sheet: 0.52 (0.36), residues: 224 loop : -1.95 (0.18), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 177 TYR 0.015 0.001 TYR F 291 PHE 0.024 0.001 PHE D 148 TRP 0.006 0.001 TRP A 184 HIS 0.004 0.001 HIS E 43 Details of bonding type rmsd covalent geometry : bond 0.00271 (19334) covalent geometry : angle 0.49788 (25984) hydrogen bonds : bond 0.03496 ( 1256) hydrogen bonds : angle 3.71593 ( 3621) *********************** 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 179 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.690 Fit side-chains REVERT: C 11 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6787 (mp) REVERT: C 100 GLN cc_start: 0.7523 (tp40) cc_final: 0.7302 (tp40) REVERT: D 11 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7014 (mp) REVERT: D 256 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8313 (mt-10) REVERT: E 11 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6774 (mp) REVERT: E 198 GLU cc_start: 0.8839 (pt0) cc_final: 0.8625 (pt0) REVERT: E 256 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8337 (mt-10) outliers start: 35 outliers final: 9 residues processed: 159 average time/residue: 0.6585 time to fit residues: 117.8487 Evaluate side-chains 156 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain G residue 113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 230 optimal weight: 0.6980 chunk 71 optimal weight: 8.9990 chunk 214 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 177 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 216 optimal weight: 0.7980 chunk 178 optimal weight: 7.9990 chunk 108 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 272 GLN E 272 GLN F 272 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.154783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.068133 restraints weight = 27073.612| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.47 r_work: 0.2549 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2427 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19334 Z= 0.169 Angle : 0.521 7.148 25984 Z= 0.268 Chirality : 0.043 0.151 2982 Planarity : 0.003 0.022 3171 Dihedral : 4.981 54.442 2898 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.65 % Allowed : 17.58 % Favored : 80.77 % 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: 1.85 (0.17), residues: 2310 helix: 3.02 (0.14), residues: 1323 sheet: 0.46 (0.36), residues: 224 loop : -2.00 (0.18), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 37 TYR 0.020 0.001 TYR F 291 PHE 0.024 0.001 PHE D 148 TRP 0.008 0.001 TRP A 184 HIS 0.004 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00407 (19334) covalent geometry : angle 0.52136 (25984) hydrogen bonds : bond 0.04143 ( 1256) hydrogen bonds : angle 3.86485 ( 3621) *********************** 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 174 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.802 Fit side-chains REVERT: A 11 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6581 (mp) REVERT: C 11 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6857 (mp) REVERT: C 100 GLN cc_start: 0.7595 (tp40) cc_final: 0.7362 (tp40) REVERT: D 11 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7031 (mp) REVERT: E 11 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6758 (mp) REVERT: E 198 GLU cc_start: 0.8778 (pt0) cc_final: 0.8563 (pt0) REVERT: E 256 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8365 (mt-10) REVERT: F 11 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6680 (mp) REVERT: G 333 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8601 (mmm) outliers start: 33 outliers final: 12 residues processed: 158 average time/residue: 0.5760 time to fit residues: 102.4946 Evaluate side-chains 159 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 333 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 3 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 113 optimal weight: 0.0980 chunk 8 optimal weight: 8.9990 chunk 211 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 197 optimal weight: 0.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.155153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.068790 restraints weight = 26962.625| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 2.47 r_work: 0.2560 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19334 Z= 0.146 Angle : 0.512 7.844 25984 Z= 0.260 Chirality : 0.042 0.152 2982 Planarity : 0.003 0.022 3171 Dihedral : 4.581 46.746 2898 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.85 % Allowed : 17.18 % Favored : 80.97 % 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: 1.88 (0.17), residues: 2310 helix: 3.06 (0.13), residues: 1323 sheet: 0.42 (0.35), residues: 224 loop : -1.98 (0.18), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 31 TYR 0.017 0.001 TYR F 291 PHE 0.030 0.001 PHE E 148 TRP 0.006 0.001 TRP A 184 HIS 0.004 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00345 (19334) covalent geometry : angle 0.51196 (25984) hydrogen bonds : bond 0.03717 ( 1256) hydrogen bonds : angle 3.78814 ( 3621) *********************** 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 180 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.597 Fit side-chains REVERT: A 11 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6558 (mp) REVERT: B 11 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6503 (mp) REVERT: C 11 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6803 (mp) REVERT: C 100 GLN cc_start: 0.7574 (tp40) cc_final: 0.7331 (tp40) REVERT: D 11 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7026 (mp) REVERT: D 99 ASN cc_start: 0.8127 (m110) cc_final: 0.7890 (m-40) REVERT: D 333 MET cc_start: 0.8640 (mmm) cc_final: 0.8258 (mmm) REVERT: E 11 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6728 (mp) REVERT: E 140 MET cc_start: 0.3513 (OUTLIER) cc_final: 0.3251 (ttp) REVERT: E 198 GLU cc_start: 0.8811 (pt0) cc_final: 0.8602 (pt0) REVERT: E 256 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8370 (mt-10) REVERT: G 11 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.6307 (mp) REVERT: G 333 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8592 (mmm) outliers start: 37 outliers final: 13 residues processed: 161 average time/residue: 0.6182 time to fit residues: 112.0689 Evaluate side-chains 170 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 333 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 223 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.156326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.069764 restraints weight = 27066.892| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.50 r_work: 0.2584 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2462 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19334 Z= 0.112 Angle : 0.505 13.662 25984 Z= 0.250 Chirality : 0.041 0.149 2982 Planarity : 0.003 0.022 3171 Dihedral : 4.290 48.124 2898 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.75 % Allowed : 17.43 % Favored : 80.82 % 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: 1.95 (0.17), residues: 2310 helix: 3.11 (0.14), residues: 1323 sheet: 0.46 (0.36), residues: 224 loop : -1.96 (0.18), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 31 TYR 0.014 0.001 TYR A 291 PHE 0.008 0.001 PHE F 209 TRP 0.007 0.001 TRP B 29 HIS 0.002 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00251 (19334) covalent geometry : angle 0.50490 (25984) hydrogen bonds : bond 0.03300 ( 1256) hydrogen bonds : angle 3.70075 ( 3621) *********************** 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 182 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 0.707 Fit side-chains REVERT: A 11 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6466 (mp) REVERT: B 11 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6455 (mp) REVERT: B 118 MET cc_start: 0.4622 (tpp) cc_final: 0.4069 (mpp) REVERT: C 11 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6748 (mp) REVERT: D 11 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7005 (mp) REVERT: D 333 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8213 (mmm) REVERT: E 11 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6742 (mp) REVERT: E 140 MET cc_start: 0.3647 (OUTLIER) cc_final: 0.3367 (ttp) REVERT: E 198 GLU cc_start: 0.8849 (pt0) cc_final: 0.8646 (pt0) REVERT: E 256 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8376 (mt-10) REVERT: F 11 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6642 (mp) REVERT: F 333 MET cc_start: 0.8651 (mmm) cc_final: 0.8274 (mmm) REVERT: G 11 LEU cc_start: 0.6613 (OUTLIER) cc_final: 0.6266 (mp) REVERT: G 227 GLU cc_start: 0.8872 (tt0) cc_final: 0.8629 (tt0) outliers start: 35 outliers final: 15 residues processed: 164 average time/residue: 0.6000 time to fit residues: 110.8807 Evaluate side-chains 170 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain G residue 319 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 186 optimal weight: 0.9990 chunk 209 optimal weight: 6.9990 chunk 196 optimal weight: 0.8980 chunk 173 optimal weight: 40.0000 chunk 29 optimal weight: 2.9990 chunk 191 optimal weight: 0.2980 chunk 102 optimal weight: 30.0000 chunk 112 optimal weight: 0.8980 chunk 192 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 198 optimal weight: 0.0050 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.158148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.072109 restraints weight = 27234.141| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.50 r_work: 0.2631 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2510 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 19334 Z= 0.089 Angle : 0.494 13.456 25984 Z= 0.241 Chirality : 0.041 0.145 2982 Planarity : 0.002 0.021 3171 Dihedral : 4.019 54.502 2898 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.30 % Allowed : 17.98 % Favored : 80.72 % 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: 2.02 (0.17), residues: 2310 helix: 3.13 (0.14), residues: 1330 sheet: 0.51 (0.36), residues: 224 loop : -1.91 (0.18), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 177 TYR 0.012 0.001 TYR G 291 PHE 0.031 0.001 PHE F 148 TRP 0.004 0.000 TRP C 29 HIS 0.002 0.000 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00181 (19334) covalent geometry : angle 0.49394 (25984) hydrogen bonds : bond 0.02838 ( 1256) hydrogen bonds : angle 3.58606 ( 3621) *********************** 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 173 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.541 Fit side-chains REVERT: B 11 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6419 (mp) REVERT: C 11 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6702 (mp) REVERT: D 11 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6897 (mp) REVERT: D 333 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8232 (mmm) REVERT: E 11 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6762 (mp) REVERT: E 198 GLU cc_start: 0.8868 (pt0) cc_final: 0.8661 (pt0) REVERT: E 256 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8378 (mt-10) REVERT: F 11 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6566 (mp) REVERT: F 333 MET cc_start: 0.8658 (mmm) cc_final: 0.8313 (mmm) REVERT: G 11 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6218 (mp) outliers start: 26 outliers final: 9 residues processed: 162 average time/residue: 0.5621 time to fit residues: 102.9475 Evaluate side-chains 160 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 113 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 26 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 132 optimal weight: 90.0000 chunk 188 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 113 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 3 optimal weight: 0.4980 chunk 85 optimal weight: 0.9980 chunk 0 optimal weight: 80.0000 chunk 134 optimal weight: 20.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.156943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.070329 restraints weight = 26867.629| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 2.50 r_work: 0.2593 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19334 Z= 0.114 Angle : 0.519 10.775 25984 Z= 0.257 Chirality : 0.042 0.148 2982 Planarity : 0.003 0.024 3171 Dihedral : 4.176 59.189 2898 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.35 % Allowed : 18.13 % Favored : 80.52 % 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: 1.96 (0.17), residues: 2310 helix: 3.09 (0.14), residues: 1330 sheet: 0.53 (0.36), residues: 224 loop : -1.96 (0.18), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 177 TYR 0.014 0.001 TYR F 291 PHE 0.026 0.001 PHE C 148 TRP 0.005 0.001 TRP A 184 HIS 0.002 0.001 HIS G 320 Details of bonding type rmsd covalent geometry : bond 0.00254 (19334) covalent geometry : angle 0.51938 (25984) hydrogen bonds : bond 0.03286 ( 1256) hydrogen bonds : angle 3.67742 ( 3621) *********************** 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 171 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.689 Fit side-chains REVERT: B 11 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6424 (mp) REVERT: C 11 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6698 (mp) REVERT: D 11 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6890 (mp) REVERT: D 333 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8247 (mmm) REVERT: E 11 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6703 (mp) REVERT: E 198 GLU cc_start: 0.8849 (pt0) cc_final: 0.8643 (pt0) REVERT: E 256 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8345 (mt-10) REVERT: F 11 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6508 (mp) REVERT: F 333 MET cc_start: 0.8692 (mmm) cc_final: 0.8225 (mmm) REVERT: G 11 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6327 (mp) REVERT: G 227 GLU cc_start: 0.8838 (tt0) cc_final: 0.8592 (tt0) outliers start: 27 outliers final: 13 residues processed: 161 average time/residue: 0.5870 time to fit residues: 106.8747 Evaluate side-chains 164 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 202 optimal weight: 8.9990 chunk 183 optimal weight: 0.0980 chunk 115 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 201 optimal weight: 7.9990 chunk 125 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.158294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.072209 restraints weight = 26929.972| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.49 r_work: 0.2634 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19334 Z= 0.093 Angle : 0.512 11.544 25984 Z= 0.250 Chirality : 0.041 0.146 2982 Planarity : 0.002 0.023 3171 Dihedral : 3.961 55.977 2898 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.30 % Allowed : 18.28 % Favored : 80.42 % 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: 2.04 (0.17), residues: 2310 helix: 3.13 (0.14), residues: 1330 sheet: 0.55 (0.36), residues: 224 loop : -1.89 (0.18), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 177 TYR 0.012 0.001 TYR A 291 PHE 0.030 0.001 PHE F 148 TRP 0.004 0.000 TRP B 29 HIS 0.001 0.000 HIS G 320 Details of bonding type rmsd covalent geometry : bond 0.00193 (19334) covalent geometry : angle 0.51206 (25984) hydrogen bonds : bond 0.02808 ( 1256) hydrogen bonds : angle 3.58518 ( 3621) ********************** 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 173 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.754 Fit side-chains REVERT: A 11 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6383 (mp) REVERT: B 11 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6381 (mp) REVERT: C 11 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6689 (mp) REVERT: D 11 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6909 (mp) REVERT: D 333 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8256 (mmm) REVERT: E 11 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6686 (mp) REVERT: E 198 GLU cc_start: 0.8852 (pt0) cc_final: 0.8641 (pt0) REVERT: E 256 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8385 (mt-10) REVERT: F 11 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.6360 (mp) REVERT: G 11 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6303 (mp) REVERT: G 227 GLU cc_start: 0.8822 (tt0) cc_final: 0.8582 (tt0) REVERT: G 333 MET cc_start: 0.8939 (tpp) cc_final: 0.8473 (mmm) outliers start: 26 outliers final: 11 residues processed: 164 average time/residue: 0.5915 time to fit residues: 110.4087 Evaluate side-chains 164 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 68 optimal weight: 40.0000 chunk 56 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 228 optimal weight: 0.9980 chunk 176 optimal weight: 8.9990 chunk 181 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 33 optimal weight: 90.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.157680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.072471 restraints weight = 26765.048| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.42 r_work: 0.2649 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19334 Z= 0.128 Angle : 0.542 12.464 25984 Z= 0.269 Chirality : 0.042 0.149 2982 Planarity : 0.003 0.024 3171 Dihedral : 4.225 53.175 2898 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.40 % Allowed : 18.38 % Favored : 80.22 % 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: 1.97 (0.17), residues: 2310 helix: 3.09 (0.14), residues: 1330 sheet: 0.56 (0.36), residues: 224 loop : -1.97 (0.18), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 177 TYR 0.015 0.001 TYR F 291 PHE 0.010 0.001 PHE G 209 TRP 0.007 0.001 TRP A 184 HIS 0.002 0.001 HIS G 320 Details of bonding type rmsd covalent geometry : bond 0.00292 (19334) covalent geometry : angle 0.54234 (25984) hydrogen bonds : bond 0.03444 ( 1256) hydrogen bonds : angle 3.71196 ( 3621) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13321.59 seconds wall clock time: 225 minutes 43.90 seconds (13543.90 seconds total)