Starting phenix.real_space_refine on Wed Mar 4 18:33:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rld_4919/03_2026/6rld_4919.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rld_4919/03_2026/6rld_4919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rld_4919/03_2026/6rld_4919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rld_4919/03_2026/6rld_4919.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rld_4919/03_2026/6rld_4919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rld_4919/03_2026/6rld_4919.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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: 5 Type Number sf(0) Gaussians P 21 5.49 5 S 42 5.16 5 C 10045 2.51 5 N 2492 2.21 5 O 2709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15309 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2025 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 5, 'TRANS': 259} Chain: "B" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2025 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 5, 'TRANS': 259} Chain: "C" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2025 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 5, 'TRANS': 259} Chain: "D" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2025 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 5, 'TRANS': 259} Chain: "E" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2025 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 5, 'TRANS': 259} Chain: "F" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2025 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 5, 'TRANS': 259} Chain: "G" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2025 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 5, 'TRANS': 259} Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.51, per 1000 atoms: 0.23 Number of scatterers: 15309 At special positions: 0 Unit cell: (97.842, 98.9055, 145.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 21 15.00 O 2709 8.00 N 2492 7.00 C 10045 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: 1.42 Conformation dependent library (CDL) restraints added in 517.0 milliseconds 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 9 sheets defined 54.0% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 22 through 58 removed outlier: 3.742A pdb=" N SER A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 90 Processing helix chain 'A' and resid 93 through 111 Processing helix chain 'A' and resid 111 through 127 Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.558A pdb=" N ALA A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 245 through 264 Processing helix chain 'B' and resid 22 through 58 removed outlier: 3.742A pdb=" N SER B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 90 Processing helix chain 'B' and resid 93 through 111 Processing helix chain 'B' and resid 111 through 127 Processing helix chain 'B' and resid 167 through 172 removed outlier: 3.558A pdb=" N ALA B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 245 through 264 Processing helix chain 'C' and resid 22 through 58 removed outlier: 3.741A pdb=" N SER C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 90 Processing helix chain 'C' and resid 93 through 111 Processing helix chain 'C' and resid 111 through 127 Processing helix chain 'C' and resid 167 through 172 removed outlier: 3.558A pdb=" N ALA C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 245 through 264 Processing helix chain 'D' and resid 22 through 58 removed outlier: 3.742A pdb=" N SER D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 90 Processing helix chain 'D' and resid 93 through 111 Processing helix chain 'D' and resid 111 through 127 Processing helix chain 'D' and resid 167 through 172 removed outlier: 3.557A pdb=" N ALA D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 245 through 264 Processing helix chain 'E' and resid 22 through 58 removed outlier: 3.741A pdb=" N SER E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 90 Processing helix chain 'E' and resid 93 through 111 Processing helix chain 'E' and resid 111 through 127 Processing helix chain 'E' and resid 167 through 172 removed outlier: 3.557A pdb=" N ALA E 172 " --> pdb=" O GLY E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 Processing helix chain 'E' and resid 245 through 264 Processing helix chain 'F' and resid 22 through 58 removed outlier: 3.741A pdb=" N SER F 58 " --> pdb=" O ARG F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 90 Processing helix chain 'F' and resid 93 through 111 Processing helix chain 'F' and resid 111 through 127 Processing helix chain 'F' and resid 167 through 172 removed outlier: 3.558A pdb=" N ALA F 172 " --> pdb=" O GLY F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 211 Processing helix chain 'F' and resid 245 through 264 Processing helix chain 'G' and resid 22 through 58 removed outlier: 3.741A pdb=" N SER G 58 " --> pdb=" O ARG G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 90 Processing helix chain 'G' and resid 93 through 111 Processing helix chain 'G' and resid 111 through 127 Processing helix chain 'G' and resid 167 through 172 removed outlier: 3.558A pdb=" N ALA G 172 " --> pdb=" O GLY G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 211 Processing helix chain 'G' and resid 245 through 264 Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 138 removed outlier: 6.925A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 164 " --> pdb=" O ILE G 175 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL G 164 " --> pdb=" O ILE F 175 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 164 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 164 " --> pdb=" O ILE A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192 removed outlier: 6.142A pdb=" N VAL A 236 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU A 225 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG A 238 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL A 223 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N TRP A 240 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET A 221 " --> pdb=" O TRP A 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 278 removed outlier: 8.463A pdb=" N MET B 273 " --> pdb=" O GLN A 272 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ASP A 274 " --> pdb=" O MET B 273 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B 275 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ASN A 276 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N PHE B 277 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS A 278 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N MET C 273 " --> pdb=" O GLN B 272 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASP B 274 " --> pdb=" O MET C 273 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL C 275 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN B 276 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N PHE C 277 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS B 278 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET A 273 " --> pdb=" O ASN G 276 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LYS G 278 " --> pdb=" O MET A 273 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL A 275 " --> pdb=" O LYS G 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192 removed outlier: 6.142A pdb=" N VAL B 236 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU B 225 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ARG B 238 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL B 223 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N TRP B 240 " --> pdb=" O MET B 221 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N MET B 221 " --> pdb=" O TRP B 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 192 removed outlier: 6.142A pdb=" N VAL C 236 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU C 225 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ARG C 238 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL C 223 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N TRP C 240 " --> pdb=" O MET C 221 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET C 221 " --> pdb=" O TRP C 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 183 through 192 removed outlier: 6.142A pdb=" N VAL D 236 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU D 225 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ARG D 238 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL D 223 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N TRP D 240 " --> pdb=" O MET D 221 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET D 221 " --> pdb=" O TRP D 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 183 through 192 removed outlier: 6.142A pdb=" N VAL E 236 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU E 225 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ARG E 238 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL E 223 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N TRP E 240 " --> pdb=" O MET E 221 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET E 221 " --> pdb=" O TRP E 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 183 through 192 removed outlier: 6.142A pdb=" N VAL F 236 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU F 225 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ARG F 238 " --> pdb=" O VAL F 223 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL F 223 " --> pdb=" O ARG F 238 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N TRP F 240 " --> pdb=" O MET F 221 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET F 221 " --> pdb=" O TRP F 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 183 through 192 removed outlier: 6.141A pdb=" N VAL G 236 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU G 225 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ARG G 238 " --> pdb=" O VAL G 223 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL G 223 " --> pdb=" O ARG G 238 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N TRP G 240 " --> pdb=" O MET G 221 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET G 221 " --> pdb=" O TRP G 240 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2925 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: 2.39 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2359 1.31 - 1.43: 3688 1.43 - 1.56: 9291 1.56 - 1.68: 55 1.68 - 1.81: 84 Bond restraints: 15477 Sorted by residual: bond pdb=" C11 PCW F 602 " pdb=" O3 PCW F 602 " ideal model delta sigma weight residual 1.326 1.400 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C11 PCW G 602 " pdb=" O3 PCW G 602 " ideal model delta sigma weight residual 1.326 1.399 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C11 PCW B 602 " pdb=" O3 PCW B 602 " ideal model delta sigma weight residual 1.326 1.399 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C11 PCW E 602 " pdb=" O3 PCW E 602 " ideal model delta sigma weight residual 1.326 1.399 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C11 PCW A 602 " pdb=" O3 PCW A 602 " ideal model delta sigma weight residual 1.326 1.399 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 15472 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 19474 2.65 - 5.31: 1036 5.31 - 7.96: 175 7.96 - 10.62: 49 10.62 - 13.27: 42 Bond angle restraints: 20776 Sorted by residual: angle pdb=" O3P PCW D 603 " pdb=" P PCW D 603 " pdb=" O4P PCW D 603 " ideal model delta sigma weight residual 96.85 110.12 -13.27 3.00e+00 1.11e-01 1.96e+01 angle pdb=" O3P PCW E 603 " pdb=" P PCW E 603 " pdb=" O4P PCW E 603 " ideal model delta sigma weight residual 96.85 110.09 -13.24 3.00e+00 1.11e-01 1.95e+01 angle pdb=" O3P PCW B 603 " pdb=" P PCW B 603 " pdb=" O4P PCW B 603 " ideal model delta sigma weight residual 96.85 110.08 -13.23 3.00e+00 1.11e-01 1.95e+01 angle pdb=" O3P PCW F 603 " pdb=" P PCW F 603 " pdb=" O4P PCW F 603 " ideal model delta sigma weight residual 96.85 110.08 -13.23 3.00e+00 1.11e-01 1.95e+01 angle pdb=" O3P PCW G 603 " pdb=" P PCW G 603 " pdb=" O4P PCW G 603 " ideal model delta sigma weight residual 96.85 110.08 -13.23 3.00e+00 1.11e-01 1.94e+01 ... (remaining 20771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.01: 9100 32.01 - 64.02: 399 64.02 - 96.03: 21 96.03 - 128.05: 21 128.05 - 160.06: 14 Dihedral angle restraints: 9555 sinusoidal: 4235 harmonic: 5320 Sorted by residual: dihedral pdb=" CA ILE E 61 " pdb=" C ILE E 61 " pdb=" N ASP E 62 " pdb=" CA ASP E 62 " ideal model delta harmonic sigma weight residual 180.00 150.04 29.96 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ILE G 61 " pdb=" C ILE G 61 " pdb=" N ASP G 62 " pdb=" CA ASP G 62 " ideal model delta harmonic sigma weight residual 180.00 150.05 29.95 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ILE A 61 " pdb=" C ILE A 61 " pdb=" N ASP A 62 " pdb=" CA ASP A 62 " ideal model delta harmonic sigma weight residual 180.00 150.06 29.94 0 5.00e+00 4.00e-02 3.59e+01 ... (remaining 9552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1520 0.045 - 0.089: 643 0.089 - 0.134: 158 0.134 - 0.179: 49 0.179 - 0.224: 45 Chirality restraints: 2415 Sorted by residual: chirality pdb=" C2 PCW G 601 " pdb=" C1 PCW G 601 " pdb=" C3 PCW G 601 " pdb=" O2 PCW G 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C2 PCW D 601 " pdb=" C1 PCW D 601 " pdb=" C3 PCW D 601 " pdb=" O2 PCW D 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C2 PCW C 601 " pdb=" C1 PCW C 601 " pdb=" C3 PCW C 601 " pdb=" O2 PCW C 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 2412 not shown) Planarity restraints: 2548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 270 " 0.047 5.00e-02 4.00e+02 7.06e-02 7.97e+00 pdb=" N PRO D 271 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 271 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 271 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR G 270 " 0.047 5.00e-02 4.00e+02 7.05e-02 7.94e+00 pdb=" N PRO G 271 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO G 271 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 271 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 270 " 0.047 5.00e-02 4.00e+02 7.03e-02 7.91e+00 pdb=" N PRO C 271 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 271 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 271 " 0.039 5.00e-02 4.00e+02 ... (remaining 2545 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 4180 2.82 - 3.34: 13201 3.34 - 3.86: 24952 3.86 - 4.38: 27209 4.38 - 4.90: 49780 Nonbonded interactions: 119322 Sorted by model distance: nonbonded pdb=" NH2 ARG D 224 " pdb=" OD1 ASP E 252 " model vdw 2.306 3.120 nonbonded pdb=" NH2 ARG E 224 " pdb=" OD1 ASP F 252 " model vdw 2.326 3.120 nonbonded pdb=" NE2 GLN A 272 " pdb=" OD2 ASP G 274 " model vdw 2.330 3.120 nonbonded pdb=" NH2 ARG B 224 " pdb=" OD1 ASP C 252 " model vdw 2.350 3.120 nonbonded pdb=" NH2 ARG F 224 " pdb=" OD1 ASP G 252 " model vdw 2.357 3.120 ... (remaining 119317 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: 0.04 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: 1.490 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.690 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 : 0.009 0.087 15477 Z= 0.415 Angle : 1.376 13.269 20776 Z= 0.602 Chirality : 0.059 0.224 2415 Planarity : 0.006 0.071 2548 Dihedral : 18.759 160.058 6125 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.47 % Allowed : 3.72 % Favored : 95.81 % 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: -3.38 (0.15), residues: 1841 helix: -2.06 (0.12), residues: 987 sheet: -1.77 (0.24), residues: 308 loop : -2.40 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 156 TYR 0.035 0.004 TYR D 75 PHE 0.040 0.005 PHE C 235 TRP 0.018 0.003 TRP F 251 Details of bonding type rmsd covalent geometry : bond 0.00920 (15477) covalent geometry : angle 1.37606 (20776) hydrogen bonds : bond 0.15341 ( 996) hydrogen bonds : angle 6.32347 ( 2925) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 322 time to evaluate : 0.534 Fit side-chains REVERT: A 35 LEU cc_start: 0.8480 (mt) cc_final: 0.8165 (mp) REVERT: A 47 MET cc_start: 0.6802 (mmp) cc_final: 0.6016 (tmm) REVERT: B 227 GLU cc_start: 0.8054 (tt0) cc_final: 0.7779 (tt0) REVERT: C 47 MET cc_start: 0.6811 (mmp) cc_final: 0.6305 (tmm) REVERT: C 273 MET cc_start: 0.8123 (ttm) cc_final: 0.7918 (ttp) REVERT: D 47 MET cc_start: 0.6751 (mmp) cc_final: 0.6133 (tmm) REVERT: D 278 LYS cc_start: 0.8379 (mtmt) cc_final: 0.8136 (mtpt) REVERT: E 47 MET cc_start: 0.6967 (mmp) cc_final: 0.6318 (tmm) REVERT: E 227 GLU cc_start: 0.8119 (tt0) cc_final: 0.7860 (tt0) REVERT: F 47 MET cc_start: 0.7138 (mmp) cc_final: 0.6509 (tmm) REVERT: F 92 GLN cc_start: 0.8455 (tt0) cc_final: 0.8163 (tt0) REVERT: F 149 GLN cc_start: 0.8214 (mt0) cc_final: 0.7998 (mt0) REVERT: G 47 MET cc_start: 0.6976 (mmp) cc_final: 0.6401 (tmm) REVERT: G 135 TYR cc_start: 0.8504 (t80) cc_final: 0.8220 (t80) REVERT: G 247 GLN cc_start: 0.8321 (tp40) cc_final: 0.8064 (tp-100) outliers start: 7 outliers final: 2 residues processed: 322 average time/residue: 0.7421 time to fit residues: 258.5985 Evaluate side-chains 192 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain B residue 68 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 0.0020 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 149 GLN B 149 GLN B 210 GLN C 50 ASN D 50 ASN D 92 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.131681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.094116 restraints weight = 21228.680| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.21 r_work: 0.3052 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15477 Z= 0.126 Angle : 0.530 8.095 20776 Z= 0.281 Chirality : 0.042 0.154 2415 Planarity : 0.005 0.068 2548 Dihedral : 20.811 143.178 2967 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.12 % Allowed : 12.69 % Favored : 84.19 % 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: -1.02 (0.18), residues: 1841 helix: 0.44 (0.15), residues: 994 sheet: -1.36 (0.25), residues: 294 loop : -2.23 (0.23), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 279 TYR 0.008 0.001 TYR G 75 PHE 0.034 0.002 PHE D 68 TRP 0.005 0.001 TRP E 251 Details of bonding type rmsd covalent geometry : bond 0.00280 (15477) covalent geometry : angle 0.52980 (20776) hydrogen bonds : bond 0.03802 ( 996) hydrogen bonds : angle 4.24714 ( 2925) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 252 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.6616 (mmp) cc_final: 0.5851 (tmm) REVERT: A 60 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6926 (ptpp) REVERT: B 181 GLU cc_start: 0.8294 (tp30) cc_final: 0.7916 (tt0) REVERT: B 227 GLU cc_start: 0.8721 (tt0) cc_final: 0.8483 (tt0) REVERT: B 278 LYS cc_start: 0.8457 (mtpt) cc_final: 0.8025 (mttt) REVERT: C 47 MET cc_start: 0.6757 (mmp) cc_final: 0.6145 (tmm) REVERT: C 149 GLN cc_start: 0.8517 (mt0) cc_final: 0.8288 (mp10) REVERT: C 273 MET cc_start: 0.8599 (ttm) cc_final: 0.8336 (ttp) REVERT: D 35 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8331 (mp) REVERT: D 47 MET cc_start: 0.6597 (mmp) cc_final: 0.5914 (tmm) REVERT: D 210 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8306 (mt0) REVERT: D 278 LYS cc_start: 0.8041 (mtmt) cc_final: 0.7814 (mtpt) REVERT: E 47 MET cc_start: 0.6739 (mmp) cc_final: 0.6125 (tmm) REVERT: E 181 GLU cc_start: 0.8506 (tp30) cc_final: 0.7888 (tt0) REVERT: E 210 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8423 (mt0) REVERT: E 227 GLU cc_start: 0.8714 (tt0) cc_final: 0.8432 (tt0) REVERT: F 47 MET cc_start: 0.6877 (mmp) cc_final: 0.6314 (tmm) REVERT: F 92 GLN cc_start: 0.8301 (tt0) cc_final: 0.7969 (tt0) REVERT: F 149 GLN cc_start: 0.8574 (mt0) cc_final: 0.8322 (mt0) REVERT: F 227 GLU cc_start: 0.8623 (tt0) cc_final: 0.8373 (tt0) REVERT: G 47 MET cc_start: 0.6924 (mmp) cc_final: 0.6196 (tmm) REVERT: G 72 LEU cc_start: 0.7401 (tp) cc_final: 0.7197 (tt) REVERT: G 135 TYR cc_start: 0.8786 (t80) cc_final: 0.8479 (t80) REVERT: G 221 MET cc_start: 0.8869 (mtm) cc_final: 0.8644 (mtm) REVERT: G 278 LYS cc_start: 0.8474 (mtpt) cc_final: 0.8008 (mtmt) outliers start: 47 outliers final: 11 residues processed: 282 average time/residue: 0.6737 time to fit residues: 207.2135 Evaluate side-chains 205 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 237 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 82 optimal weight: 7.9990 chunk 169 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 112 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 149 GLN B 92 GLN B 149 GLN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN D 92 GLN E 92 GLN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN G 92 GLN G 149 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.129743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.091648 restraints weight = 21352.376| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.20 r_work: 0.3010 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15477 Z= 0.138 Angle : 0.494 7.599 20776 Z= 0.264 Chirality : 0.041 0.154 2415 Planarity : 0.004 0.062 2548 Dihedral : 19.506 149.393 2961 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.79 % Allowed : 16.61 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.19), residues: 1841 helix: 1.59 (0.16), residues: 987 sheet: -0.84 (0.25), residues: 308 loop : -1.95 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 279 TYR 0.008 0.001 TYR B 75 PHE 0.029 0.002 PHE G 68 TRP 0.003 0.001 TRP C 240 Details of bonding type rmsd covalent geometry : bond 0.00323 (15477) covalent geometry : angle 0.49351 (20776) hydrogen bonds : bond 0.03636 ( 996) hydrogen bonds : angle 4.02945 ( 2925) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 208 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.6594 (mmp) cc_final: 0.5751 (tmt) REVERT: A 60 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.6922 (ptpp) REVERT: A 181 GLU cc_start: 0.8284 (tp30) cc_final: 0.7636 (tt0) REVERT: B 134 GLU cc_start: 0.8575 (tt0) cc_final: 0.8336 (tt0) REVERT: B 181 GLU cc_start: 0.8260 (tp30) cc_final: 0.7829 (tt0) REVERT: B 227 GLU cc_start: 0.8663 (tt0) cc_final: 0.8431 (tt0) REVERT: B 278 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8002 (mttt) REVERT: C 47 MET cc_start: 0.6781 (mmp) cc_final: 0.6052 (tmm) REVERT: C 273 MET cc_start: 0.8577 (ttm) cc_final: 0.8329 (ttp) REVERT: D 47 MET cc_start: 0.6583 (mmp) cc_final: 0.5998 (tmm) REVERT: D 126 MET cc_start: 0.7866 (tmt) cc_final: 0.7644 (tmt) REVERT: D 169 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.9119 (ttmm) REVERT: D 210 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8279 (mt0) REVERT: D 227 GLU cc_start: 0.8684 (tt0) cc_final: 0.8446 (tt0) REVERT: E 47 MET cc_start: 0.6679 (mmp) cc_final: 0.6074 (tmm) REVERT: E 60 LYS cc_start: 0.7388 (ptmm) cc_final: 0.7052 (ptpp) REVERT: E 181 GLU cc_start: 0.8523 (tp30) cc_final: 0.7912 (tt0) REVERT: E 210 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8303 (mt0) REVERT: E 227 GLU cc_start: 0.8670 (tt0) cc_final: 0.8367 (tt0) REVERT: F 47 MET cc_start: 0.6760 (mmp) cc_final: 0.6138 (tmm) REVERT: F 92 GLN cc_start: 0.8306 (tt0) cc_final: 0.7989 (tt0) REVERT: F 227 GLU cc_start: 0.8636 (tt0) cc_final: 0.8393 (tt0) REVERT: G 47 MET cc_start: 0.6876 (mmp) cc_final: 0.6164 (tmm) REVERT: G 72 LEU cc_start: 0.7395 (tp) cc_final: 0.7144 (tt) outliers start: 57 outliers final: 16 residues processed: 243 average time/residue: 0.6647 time to fit residues: 176.9108 Evaluate side-chains 212 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 237 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 149 GLN B 53 ASN C 92 GLN D 92 GLN E 92 GLN G 92 GLN G 149 GLN G 210 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.130539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.092703 restraints weight = 21305.250| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.19 r_work: 0.3023 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15477 Z= 0.114 Angle : 0.470 9.652 20776 Z= 0.248 Chirality : 0.041 0.146 2415 Planarity : 0.004 0.062 2548 Dihedral : 18.629 152.475 2961 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.25 % Allowed : 17.74 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.19), residues: 1841 helix: 2.15 (0.16), residues: 987 sheet: -0.69 (0.26), residues: 294 loop : -1.50 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 279 TYR 0.006 0.001 TYR B 75 PHE 0.025 0.002 PHE E 68 TRP 0.002 0.000 TRP D 16 Details of bonding type rmsd covalent geometry : bond 0.00259 (15477) covalent geometry : angle 0.46974 (20776) hydrogen bonds : bond 0.03331 ( 996) hydrogen bonds : angle 3.83499 ( 2925) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 215 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.6477 (mmp) cc_final: 0.5806 (tmt) REVERT: A 159 ASP cc_start: 0.8412 (t0) cc_final: 0.8195 (t0) REVERT: A 181 GLU cc_start: 0.8345 (tp30) cc_final: 0.7726 (tt0) REVERT: B 68 PHE cc_start: 0.6202 (OUTLIER) cc_final: 0.5891 (OUTLIER) REVERT: B 159 ASP cc_start: 0.8238 (t0) cc_final: 0.8023 (t0) REVERT: B 171 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8673 (mp) REVERT: B 181 GLU cc_start: 0.8275 (tp30) cc_final: 0.7881 (tt0) REVERT: B 227 GLU cc_start: 0.8721 (tt0) cc_final: 0.8508 (tt0) REVERT: B 253 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8346 (t) REVERT: B 277 PHE cc_start: 0.8093 (t80) cc_final: 0.7004 (t80) REVERT: B 278 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8124 (mttt) REVERT: C 47 MET cc_start: 0.6811 (mmp) cc_final: 0.6033 (tmt) REVERT: C 149 GLN cc_start: 0.8514 (mt0) cc_final: 0.7983 (mm110) REVERT: C 155 MET cc_start: 0.8986 (ptt) cc_final: 0.8702 (ptt) REVERT: C 273 MET cc_start: 0.8612 (ttm) cc_final: 0.8364 (ttp) REVERT: C 277 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7801 (m-80) REVERT: D 47 MET cc_start: 0.6648 (mmp) cc_final: 0.5945 (tmm) REVERT: D 126 MET cc_start: 0.7923 (tmt) cc_final: 0.7683 (tmt) REVERT: D 181 GLU cc_start: 0.8348 (tp30) cc_final: 0.7797 (tt0) REVERT: D 227 GLU cc_start: 0.8690 (tt0) cc_final: 0.8465 (tt0) REVERT: D 253 VAL cc_start: 0.8658 (OUTLIER) cc_final: 0.8427 (t) REVERT: E 47 MET cc_start: 0.6751 (mmp) cc_final: 0.6143 (tmt) REVERT: E 60 LYS cc_start: 0.7343 (ptmm) cc_final: 0.7074 (ptpp) REVERT: E 227 GLU cc_start: 0.8694 (tt0) cc_final: 0.8402 (tt0) REVERT: E 278 LYS cc_start: 0.7972 (mtpt) cc_final: 0.7556 (mtmt) REVERT: F 47 MET cc_start: 0.7002 (mmp) cc_final: 0.6273 (tmm) REVERT: F 92 GLN cc_start: 0.8183 (tt0) cc_final: 0.7848 (tt0) REVERT: F 105 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8174 (tt) REVERT: F 227 GLU cc_start: 0.8626 (tt0) cc_final: 0.8399 (tt0) REVERT: F 253 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.8340 (t) REVERT: F 273 MET cc_start: 0.8446 (ttm) cc_final: 0.8093 (ttp) REVERT: G 47 MET cc_start: 0.6772 (mmp) cc_final: 0.6186 (tmm) REVERT: G 72 LEU cc_start: 0.7435 (tp) cc_final: 0.7163 (tt) REVERT: G 278 LYS cc_start: 0.8357 (mtpt) cc_final: 0.7872 (mtmt) outliers start: 64 outliers final: 15 residues processed: 262 average time/residue: 0.6384 time to fit residues: 184.0946 Evaluate side-chains 218 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 237 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 0.0050 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 149 GLN B 203 GLN C 92 GLN D 53 ASN D 92 GLN E 92 GLN G 149 GLN G 210 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.129069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.091238 restraints weight = 21853.646| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.30 r_work: 0.2973 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15477 Z= 0.133 Angle : 0.477 7.744 20776 Z= 0.251 Chirality : 0.041 0.148 2415 Planarity : 0.004 0.059 2548 Dihedral : 18.368 154.420 2961 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.59 % Allowed : 19.67 % Favored : 76.74 % 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: 1.18 (0.19), residues: 1841 helix: 2.38 (0.16), residues: 987 sheet: -0.45 (0.26), residues: 308 loop : -1.52 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 279 TYR 0.005 0.001 TYR B 75 PHE 0.023 0.002 PHE A 68 TRP 0.002 0.000 TRP D 16 Details of bonding type rmsd covalent geometry : bond 0.00314 (15477) covalent geometry : angle 0.47716 (20776) hydrogen bonds : bond 0.03437 ( 996) hydrogen bonds : angle 3.85531 ( 2925) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 205 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.6376 (mmp) cc_final: 0.5690 (tmt) REVERT: A 60 LYS cc_start: 0.7425 (ptmm) cc_final: 0.6991 (ptpp) REVERT: A 149 GLN cc_start: 0.8296 (mt0) cc_final: 0.7780 (mm110) REVERT: A 159 ASP cc_start: 0.8399 (t0) cc_final: 0.8128 (t0) REVERT: A 161 LYS cc_start: 0.8827 (ptpt) cc_final: 0.8317 (mtmm) REVERT: A 203 GLN cc_start: 0.8024 (tt0) cc_final: 0.7664 (tp40) REVERT: B 68 PHE cc_start: 0.6262 (OUTLIER) cc_final: 0.5943 (OUTLIER) REVERT: B 159 ASP cc_start: 0.8210 (t0) cc_final: 0.7926 (t0) REVERT: B 171 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8528 (mp) REVERT: B 181 GLU cc_start: 0.8358 (tp30) cc_final: 0.7690 (tt0) REVERT: B 227 GLU cc_start: 0.8733 (tt0) cc_final: 0.8523 (tt0) REVERT: B 253 VAL cc_start: 0.8449 (OUTLIER) cc_final: 0.8248 (t) REVERT: B 278 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8009 (mttt) REVERT: C 47 MET cc_start: 0.6670 (mmp) cc_final: 0.5905 (tmt) REVERT: C 149 GLN cc_start: 0.8477 (mt0) cc_final: 0.7921 (mm110) REVERT: C 155 MET cc_start: 0.9058 (ptt) cc_final: 0.8812 (ptt) REVERT: C 181 GLU cc_start: 0.8531 (tp30) cc_final: 0.7735 (mp0) REVERT: C 273 MET cc_start: 0.8495 (ttm) cc_final: 0.8233 (ttp) REVERT: D 35 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8210 (mp) REVERT: D 47 MET cc_start: 0.6772 (mmp) cc_final: 0.6062 (tmm) REVERT: D 126 MET cc_start: 0.7966 (tmt) cc_final: 0.7689 (tmt) REVERT: D 227 GLU cc_start: 0.8693 (tt0) cc_final: 0.8438 (tt0) REVERT: D 253 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8327 (t) REVERT: E 47 MET cc_start: 0.6654 (mmp) cc_final: 0.6043 (tmt) REVERT: E 60 LYS cc_start: 0.7246 (ptmm) cc_final: 0.6989 (ptpp) REVERT: E 181 GLU cc_start: 0.8554 (tp30) cc_final: 0.7797 (tt0) REVERT: E 227 GLU cc_start: 0.8703 (tt0) cc_final: 0.8367 (tt0) REVERT: F 47 MET cc_start: 0.6947 (mmp) cc_final: 0.6215 (tmm) REVERT: F 92 GLN cc_start: 0.8232 (tt0) cc_final: 0.7922 (tt0) REVERT: F 105 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8087 (tt) REVERT: F 155 MET cc_start: 0.8771 (ptt) cc_final: 0.8347 (ptm) REVERT: F 253 VAL cc_start: 0.8439 (OUTLIER) cc_final: 0.8232 (t) REVERT: F 273 MET cc_start: 0.8351 (ttm) cc_final: 0.8048 (ttp) REVERT: G 47 MET cc_start: 0.6716 (mmp) cc_final: 0.6127 (tmm) REVERT: G 247 GLN cc_start: 0.8585 (tp40) cc_final: 0.8305 (tp-100) REVERT: G 278 LYS cc_start: 0.8391 (mtpt) cc_final: 0.7921 (mtmt) outliers start: 54 outliers final: 17 residues processed: 240 average time/residue: 0.6786 time to fit residues: 178.0816 Evaluate side-chains 215 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 154 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 149 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 56 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN C 53 ASN C 92 GLN D 92 GLN E 92 GLN F 53 ASN G 149 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.129745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.091709 restraints weight = 21225.183| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.18 r_work: 0.3024 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15477 Z= 0.119 Angle : 0.472 8.959 20776 Z= 0.248 Chirality : 0.040 0.144 2415 Planarity : 0.004 0.060 2548 Dihedral : 17.957 156.301 2961 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.79 % Allowed : 20.86 % Favored : 76.35 % 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: 1.39 (0.19), residues: 1841 helix: 2.53 (0.16), residues: 994 sheet: -0.35 (0.26), residues: 308 loop : -1.44 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 279 TYR 0.004 0.001 TYR G 75 PHE 0.020 0.002 PHE A 68 TRP 0.002 0.000 TRP D 16 Details of bonding type rmsd covalent geometry : bond 0.00274 (15477) covalent geometry : angle 0.47218 (20776) hydrogen bonds : bond 0.03343 ( 996) hydrogen bonds : angle 3.78006 ( 2925) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 203 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.6671 (mmp) cc_final: 0.5815 (tmm) REVERT: A 60 LYS cc_start: 0.7272 (ptmm) cc_final: 0.6861 (ptpp) REVERT: A 149 GLN cc_start: 0.8344 (mt0) cc_final: 0.7893 (mm110) REVERT: A 159 ASP cc_start: 0.8403 (t0) cc_final: 0.8191 (t0) REVERT: A 161 LYS cc_start: 0.8911 (ptpt) cc_final: 0.8441 (mtmm) REVERT: A 181 GLU cc_start: 0.8359 (tp30) cc_final: 0.7755 (tt0) REVERT: A 203 GLN cc_start: 0.8020 (tt0) cc_final: 0.7771 (tp40) REVERT: B 25 LEU cc_start: 0.8068 (tt) cc_final: 0.7815 (pp) REVERT: B 47 MET cc_start: 0.6897 (mmp) cc_final: 0.6321 (tmm) REVERT: B 68 PHE cc_start: 0.6339 (OUTLIER) cc_final: 0.5996 (OUTLIER) REVERT: B 159 ASP cc_start: 0.8219 (t0) cc_final: 0.7934 (t0) REVERT: B 181 GLU cc_start: 0.8247 (tp30) cc_final: 0.7734 (tt0) REVERT: B 227 GLU cc_start: 0.8703 (tt0) cc_final: 0.8501 (tt0) REVERT: B 278 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8094 (mttt) REVERT: C 47 MET cc_start: 0.6759 (mmp) cc_final: 0.5993 (tmt) REVERT: C 149 GLN cc_start: 0.8443 (mt0) cc_final: 0.7990 (mm-40) REVERT: C 155 MET cc_start: 0.8988 (ptt) cc_final: 0.8748 (ptt) REVERT: C 273 MET cc_start: 0.8548 (ttm) cc_final: 0.8283 (ttp) REVERT: D 35 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8313 (mp) REVERT: D 47 MET cc_start: 0.6811 (mmp) cc_final: 0.6081 (tmm) REVERT: D 126 MET cc_start: 0.7918 (tmt) cc_final: 0.7649 (tmt) REVERT: D 181 GLU cc_start: 0.8317 (tp30) cc_final: 0.7745 (tt0) REVERT: D 227 GLU cc_start: 0.8684 (tt0) cc_final: 0.8446 (tt0) REVERT: E 47 MET cc_start: 0.6678 (mmp) cc_final: 0.6163 (tmt) REVERT: E 60 LYS cc_start: 0.7258 (ptmm) cc_final: 0.6908 (ptpp) REVERT: E 227 GLU cc_start: 0.8668 (tt0) cc_final: 0.8347 (tt0) REVERT: F 47 MET cc_start: 0.7069 (mmp) cc_final: 0.6351 (tmm) REVERT: F 92 GLN cc_start: 0.8220 (tt0) cc_final: 0.7907 (tt0) REVERT: F 105 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8145 (tt) REVERT: F 149 GLN cc_start: 0.8441 (mt0) cc_final: 0.8170 (mm110) REVERT: F 155 MET cc_start: 0.8748 (ptt) cc_final: 0.8379 (ptm) REVERT: F 181 GLU cc_start: 0.8356 (tp30) cc_final: 0.8042 (mt-10) REVERT: F 203 GLN cc_start: 0.8169 (tt0) cc_final: 0.7916 (tp40) REVERT: F 210 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8262 (mt0) REVERT: F 273 MET cc_start: 0.8371 (ttm) cc_final: 0.8054 (ttp) REVERT: G 47 MET cc_start: 0.6775 (mmp) cc_final: 0.6145 (tmm) REVERT: G 247 GLN cc_start: 0.8613 (tp40) cc_final: 0.8354 (tp-100) REVERT: G 278 LYS cc_start: 0.8433 (mtpt) cc_final: 0.7976 (mtmt) outliers start: 42 outliers final: 17 residues processed: 235 average time/residue: 0.6995 time to fit residues: 179.2341 Evaluate side-chains 210 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 237 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 168 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 149 optimal weight: 0.1980 chunk 31 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 92 GLN B 203 GLN C 92 GLN D 92 GLN E 92 GLN G 149 GLN G 210 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.129699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.091607 restraints weight = 21050.184| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.17 r_work: 0.3007 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15477 Z= 0.119 Angle : 0.465 8.929 20776 Z= 0.244 Chirality : 0.040 0.144 2415 Planarity : 0.004 0.059 2548 Dihedral : 17.615 159.027 2961 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.12 % Allowed : 21.13 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.59 (0.20), residues: 1841 helix: 2.66 (0.16), residues: 987 sheet: -0.34 (0.27), residues: 294 loop : -1.16 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 279 TYR 0.005 0.001 TYR D 250 PHE 0.017 0.002 PHE A 68 TRP 0.002 0.000 TRP E 16 Details of bonding type rmsd covalent geometry : bond 0.00272 (15477) covalent geometry : angle 0.46506 (20776) hydrogen bonds : bond 0.03325 ( 996) hydrogen bonds : angle 3.75763 ( 2925) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.6689 (mmp) cc_final: 0.5784 (tmt) REVERT: A 60 LYS cc_start: 0.7423 (ptmm) cc_final: 0.7003 (ptpp) REVERT: A 149 GLN cc_start: 0.8428 (mt0) cc_final: 0.7957 (mm110) REVERT: A 155 MET cc_start: 0.9097 (ptt) cc_final: 0.8798 (ptt) REVERT: A 181 GLU cc_start: 0.8527 (tp30) cc_final: 0.7827 (tt0) REVERT: A 203 GLN cc_start: 0.8234 (tt0) cc_final: 0.7954 (tp40) REVERT: B 25 LEU cc_start: 0.7962 (tt) cc_final: 0.7744 (pp) REVERT: B 47 MET cc_start: 0.6937 (mmp) cc_final: 0.6287 (tmm) REVERT: B 68 PHE cc_start: 0.6253 (OUTLIER) cc_final: 0.5917 (OUTLIER) REVERT: B 149 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8063 (mm110) REVERT: B 159 ASP cc_start: 0.8577 (t0) cc_final: 0.8285 (t0) REVERT: B 181 GLU cc_start: 0.8453 (tp30) cc_final: 0.7815 (tt0) REVERT: B 278 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8158 (mttt) REVERT: C 47 MET cc_start: 0.6891 (mmp) cc_final: 0.6043 (tmt) REVERT: C 149 GLN cc_start: 0.8536 (mt0) cc_final: 0.8044 (mm-40) REVERT: C 155 MET cc_start: 0.9139 (ptt) cc_final: 0.8920 (ptt) REVERT: C 159 ASP cc_start: 0.8629 (t0) cc_final: 0.8415 (t0) REVERT: C 181 GLU cc_start: 0.8595 (tp30) cc_final: 0.7936 (mp0) REVERT: C 203 GLN cc_start: 0.8393 (tt0) cc_final: 0.8023 (tp40) REVERT: C 273 MET cc_start: 0.8742 (ttm) cc_final: 0.8496 (ttp) REVERT: D 47 MET cc_start: 0.6802 (mmp) cc_final: 0.6062 (tmm) REVERT: D 126 MET cc_start: 0.8110 (tmt) cc_final: 0.7841 (tmt) REVERT: D 149 GLN cc_start: 0.8565 (mt0) cc_final: 0.8102 (mm110) REVERT: D 181 GLU cc_start: 0.8539 (tp30) cc_final: 0.7885 (tt0) REVERT: D 203 GLN cc_start: 0.8363 (tm-30) cc_final: 0.7988 (tp40) REVERT: D 227 GLU cc_start: 0.8905 (tt0) cc_final: 0.8690 (tt0) REVERT: E 47 MET cc_start: 0.6694 (mmp) cc_final: 0.6097 (tmt) REVERT: E 60 LYS cc_start: 0.7338 (ptmm) cc_final: 0.6955 (ptpp) REVERT: E 181 GLU cc_start: 0.8615 (tp30) cc_final: 0.7967 (tt0) REVERT: E 203 GLN cc_start: 0.8371 (tt0) cc_final: 0.8118 (tp40) REVERT: E 227 GLU cc_start: 0.8865 (tt0) cc_final: 0.8578 (tt0) REVERT: F 47 MET cc_start: 0.7096 (mmp) cc_final: 0.6327 (tmm) REVERT: F 92 GLN cc_start: 0.8235 (tt0) cc_final: 0.7945 (tt0) REVERT: F 105 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8189 (tt) REVERT: F 149 GLN cc_start: 0.8553 (mt0) cc_final: 0.8260 (mm110) REVERT: F 155 MET cc_start: 0.8901 (ptt) cc_final: 0.8575 (ptm) REVERT: F 181 GLU cc_start: 0.8549 (tp30) cc_final: 0.7962 (mp0) REVERT: F 194 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.8425 (m-80) REVERT: F 203 GLN cc_start: 0.8395 (tt0) cc_final: 0.8090 (tp40) REVERT: F 210 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8468 (mt0) REVERT: F 273 MET cc_start: 0.8570 (ttm) cc_final: 0.8301 (ttp) REVERT: G 47 MET cc_start: 0.6817 (mmp) cc_final: 0.6122 (tmm) REVERT: G 60 LYS cc_start: 0.7547 (ptmm) cc_final: 0.7113 (ptpp) REVERT: G 149 GLN cc_start: 0.8591 (mt0) cc_final: 0.8066 (mm110) REVERT: G 203 GLN cc_start: 0.8320 (tm-30) cc_final: 0.8082 (tp40) REVERT: G 247 GLN cc_start: 0.8800 (tp40) cc_final: 0.8518 (tp-100) REVERT: G 278 LYS cc_start: 0.8428 (mtpt) cc_final: 0.7947 (mtmt) outliers start: 47 outliers final: 17 residues processed: 248 average time/residue: 0.6977 time to fit residues: 188.6626 Evaluate side-chains 215 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 194 TYR Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 237 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 0.6980 chunk 161 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 143 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 150 optimal weight: 0.0070 chunk 54 optimal weight: 0.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN C 92 GLN D 92 GLN E 92 GLN G 210 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.130684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.092537 restraints weight = 21278.760| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.19 r_work: 0.3018 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15477 Z= 0.107 Angle : 0.479 10.472 20776 Z= 0.244 Chirality : 0.040 0.141 2415 Planarity : 0.004 0.059 2548 Dihedral : 17.188 161.069 2961 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.46 % Allowed : 22.33 % Favored : 75.22 % 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: 1.75 (0.20), residues: 1841 helix: 2.77 (0.16), residues: 987 sheet: -0.27 (0.27), residues: 294 loop : -1.06 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 46 TYR 0.006 0.001 TYR D 135 PHE 0.016 0.002 PHE C 68 TRP 0.002 0.000 TRP C 16 Details of bonding type rmsd covalent geometry : bond 0.00238 (15477) covalent geometry : angle 0.47871 (20776) hydrogen bonds : bond 0.03213 ( 996) hydrogen bonds : angle 3.71586 ( 2925) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.6644 (mmp) cc_final: 0.5877 (tmt) REVERT: A 60 LYS cc_start: 0.7201 (ptmm) cc_final: 0.6833 (ptpp) REVERT: A 149 GLN cc_start: 0.8343 (mt0) cc_final: 0.7907 (mm110) REVERT: A 155 MET cc_start: 0.8995 (ptt) cc_final: 0.8718 (ptt) REVERT: A 161 LYS cc_start: 0.8936 (ptpt) cc_final: 0.8579 (mtmp) REVERT: A 181 GLU cc_start: 0.8401 (tp30) cc_final: 0.7805 (tt0) REVERT: A 278 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8101 (mtpt) REVERT: B 47 MET cc_start: 0.6891 (mmp) cc_final: 0.6298 (tmm) REVERT: B 68 PHE cc_start: 0.6363 (OUTLIER) cc_final: 0.6030 (OUTLIER) REVERT: B 149 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7988 (mm110) REVERT: B 159 ASP cc_start: 0.8315 (t0) cc_final: 0.7995 (t0) REVERT: B 278 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.7968 (mttt) REVERT: C 47 MET cc_start: 0.6805 (mmp) cc_final: 0.6056 (tmt) REVERT: C 149 GLN cc_start: 0.8451 (mt0) cc_final: 0.7996 (mm110) REVERT: C 159 ASP cc_start: 0.8311 (t0) cc_final: 0.8083 (t0) REVERT: C 181 GLU cc_start: 0.8426 (tp30) cc_final: 0.7743 (mp0) REVERT: C 203 GLN cc_start: 0.8166 (tt0) cc_final: 0.7920 (tp40) REVERT: C 273 MET cc_start: 0.8566 (ttm) cc_final: 0.8286 (ttp) REVERT: D 47 MET cc_start: 0.6853 (mmp) cc_final: 0.6113 (tmm) REVERT: D 126 MET cc_start: 0.7906 (tmt) cc_final: 0.7644 (tmt) REVERT: D 149 GLN cc_start: 0.8465 (mt0) cc_final: 0.8062 (mm110) REVERT: D 181 GLU cc_start: 0.8358 (tp30) cc_final: 0.7799 (tt0) REVERT: D 203 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7828 (tp-100) REVERT: D 227 GLU cc_start: 0.8675 (tt0) cc_final: 0.8423 (tt0) REVERT: E 47 MET cc_start: 0.6614 (mmp) cc_final: 0.6090 (tmt) REVERT: E 60 LYS cc_start: 0.7157 (ptmm) cc_final: 0.6907 (ptpp) REVERT: E 159 ASP cc_start: 0.8394 (t0) cc_final: 0.8193 (t0) REVERT: E 181 GLU cc_start: 0.8423 (tp30) cc_final: 0.7797 (tt0) REVERT: E 227 GLU cc_start: 0.8671 (tt0) cc_final: 0.8461 (tt0) REVERT: F 47 MET cc_start: 0.7071 (mmp) cc_final: 0.6355 (tmm) REVERT: F 92 GLN cc_start: 0.8235 (tt0) cc_final: 0.7920 (tt0) REVERT: F 105 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8147 (tt) REVERT: F 149 GLN cc_start: 0.8516 (mt0) cc_final: 0.8257 (mm110) REVERT: F 155 MET cc_start: 0.8729 (ptt) cc_final: 0.8400 (ptm) REVERT: F 181 GLU cc_start: 0.8337 (tp30) cc_final: 0.7787 (mp0) REVERT: F 194 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.8422 (m-80) REVERT: F 273 MET cc_start: 0.8360 (ttm) cc_final: 0.8028 (ttp) REVERT: G 47 MET cc_start: 0.6810 (mmp) cc_final: 0.6134 (tmm) REVERT: G 60 LYS cc_start: 0.7420 (ptmm) cc_final: 0.7023 (ptpp) REVERT: G 149 GLN cc_start: 0.8470 (mt0) cc_final: 0.8008 (mm110) REVERT: G 247 GLN cc_start: 0.8602 (tp40) cc_final: 0.8314 (tp-100) REVERT: G 278 LYS cc_start: 0.8393 (mtpt) cc_final: 0.7895 (mtmt) outliers start: 37 outliers final: 17 residues processed: 226 average time/residue: 0.7330 time to fit residues: 179.7988 Evaluate side-chains 212 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 194 TYR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 154 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 47 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN B 203 GLN B 234 ASN C 92 GLN D 92 GLN E 92 GLN F 207 ASN G 53 ASN G 92 GLN G 207 ASN G 210 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.130014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.091812 restraints weight = 21288.588| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.20 r_work: 0.3010 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15477 Z= 0.116 Angle : 0.488 10.231 20776 Z= 0.247 Chirality : 0.040 0.145 2415 Planarity : 0.004 0.059 2548 Dihedral : 16.965 162.621 2961 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.26 % Allowed : 22.66 % Favored : 75.08 % 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: 1.80 (0.20), residues: 1841 helix: 2.76 (0.16), residues: 994 sheet: -0.23 (0.27), residues: 294 loop : -0.98 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 46 TYR 0.014 0.001 TYR E 27 PHE 0.016 0.002 PHE C 68 TRP 0.002 0.000 TRP A 16 Details of bonding type rmsd covalent geometry : bond 0.00264 (15477) covalent geometry : angle 0.48806 (20776) hydrogen bonds : bond 0.03276 ( 996) hydrogen bonds : angle 3.74171 ( 2925) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 198 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.6630 (mmp) cc_final: 0.5777 (tmm) REVERT: A 60 LYS cc_start: 0.7169 (ptmm) cc_final: 0.6877 (ptpp) REVERT: A 149 GLN cc_start: 0.8332 (mt0) cc_final: 0.7916 (mm110) REVERT: A 155 MET cc_start: 0.9017 (ptt) cc_final: 0.8725 (ptt) REVERT: A 161 LYS cc_start: 0.8903 (ptpt) cc_final: 0.8587 (mtmp) REVERT: A 181 GLU cc_start: 0.8353 (tp30) cc_final: 0.7703 (tt0) REVERT: A 278 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8093 (mtpt) REVERT: B 47 MET cc_start: 0.6909 (mmp) cc_final: 0.6305 (tmm) REVERT: B 68 PHE cc_start: 0.6369 (OUTLIER) cc_final: 0.6027 (OUTLIER) REVERT: B 159 ASP cc_start: 0.8331 (t0) cc_final: 0.8030 (t0) REVERT: B 171 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8516 (mp) REVERT: B 278 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8310 (mtpt) REVERT: C 47 MET cc_start: 0.6762 (mmp) cc_final: 0.6053 (tmm) REVERT: C 149 GLN cc_start: 0.8451 (mt0) cc_final: 0.8005 (mm110) REVERT: C 159 ASP cc_start: 0.8307 (t0) cc_final: 0.8070 (t0) REVERT: C 181 GLU cc_start: 0.8427 (tp30) cc_final: 0.7719 (mp0) REVERT: C 203 GLN cc_start: 0.8173 (tt0) cc_final: 0.7894 (tp40) REVERT: C 273 MET cc_start: 0.8572 (ttm) cc_final: 0.8297 (ttp) REVERT: C 277 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7791 (m-80) REVERT: D 47 MET cc_start: 0.6825 (mmp) cc_final: 0.6079 (tmm) REVERT: D 60 LYS cc_start: 0.7435 (ptmm) cc_final: 0.7126 (ptpp) REVERT: D 126 MET cc_start: 0.7906 (tmt) cc_final: 0.7650 (tmt) REVERT: D 149 GLN cc_start: 0.8453 (mt0) cc_final: 0.8056 (mm110) REVERT: D 181 GLU cc_start: 0.8378 (tp30) cc_final: 0.7798 (tt0) REVERT: D 203 GLN cc_start: 0.8148 (tm-30) cc_final: 0.7857 (tp-100) REVERT: D 227 GLU cc_start: 0.8665 (tt0) cc_final: 0.8425 (tt0) REVERT: E 47 MET cc_start: 0.6590 (mmp) cc_final: 0.6101 (tmt) REVERT: E 60 LYS cc_start: 0.7144 (ptmm) cc_final: 0.6915 (ptpp) REVERT: E 175 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7627 (pp) REVERT: E 181 GLU cc_start: 0.8440 (tp30) cc_final: 0.7820 (tt0) REVERT: E 227 GLU cc_start: 0.8664 (tt0) cc_final: 0.8448 (tt0) REVERT: F 47 MET cc_start: 0.7073 (mmp) cc_final: 0.6348 (tmm) REVERT: F 92 GLN cc_start: 0.8261 (tt0) cc_final: 0.7954 (tt0) REVERT: F 105 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8153 (tt) REVERT: F 149 GLN cc_start: 0.8534 (mt0) cc_final: 0.8253 (mm110) REVERT: F 155 MET cc_start: 0.8757 (ptt) cc_final: 0.8436 (ptm) REVERT: F 181 GLU cc_start: 0.8338 (tp30) cc_final: 0.7762 (mp0) REVERT: F 194 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.8450 (m-80) REVERT: F 227 GLU cc_start: 0.8638 (tt0) cc_final: 0.8379 (tt0) REVERT: F 273 MET cc_start: 0.8362 (ttm) cc_final: 0.8025 (ttp) REVERT: G 47 MET cc_start: 0.6802 (mmp) cc_final: 0.6140 (tmm) REVERT: G 60 LYS cc_start: 0.7349 (ptmm) cc_final: 0.6971 (ptpp) REVERT: G 149 GLN cc_start: 0.8470 (mt0) cc_final: 0.8021 (mm110) REVERT: G 203 GLN cc_start: 0.8109 (tp40) cc_final: 0.7903 (tp40) REVERT: G 247 GLN cc_start: 0.8609 (tp40) cc_final: 0.8321 (tp-100) REVERT: G 278 LYS cc_start: 0.8388 (mtpt) cc_final: 0.7881 (mtmt) outliers start: 34 outliers final: 14 residues processed: 220 average time/residue: 0.7445 time to fit residues: 177.2521 Evaluate side-chains 213 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 194 TYR Chi-restraints excluded: chain F residue 237 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 134 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 38 optimal weight: 0.3980 chunk 109 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 210 GLN B 203 GLN C 92 GLN D 92 GLN E 92 GLN F 203 GLN F 207 ASN G 210 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.128153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.089635 restraints weight = 21319.564| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.19 r_work: 0.2974 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15477 Z= 0.157 Angle : 0.527 11.215 20776 Z= 0.266 Chirality : 0.041 0.152 2415 Planarity : 0.004 0.060 2548 Dihedral : 16.972 164.108 2961 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.99 % Allowed : 22.99 % Favored : 75.02 % 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: 1.72 (0.20), residues: 1841 helix: 2.64 (0.16), residues: 994 sheet: -0.22 (0.27), residues: 294 loop : -0.93 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 46 TYR 0.017 0.001 TYR B 194 PHE 0.017 0.002 PHE C 68 TRP 0.003 0.000 TRP B 240 Details of bonding type rmsd covalent geometry : bond 0.00375 (15477) covalent geometry : angle 0.52658 (20776) hydrogen bonds : bond 0.03543 ( 996) hydrogen bonds : angle 3.84748 ( 2925) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.6731 (mmp) cc_final: 0.5903 (tmt) REVERT: A 60 LYS cc_start: 0.7284 (ptmm) cc_final: 0.6992 (ptpp) REVERT: A 149 GLN cc_start: 0.8389 (mt0) cc_final: 0.7948 (mm110) REVERT: A 155 MET cc_start: 0.9177 (ptt) cc_final: 0.8891 (ptt) REVERT: A 161 LYS cc_start: 0.9029 (ptpt) cc_final: 0.8730 (mtmp) REVERT: A 278 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8051 (mtpt) REVERT: B 47 MET cc_start: 0.7000 (mmp) cc_final: 0.6335 (tmm) REVERT: B 60 LYS cc_start: 0.7367 (ptmm) cc_final: 0.7167 (ptpp) REVERT: B 68 PHE cc_start: 0.6407 (OUTLIER) cc_final: 0.6045 (OUTLIER) REVERT: B 149 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8052 (mm110) REVERT: B 159 ASP cc_start: 0.8561 (t0) cc_final: 0.8284 (t0) REVERT: B 171 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8655 (mp) REVERT: B 203 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8061 (tp40) REVERT: B 278 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8367 (mtpt) REVERT: C 47 MET cc_start: 0.6854 (mmp) cc_final: 0.6056 (tmm) REVERT: C 149 GLN cc_start: 0.8506 (mt0) cc_final: 0.8036 (mm110) REVERT: C 159 ASP cc_start: 0.8664 (t0) cc_final: 0.8422 (t0) REVERT: C 181 GLU cc_start: 0.8626 (tp30) cc_final: 0.7901 (mp0) REVERT: C 203 GLN cc_start: 0.8398 (tt0) cc_final: 0.8035 (tp40) REVERT: C 273 MET cc_start: 0.8705 (ttm) cc_final: 0.8438 (ttp) REVERT: D 47 MET cc_start: 0.6843 (mmp) cc_final: 0.6054 (tmm) REVERT: D 60 LYS cc_start: 0.7496 (ptmm) cc_final: 0.7178 (ptpp) REVERT: D 126 MET cc_start: 0.8225 (tmt) cc_final: 0.7902 (tmt) REVERT: D 149 GLN cc_start: 0.8556 (mt0) cc_final: 0.8136 (mm110) REVERT: D 161 LYS cc_start: 0.8981 (ptpt) cc_final: 0.8710 (mtmm) REVERT: D 181 GLU cc_start: 0.8586 (tp30) cc_final: 0.7916 (tt0) REVERT: D 203 GLN cc_start: 0.8362 (tm-30) cc_final: 0.7961 (tp40) REVERT: D 227 GLU cc_start: 0.8900 (tt0) cc_final: 0.8698 (tt0) REVERT: E 47 MET cc_start: 0.6733 (mmp) cc_final: 0.6143 (tmt) REVERT: E 60 LYS cc_start: 0.7261 (ptmm) cc_final: 0.6988 (ptpp) REVERT: E 227 GLU cc_start: 0.8892 (tt0) cc_final: 0.8629 (tt0) REVERT: F 47 MET cc_start: 0.7122 (mmp) cc_final: 0.6344 (tmm) REVERT: F 92 GLN cc_start: 0.8400 (tt0) cc_final: 0.8132 (tt0) REVERT: F 105 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8207 (tt) REVERT: F 149 GLN cc_start: 0.8626 (mt0) cc_final: 0.8295 (mm110) REVERT: F 155 MET cc_start: 0.8957 (ptt) cc_final: 0.8632 (ptm) REVERT: F 227 GLU cc_start: 0.8853 (tt0) cc_final: 0.8611 (tt0) REVERT: F 273 MET cc_start: 0.8572 (ttm) cc_final: 0.8282 (ttp) REVERT: G 47 MET cc_start: 0.6873 (mmp) cc_final: 0.6148 (tmm) REVERT: G 60 LYS cc_start: 0.7437 (ptmm) cc_final: 0.7035 (ptpp) REVERT: G 149 GLN cc_start: 0.8565 (mt0) cc_final: 0.8068 (mm110) REVERT: G 247 GLN cc_start: 0.8813 (tp40) cc_final: 0.8543 (tp-100) REVERT: G 278 LYS cc_start: 0.8396 (mtpt) cc_final: 0.7872 (mtmt) outliers start: 30 outliers final: 15 residues processed: 218 average time/residue: 0.7410 time to fit residues: 174.8815 Evaluate side-chains 210 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 237 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 50 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 174 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN C 92 GLN D 92 GLN E 92 GLN G 210 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.129381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.090995 restraints weight = 21117.366| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.19 r_work: 0.2992 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15477 Z= 0.118 Angle : 0.520 11.330 20776 Z= 0.261 Chirality : 0.041 0.141 2415 Planarity : 0.004 0.059 2548 Dihedral : 16.860 164.157 2961 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.79 % Allowed : 23.46 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.77 (0.20), residues: 1841 helix: 2.68 (0.16), residues: 994 sheet: -0.19 (0.27), residues: 294 loop : -0.90 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 46 TYR 0.021 0.001 TYR E 27 PHE 0.017 0.002 PHE C 68 TRP 0.003 0.000 TRP E 16 Details of bonding type rmsd covalent geometry : bond 0.00268 (15477) covalent geometry : angle 0.51992 (20776) hydrogen bonds : bond 0.03388 ( 996) hydrogen bonds : angle 3.79991 ( 2925) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5344.20 seconds wall clock time: 91 minutes 33.62 seconds (5493.62 seconds total)