Starting phenix.real_space_refine on Thu Jul 2 21:05:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ov1_70886/07_2026/9ov1_70886.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ov1_70886/07_2026/9ov1_70886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ov1_70886/07_2026/9ov1_70886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ov1_70886/07_2026/9ov1_70886.map" model { file = "/net/cci-nas-00/data/ceres_data/9ov1_70886/07_2026/9ov1_70886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ov1_70886/07_2026/9ov1_70886.cif" } resolution = 2.36 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 12 5.21 5 S 42 5.16 5 C 6474 2.51 5 N 1728 2.21 5 O 1908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10170 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1688 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "B" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1688 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "C" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1688 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "D" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1688 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "E" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1688 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "F" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1688 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.34, per 1000 atoms: 0.23 Number of scatterers: 10170 At special positions: 0 Unit cell: (108.075, 105.6, 68.475, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 6 15.00 Mg 12 11.99 O 1908 8.00 N 1728 7.00 C 6474 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: 1.00 Conformation dependent library (CDL) restraints added in 361.9 milliseconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2376 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 71.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.610A pdb=" N HIS A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP A 121 " --> pdb=" O HIS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 138 Processing helix chain 'A' and resid 138 through 143 removed outlier: 3.765A pdb=" N TYR A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 177 removed outlier: 3.598A pdb=" N SER A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 192 Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 216 through 233 removed outlier: 3.502A pdb=" N ASP A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 248 removed outlier: 4.510A pdb=" N MET A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 263 through 289 removed outlier: 3.523A pdb=" N TYR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.528A pdb=" N GLU A 302 " --> pdb=" O PHE A 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.662A pdb=" N HIS B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP B 121 " --> pdb=" O HIS B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 138 Processing helix chain 'B' and resid 138 through 143 removed outlier: 3.795A pdb=" N TYR B 143 " --> pdb=" O GLN B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 177 removed outlier: 3.617A pdb=" N SER B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 192 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 216 through 232 removed outlier: 3.689A pdb=" N VAL B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 248 removed outlier: 4.469A pdb=" N MET B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 263 through 289 removed outlier: 3.528A pdb=" N TYR B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS B 288 " --> pdb=" O LYS B 284 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 302 Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.662A pdb=" N HIS C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP C 121 " --> pdb=" O HIS C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 138 Processing helix chain 'C' and resid 138 through 143 removed outlier: 3.794A pdb=" N TYR C 143 " --> pdb=" O GLN C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 177 removed outlier: 3.615A pdb=" N SER C 172 " --> pdb=" O ARG C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 192 Processing helix chain 'C' and resid 195 through 200 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 216 through 232 removed outlier: 3.679A pdb=" N VAL C 226 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 248 removed outlier: 4.500A pdb=" N MET C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 263 through 289 removed outlier: 3.534A pdb=" N TYR C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS C 288 " --> pdb=" O LYS C 284 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 289 " --> pdb=" O ALA C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 302 removed outlier: 3.514A pdb=" N GLU C 302 " --> pdb=" O PHE C 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 121 removed outlier: 3.609A pdb=" N HIS D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 120 " --> pdb=" O SER D 116 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP D 121 " --> pdb=" O HIS D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 138 Processing helix chain 'D' and resid 138 through 143 removed outlier: 3.786A pdb=" N TYR D 143 " --> pdb=" O GLN D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 177 removed outlier: 3.600A pdb=" N SER D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 195 through 200 Processing helix chain 'D' and resid 209 through 215 Processing helix chain 'D' and resid 216 through 233 removed outlier: 3.721A pdb=" N VAL D 226 " --> pdb=" O SER D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 248 removed outlier: 4.485A pdb=" N MET D 240 " --> pdb=" O GLY D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 263 through 289 removed outlier: 3.522A pdb=" N TYR D 271 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS D 288 " --> pdb=" O LYS D 284 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR D 289 " --> pdb=" O ALA D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 302 removed outlier: 3.563A pdb=" N GLU D 302 " --> pdb=" O PHE D 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 121 removed outlier: 3.852A pdb=" N HIS E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR E 118 " --> pdb=" O GLU E 114 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU E 120 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP E 121 " --> pdb=" O HIS E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 138 Processing helix chain 'E' and resid 138 through 143 removed outlier: 3.765A pdb=" N TYR E 143 " --> pdb=" O GLN E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 177 removed outlier: 3.557A pdb=" N SER E 172 " --> pdb=" O ARG E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 192 Processing helix chain 'E' and resid 195 through 200 Processing helix chain 'E' and resid 209 through 215 Processing helix chain 'E' and resid 215 through 233 removed outlier: 4.360A pdb=" N SER E 219 " --> pdb=" O LEU E 215 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP E 223 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL E 225 " --> pdb=" O ALA E 221 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 248 removed outlier: 4.536A pdb=" N MET E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 256 Processing helix chain 'E' and resid 263 through 289 removed outlier: 3.604A pdb=" N TYR E 271 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS E 288 " --> pdb=" O LYS E 284 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR E 289 " --> pdb=" O ALA E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 302 removed outlier: 3.513A pdb=" N GLU E 302 " --> pdb=" O PHE E 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 121 removed outlier: 3.859A pdb=" N HIS F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR F 118 " --> pdb=" O GLU F 114 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU F 120 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP F 121 " --> pdb=" O HIS F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 138 Processing helix chain 'F' and resid 138 through 143 removed outlier: 3.768A pdb=" N TYR F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 177 removed outlier: 3.560A pdb=" N SER F 172 " --> pdb=" O ARG F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 192 Processing helix chain 'F' and resid 195 through 200 Processing helix chain 'F' and resid 209 through 215 Processing helix chain 'F' and resid 215 through 233 removed outlier: 4.370A pdb=" N SER F 219 " --> pdb=" O LEU F 215 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP F 223 " --> pdb=" O SER F 219 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL F 226 " --> pdb=" O SER F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 248 removed outlier: 4.531A pdb=" N MET F 240 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 256 Processing helix chain 'F' and resid 263 through 289 removed outlier: 3.530A pdb=" N TYR F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS F 288 " --> pdb=" O LYS F 284 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR F 289 " --> pdb=" O ALA F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 302 removed outlier: 3.505A pdb=" N GLU F 302 " --> pdb=" O PHE F 299 " (cutoff:3.500A) 544 hydrogen bonds defined for protein. 1575 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: 1.47 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1679 1.32 - 1.44: 2740 1.44 - 1.56: 5883 1.56 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 10374 Sorted by residual: bond pdb=" O3 PO4 F 403 " pdb=" P PO4 F 403 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.36e+00 bond pdb=" O3 PO4 A1003 " pdb=" P PO4 A1003 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.17e+00 bond pdb=" O3 PO4 E1002 " pdb=" P PO4 E1002 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.14e+00 bond pdb=" O4 PO4 B 402 " pdb=" P PO4 B 402 " ideal model delta sigma weight residual 1.568 1.508 0.060 2.00e-02 2.50e+03 9.07e+00 bond pdb=" O4 PO4 F 403 " pdb=" P PO4 F 403 " ideal model delta sigma weight residual 1.568 1.508 0.060 2.00e-02 2.50e+03 9.03e+00 ... (remaining 10369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 13676 1.06 - 2.12: 250 2.12 - 3.18: 65 3.18 - 4.25: 15 4.25 - 5.31: 4 Bond angle restraints: 14010 Sorted by residual: angle pdb=" N ASP E 223 " pdb=" CA ASP E 223 " pdb=" C ASP E 223 " ideal model delta sigma weight residual 112.68 107.96 4.72 1.33e+00 5.65e-01 1.26e+01 angle pdb=" N ASP F 223 " pdb=" CA ASP F 223 " pdb=" C ASP F 223 " ideal model delta sigma weight residual 113.97 109.45 4.52 1.28e+00 6.10e-01 1.25e+01 angle pdb=" N GLU F 224 " pdb=" CA GLU F 224 " pdb=" C GLU F 224 " ideal model delta sigma weight residual 112.23 108.20 4.03 1.26e+00 6.30e-01 1.02e+01 angle pdb=" O ALA E 221 " pdb=" C ALA E 221 " pdb=" N SER E 222 " ideal model delta sigma weight residual 122.27 118.53 3.74 1.23e+00 6.61e-01 9.24e+00 angle pdb=" N VAL A 225 " pdb=" CA VAL A 225 " pdb=" C VAL A 225 " ideal model delta sigma weight residual 111.00 107.92 3.08 1.09e+00 8.42e-01 8.01e+00 ... (remaining 14005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 5629 17.22 - 34.44: 545 34.44 - 51.66: 84 51.66 - 68.88: 21 68.88 - 86.10: 3 Dihedral angle restraints: 6282 sinusoidal: 2580 harmonic: 3702 Sorted by residual: dihedral pdb=" CB GLU F 224 " pdb=" CG GLU F 224 " pdb=" CD GLU F 224 " pdb=" OE1 GLU F 224 " ideal model delta sinusoidal sigma weight residual 0.00 86.10 -86.10 1 3.00e+01 1.11e-03 9.94e+00 dihedral pdb=" CG LYS B 196 " pdb=" CD LYS B 196 " pdb=" CE LYS B 196 " pdb=" NZ LYS B 196 " ideal model delta sinusoidal sigma weight residual -60.00 -116.58 56.58 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CG LYS C 196 " pdb=" CD LYS C 196 " pdb=" CE LYS C 196 " pdb=" NZ LYS C 196 " ideal model delta sinusoidal sigma weight residual -60.00 -116.28 56.28 3 1.50e+01 4.44e-03 9.39e+00 ... (remaining 6279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1016 0.029 - 0.057: 313 0.057 - 0.085: 150 0.085 - 0.114: 57 0.114 - 0.142: 6 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CA GLU D 302 " pdb=" N GLU D 302 " pdb=" C GLU D 302 " pdb=" CB GLU D 302 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA ASP F 223 " pdb=" N ASP F 223 " pdb=" C ASP F 223 " pdb=" CB ASP F 223 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA SER E 222 " pdb=" N SER E 222 " pdb=" C SER E 222 " pdb=" CB SER E 222 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.07e-01 ... (remaining 1539 not shown) Planarity restraints: 1782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 221 " -0.015 2.00e-02 2.50e+03 2.82e-02 7.93e+00 pdb=" C ALA E 221 " 0.049 2.00e-02 2.50e+03 pdb=" O ALA E 221 " -0.018 2.00e-02 2.50e+03 pdb=" N SER E 222 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 223 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.91e+00 pdb=" C ASP E 223 " -0.024 2.00e-02 2.50e+03 pdb=" O ASP E 223 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU E 224 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 220 " 0.006 2.00e-02 2.50e+03 1.13e-02 1.28e+00 pdb=" C ILE A 220 " -0.020 2.00e-02 2.50e+03 pdb=" O ILE A 220 " 0.007 2.00e-02 2.50e+03 pdb=" N ALA A 221 " 0.007 2.00e-02 2.50e+03 ... (remaining 1779 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 78 2.51 - 3.11: 6839 3.11 - 3.71: 15300 3.71 - 4.30: 23994 4.30 - 4.90: 37900 Nonbonded interactions: 84111 Sorted by model distance: nonbonded pdb=" O1 PO4 B 402 " pdb="MG MG B 403 " model vdw 1.918 2.170 nonbonded pdb=" O1 PO4 C 401 " pdb="MG MG C 402 " model vdw 1.919 2.170 nonbonded pdb="MG MG A1001 " pdb=" O1 PO4 A1003 " model vdw 1.927 2.170 nonbonded pdb="MG MG D1001 " pdb=" O1 PO4 D1003 " model vdw 1.927 2.170 nonbonded pdb="MG MG F 402 " pdb=" O1 PO4 F 403 " model vdw 1.931 2.170 ... (remaining 84106 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 105 through 313) selection = (chain 'B' and resid 105 through 313) selection = (chain 'C' and resid 105 through 313) selection = (chain 'D' and resid 105 through 313) selection = (chain 'E' and resid 105 through 313) selection = (chain 'F' and resid 105 through 313) } 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: 1.800 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.320 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 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 : 0.004 0.061 10374 Z= 0.218 Angle : 0.419 5.307 14010 Z= 0.245 Chirality : 0.037 0.142 1542 Planarity : 0.003 0.036 1782 Dihedral : 13.494 86.097 3906 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.09 % Allowed : 0.36 % Favored : 99.55 % 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: -0.26 (0.20), residues: 1242 helix: 0.12 (0.16), residues: 738 sheet: None (None), residues: 0 loop : -0.43 (0.22), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 230 TYR 0.011 0.001 TYR E 255 PHE 0.005 0.001 PHE D 306 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.22 (10374) covalent geometry : angle 0.41875 / 0.24 (14010) hydrogen bonds : bond 0.25802 / 17.27 ( 544) hydrogen bonds : angle 5.94590 / 4.29 ( 1575) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 248 time to evaluate : 0.432 Fit side-chains REVERT: A 114 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7873 (mm-30) REVERT: B 114 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7903 (mm-30) REVERT: C 114 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7914 (mm-30) REVERT: D 114 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7918 (mm-30) REVERT: E 223 ASP cc_start: 0.6950 (OUTLIER) cc_final: 0.6618 (p0) REVERT: F 227 GLU cc_start: 0.7716 (pp20) cc_final: 0.7307 (mm-30) outliers start: 1 outliers final: 0 residues processed: 249 average time/residue: 0.9212 time to fit residues: 240.0809 Evaluate side-chains 207 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 HIS B 308 ASN C 151 HIS C 308 ASN D 151 HIS E 151 HIS F 151 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.130454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.106015 restraints weight = 9738.788| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.46 r_work: 0.2977 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10374 Z= 0.133 Angle : 0.471 3.677 14010 Z= 0.264 Chirality : 0.038 0.112 1542 Planarity : 0.004 0.053 1782 Dihedral : 4.087 39.283 1394 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.45 % Allowed : 6.43 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.21), residues: 1242 helix: 1.32 (0.17), residues: 798 sheet: None (None), residues: 0 loop : -0.02 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 243 TYR 0.009 0.001 TYR E 255 PHE 0.007 0.001 PHE D 306 HIS 0.006 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (10374) covalent geometry : angle 0.47087 / 0.26 (14010) hydrogen bonds : bond 0.06912 / 4.65 ( 544) hydrogen bonds : angle 3.77978 / 2.74 ( 1575) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 228 time to evaluate : 0.419 Fit side-chains REVERT: A 114 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7958 (mm-30) REVERT: A 230 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.6995 (tmm160) REVERT: A 252 LYS cc_start: 0.8620 (mtpt) cc_final: 0.8279 (mttm) REVERT: A 283 GLU cc_start: 0.7490 (tt0) cc_final: 0.7288 (tp30) REVERT: A 287 LYS cc_start: 0.7359 (tppt) cc_final: 0.6939 (tptp) REVERT: A 302 GLU cc_start: 0.7952 (mp0) cc_final: 0.7672 (mp0) REVERT: A 310 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7585 (mt-10) REVERT: B 114 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8100 (mm-30) REVERT: C 114 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8118 (mm-30) REVERT: C 252 LYS cc_start: 0.8567 (mtpt) cc_final: 0.8192 (mttm) REVERT: C 287 LYS cc_start: 0.6869 (ttmt) cc_final: 0.6516 (tptp) REVERT: D 114 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7965 (mm-30) REVERT: D 230 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7341 (tmm160) REVERT: D 252 LYS cc_start: 0.8579 (mtpt) cc_final: 0.8284 (mttt) REVERT: D 287 LYS cc_start: 0.7320 (tppt) cc_final: 0.6864 (tptp) REVERT: D 302 GLU cc_start: 0.8117 (mp0) cc_final: 0.7757 (mp0) REVERT: E 223 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.6947 (p0) REVERT: E 230 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7701 (tmm160) REVERT: E 252 LYS cc_start: 0.8550 (mtpt) cc_final: 0.8271 (mttt) REVERT: E 287 LYS cc_start: 0.7310 (tppt) cc_final: 0.6647 (tptp) REVERT: F 230 ARG cc_start: 0.7832 (tmm160) cc_final: 0.7578 (tmm160) REVERT: F 252 LYS cc_start: 0.8606 (mtpt) cc_final: 0.7781 (mmpt) REVERT: F 287 LYS cc_start: 0.7306 (tppt) cc_final: 0.6650 (tptp) outliers start: 16 outliers final: 3 residues processed: 231 average time/residue: 0.8834 time to fit residues: 213.9141 Evaluate side-chains 212 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 204 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 230 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 40 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 114 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 HIS B 151 HIS B 308 ASN C 151 HIS C 308 ASN D 151 HIS E 151 HIS E 308 ASN F 151 HIS F 308 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.124276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.099314 restraints weight = 9784.166| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.48 r_work: 0.2875 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10374 Z= 0.253 Angle : 0.630 4.641 14010 Z= 0.348 Chirality : 0.046 0.123 1542 Planarity : 0.006 0.102 1782 Dihedral : 4.718 51.942 1394 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 1.45 % Allowed : 8.24 % Favored : 90.31 % 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: 1.24 (0.21), residues: 1242 helix: 1.55 (0.17), residues: 756 sheet: None (None), residues: 0 loop : -0.25 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 243 TYR 0.012 0.002 TYR C 255 PHE 0.011 0.002 PHE D 306 HIS 0.008 0.002 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.25 (10374) covalent geometry : angle 0.62962 / 0.35 (14010) hydrogen bonds : bond 0.09623 / 6.45 ( 544) hydrogen bonds : angle 3.98568 / 2.87 ( 1575) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 207 time to evaluate : 0.431 Fit side-chains REVERT: A 114 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7915 (mm-30) REVERT: A 230 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7294 (tmm160) REVERT: A 287 LYS cc_start: 0.7576 (tppt) cc_final: 0.7099 (tptp) REVERT: A 310 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7648 (mt-10) REVERT: B 114 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8092 (mm-30) REVERT: C 114 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8112 (mm-30) REVERT: C 252 LYS cc_start: 0.8577 (mtpt) cc_final: 0.8199 (mttm) REVERT: C 287 LYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6834 (tptp) REVERT: D 114 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7919 (mm-30) REVERT: D 140 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6620 (mp0) REVERT: D 230 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7597 (tmm160) REVERT: D 283 GLU cc_start: 0.7795 (tp30) cc_final: 0.7330 (tp30) REVERT: D 287 LYS cc_start: 0.7529 (tppt) cc_final: 0.7057 (tptp) REVERT: D 310 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7780 (mt-10) outliers start: 16 outliers final: 4 residues processed: 210 average time/residue: 0.8605 time to fit residues: 189.6614 Evaluate side-chains 200 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 191 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 230 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 34 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 HIS B 151 HIS C 151 HIS D 151 HIS E 117 HIS E 151 HIS E 308 ASN F 151 HIS F 308 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.131049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.106525 restraints weight = 9864.688| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.48 r_work: 0.2990 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10374 Z= 0.112 Angle : 0.435 3.768 14010 Z= 0.244 Chirality : 0.037 0.114 1542 Planarity : 0.004 0.067 1782 Dihedral : 4.160 52.692 1394 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.82 % Allowed : 8.51 % Favored : 90.67 % 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: 1.74 (0.22), residues: 1242 helix: 1.82 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.04 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 243 TYR 0.008 0.001 TYR C 255 PHE 0.006 0.001 PHE D 306 HIS 0.006 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (10374) covalent geometry : angle 0.43497 / 0.24 (14010) hydrogen bonds : bond 0.05525 / 3.72 ( 544) hydrogen bonds : angle 3.55154 / 2.59 ( 1575) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 209 time to evaluate : 0.472 Fit side-chains REVERT: A 114 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7931 (mm-30) REVERT: A 227 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7107 (tm-30) REVERT: A 252 LYS cc_start: 0.8526 (mtmt) cc_final: 0.8314 (mttm) REVERT: A 287 LYS cc_start: 0.7305 (tppt) cc_final: 0.6845 (tptp) REVERT: A 310 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7520 (mt-10) REVERT: B 114 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8010 (mm-30) REVERT: B 288 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7334 (mtmt) REVERT: C 114 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8034 (mm-30) REVERT: C 252 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8205 (mttm) REVERT: C 287 LYS cc_start: 0.6713 (ttmt) cc_final: 0.6361 (tptp) REVERT: D 114 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7920 (mm-30) REVERT: D 230 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7158 (tmm160) REVERT: D 252 LYS cc_start: 0.8555 (mtmt) cc_final: 0.8272 (mttm) REVERT: D 287 LYS cc_start: 0.7186 (tppt) cc_final: 0.6750 (tptp) REVERT: E 223 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7425 (p0) REVERT: E 230 ARG cc_start: 0.7773 (tmm160) cc_final: 0.7504 (tmm160) REVERT: E 252 LYS cc_start: 0.8652 (mtpt) cc_final: 0.8225 (mttt) REVERT: F 252 LYS cc_start: 0.8490 (mtmt) cc_final: 0.8282 (mttt) outliers start: 9 outliers final: 1 residues processed: 211 average time/residue: 0.8463 time to fit residues: 187.5678 Evaluate side-chains 196 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 190 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain E residue 223 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 118 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 HIS B 151 HIS B 308 ASN C 151 HIS C 308 ASN D 151 HIS E 151 HIS E 308 ASN F 151 HIS F 308 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.128235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.103444 restraints weight = 9818.508| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.49 r_work: 0.2922 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10374 Z= 0.148 Angle : 0.500 4.339 14010 Z= 0.277 Chirality : 0.039 0.108 1542 Planarity : 0.004 0.104 1782 Dihedral : 4.300 52.790 1394 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.82 % Allowed : 9.69 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.90 (0.22), residues: 1242 helix: 2.11 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -0.05 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 243 TYR 0.012 0.001 TYR F 255 PHE 0.008 0.001 PHE D 306 HIS 0.006 0.001 HIS D 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (10374) covalent geometry : angle 0.49976 / 0.28 (14010) hydrogen bonds : bond 0.06974 / 4.69 ( 544) hydrogen bonds : angle 3.67863 / 2.66 ( 1575) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 205 time to evaluate : 0.417 Fit side-chains REVERT: A 114 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7929 (mm-30) REVERT: A 139 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: A 283 GLU cc_start: 0.7713 (tp30) cc_final: 0.7232 (tp30) REVERT: A 287 LYS cc_start: 0.7363 (tppt) cc_final: 0.6975 (tptp) REVERT: A 310 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7500 (mt-10) REVERT: B 114 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8064 (mm-30) REVERT: B 288 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7391 (mtmt) REVERT: C 114 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8083 (mm-30) REVERT: C 287 LYS cc_start: 0.6898 (ttmt) cc_final: 0.6611 (tptp) REVERT: D 114 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7930 (mm-30) REVERT: D 140 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6585 (mp0) REVERT: D 230 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7281 (tmm160) REVERT: D 252 LYS cc_start: 0.8624 (mtmt) cc_final: 0.8353 (mttm) REVERT: D 287 LYS cc_start: 0.7319 (tppt) cc_final: 0.6879 (tptp) REVERT: E 230 ARG cc_start: 0.7807 (tmm160) cc_final: 0.7537 (tmm160) REVERT: E 252 LYS cc_start: 0.8638 (mtpt) cc_final: 0.8190 (mttt) REVERT: E 287 LYS cc_start: 0.7292 (tppt) cc_final: 0.6936 (ttmt) REVERT: F 287 LYS cc_start: 0.7292 (tppt) cc_final: 0.6931 (ttmt) outliers start: 9 outliers final: 3 residues processed: 206 average time/residue: 0.8074 time to fit residues: 174.6900 Evaluate side-chains 205 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 197 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain E residue 223 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 67 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 HIS B 151 HIS B 308 ASN C 151 HIS C 308 ASN D 151 HIS E 151 HIS E 308 ASN F 151 HIS F 308 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.129690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.104988 restraints weight = 9926.987| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.49 r_work: 0.2947 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10374 Z= 0.127 Angle : 0.464 4.666 14010 Z= 0.258 Chirality : 0.037 0.112 1542 Planarity : 0.003 0.032 1782 Dihedral : 4.165 53.346 1394 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.00 % Allowed : 9.33 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.22), residues: 1242 helix: 1.90 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.09 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 243 TYR 0.011 0.001 TYR F 255 PHE 0.007 0.001 PHE D 306 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (10374) covalent geometry : angle 0.46361 / 0.26 (14010) hydrogen bonds : bond 0.06066 / 4.08 ( 544) hydrogen bonds : angle 3.57388 / 2.59 ( 1575) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 0.343 Fit side-chains REVERT: A 114 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8003 (mm-30) REVERT: A 139 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: A 230 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.6982 (tmm160) REVERT: A 283 GLU cc_start: 0.7664 (tp30) cc_final: 0.7195 (tt0) REVERT: A 287 LYS cc_start: 0.7299 (tppt) cc_final: 0.6928 (tptp) REVERT: A 310 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: B 114 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8027 (mm-30) REVERT: B 288 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7384 (mtmt) REVERT: C 114 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8035 (mm-30) REVERT: C 252 LYS cc_start: 0.8397 (mtmt) cc_final: 0.8163 (mttm) REVERT: C 287 LYS cc_start: 0.6748 (ttmt) cc_final: 0.6395 (tptp) REVERT: D 114 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7952 (mm-30) REVERT: D 230 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7213 (tmm160) REVERT: D 252 LYS cc_start: 0.8609 (mtmt) cc_final: 0.8356 (mttm) REVERT: D 287 LYS cc_start: 0.7223 (tppt) cc_final: 0.6761 (tptp) REVERT: E 223 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7409 (p0) REVERT: E 230 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7529 (tmm160) REVERT: E 252 LYS cc_start: 0.8639 (mtpt) cc_final: 0.8212 (mttt) REVERT: F 223 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7405 (p0) REVERT: F 252 LYS cc_start: 0.8581 (mtpt) cc_final: 0.8281 (mttt) outliers start: 11 outliers final: 2 residues processed: 205 average time/residue: 0.7989 time to fit residues: 172.0717 Evaluate side-chains 204 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 194 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 230 ARG Chi-restraints excluded: chain F residue 223 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 50 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 chunk 110 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 HIS B 151 HIS B 308 ASN C 308 ASN D 151 HIS E 151 HIS E 308 ASN F 151 HIS F 308 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.132851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.108578 restraints weight = 9821.559| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.48 r_work: 0.3019 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10374 Z= 0.109 Angle : 0.446 5.241 14010 Z= 0.247 Chirality : 0.036 0.114 1542 Planarity : 0.003 0.023 1782 Dihedral : 3.960 54.825 1394 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.82 % Allowed : 9.42 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.23), residues: 1242 helix: 2.08 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.16 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 243 TYR 0.010 0.001 TYR F 255 PHE 0.005 0.001 PHE D 306 HIS 0.006 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (10374) covalent geometry : angle 0.44627 / 0.25 (14010) hydrogen bonds : bond 0.04987 / 3.35 ( 544) hydrogen bonds : angle 3.45766 / 2.51 ( 1575) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 200 time to evaluate : 0.405 Fit side-chains REVERT: A 114 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7944 (mm-30) REVERT: A 139 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: A 230 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6920 (tmm160) REVERT: A 287 LYS cc_start: 0.7123 (tppt) cc_final: 0.6770 (tptp) REVERT: A 310 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7334 (mt-10) REVERT: B 114 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7940 (mm-30) REVERT: C 114 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7967 (mm-30) REVERT: C 252 LYS cc_start: 0.8288 (mtmt) cc_final: 0.8065 (mttm) REVERT: D 114 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7987 (mm-30) REVERT: D 252 LYS cc_start: 0.8591 (mtmt) cc_final: 0.8359 (mttm) REVERT: E 139 GLN cc_start: 0.8139 (tt0) cc_final: 0.7891 (tt0) REVERT: E 223 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7515 (p0) REVERT: E 230 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7493 (tmm160) REVERT: E 252 LYS cc_start: 0.8582 (mtpt) cc_final: 0.8093 (mttt) REVERT: F 223 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7409 (p0) REVERT: F 252 LYS cc_start: 0.8501 (mtpt) cc_final: 0.8227 (mttt) outliers start: 9 outliers final: 1 residues processed: 202 average time/residue: 0.6916 time to fit residues: 146.9613 Evaluate side-chains 197 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 190 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 230 ARG Chi-restraints excluded: chain F residue 223 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 47 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 HIS B 117 HIS B 151 HIS B 308 ASN C 117 HIS C 308 ASN D 151 HIS D 308 ASN E 151 HIS E 308 ASN F 151 HIS F 308 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.126307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.101293 restraints weight = 9838.970| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.50 r_work: 0.2897 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10374 Z= 0.199 Angle : 0.568 4.993 14010 Z= 0.314 Chirality : 0.042 0.119 1542 Planarity : 0.004 0.025 1782 Dihedral : 4.484 53.599 1394 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.27 % Allowed : 9.60 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.22), residues: 1242 helix: 1.95 (0.17), residues: 756 sheet: None (None), residues: 0 loop : -0.10 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 243 TYR 0.015 0.002 TYR F 255 PHE 0.010 0.002 PHE D 306 HIS 0.007 0.002 HIS D 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (10374) covalent geometry : angle 0.56796 / 0.31 (14010) hydrogen bonds : bond 0.08207 / 5.52 ( 544) hydrogen bonds : angle 3.82382 / 2.76 ( 1575) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 0.335 Fit side-chains REVERT: A 114 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7972 (mm-30) REVERT: A 139 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8215 (tt0) REVERT: A 230 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7142 (tmm160) REVERT: A 287 LYS cc_start: 0.7466 (tppt) cc_final: 0.7058 (tptp) REVERT: A 310 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: B 114 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8008 (mm-30) REVERT: C 114 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7998 (mm-30) REVERT: C 252 LYS cc_start: 0.8445 (mtmt) cc_final: 0.8161 (mttm) REVERT: C 283 GLU cc_start: 0.8059 (tp30) cc_final: 0.7851 (tp30) REVERT: C 287 LYS cc_start: 0.7051 (ttmt) cc_final: 0.6711 (tptp) REVERT: D 114 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7967 (mm-30) REVERT: D 140 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6648 (mp0) REVERT: D 252 LYS cc_start: 0.8640 (mtmt) cc_final: 0.8362 (mttm) REVERT: D 287 LYS cc_start: 0.7388 (tppt) cc_final: 0.6950 (tptp) REVERT: E 252 LYS cc_start: 0.8655 (mtpt) cc_final: 0.8209 (mttt) REVERT: E 287 LYS cc_start: 0.7315 (tppt) cc_final: 0.6960 (ttmt) REVERT: F 141 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8176 (mtp180) REVERT: F 252 LYS cc_start: 0.8583 (mtpt) cc_final: 0.8271 (mttt) REVERT: F 287 LYS cc_start: 0.7312 (tppt) cc_final: 0.6758 (tptp) outliers start: 14 outliers final: 3 residues processed: 200 average time/residue: 0.7488 time to fit residues: 157.4195 Evaluate side-chains 202 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 194 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain F residue 141 ARG Chi-restraints excluded: chain F residue 222 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 24 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 HIS B 117 HIS B 151 HIS B 308 ASN C 117 HIS C 308 ASN D 151 HIS E 151 HIS E 308 ASN F 151 HIS F 308 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.127827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.103061 restraints weight = 9830.639| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.49 r_work: 0.2927 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10374 Z= 0.153 Angle : 0.511 4.534 14010 Z= 0.283 Chirality : 0.039 0.122 1542 Planarity : 0.003 0.025 1782 Dihedral : 4.369 54.243 1394 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.91 % Allowed : 9.87 % Favored : 89.22 % 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: 1.80 (0.22), residues: 1242 helix: 2.06 (0.17), residues: 756 sheet: None (None), residues: 0 loop : -0.15 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 243 TYR 0.013 0.001 TYR F 255 PHE 0.008 0.001 PHE D 306 HIS 0.006 0.001 HIS D 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (10374) covalent geometry : angle 0.51141 / 0.28 (14010) hydrogen bonds : bond 0.06956 / 4.68 ( 544) hydrogen bonds : angle 3.68861 / 2.67 ( 1575) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 198 time to evaluate : 0.412 Fit side-chains REVERT: A 114 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7969 (mm-30) REVERT: A 139 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: A 230 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7066 (tmm160) REVERT: A 287 LYS cc_start: 0.7388 (tppt) cc_final: 0.6967 (tptp) REVERT: A 310 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: B 114 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8004 (mm-30) REVERT: C 114 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7970 (mm-30) REVERT: C 252 LYS cc_start: 0.8368 (mtmt) cc_final: 0.8104 (mttm) REVERT: C 283 GLU cc_start: 0.8031 (tp30) cc_final: 0.7828 (tp30) REVERT: C 287 LYS cc_start: 0.6823 (ttmt) cc_final: 0.6476 (tptp) REVERT: D 114 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7964 (mm-30) REVERT: D 140 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6676 (mp0) REVERT: D 230 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7286 (tmm160) REVERT: D 252 LYS cc_start: 0.8620 (mtmt) cc_final: 0.8404 (mttm) REVERT: D 287 LYS cc_start: 0.7298 (tppt) cc_final: 0.6870 (tptp) REVERT: E 252 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8189 (mttt) REVERT: E 283 GLU cc_start: 0.7814 (tp30) cc_final: 0.7604 (tp30) REVERT: E 287 LYS cc_start: 0.7295 (tppt) cc_final: 0.6893 (ttmt) REVERT: F 117 HIS cc_start: 0.8488 (m-70) cc_final: 0.8272 (m90) REVERT: F 141 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8174 (mtp180) REVERT: F 252 LYS cc_start: 0.8576 (mtpt) cc_final: 0.8104 (mttt) REVERT: F 283 GLU cc_start: 0.7827 (tp30) cc_final: 0.7616 (tp30) REVERT: F 287 LYS cc_start: 0.7286 (tppt) cc_final: 0.6883 (ttmt) outliers start: 10 outliers final: 2 residues processed: 201 average time/residue: 0.7915 time to fit residues: 167.3104 Evaluate side-chains 203 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 195 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain F residue 141 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 80 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 HIS A 151 HIS B 151 HIS B 308 ASN C 308 ASN D 151 HIS E 117 HIS E 151 HIS E 308 ASN F 151 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.132487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.108064 restraints weight = 9774.664| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.48 r_work: 0.3000 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10374 Z= 0.115 Angle : 0.460 6.858 14010 Z= 0.255 Chirality : 0.037 0.121 1542 Planarity : 0.003 0.024 1782 Dihedral : 4.069 55.115 1394 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.72 % Allowed : 10.24 % Favored : 89.04 % 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: 1.94 (0.23), residues: 1242 helix: 2.00 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.06 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 243 TYR 0.013 0.001 TYR F 255 PHE 0.006 0.001 PHE A 306 HIS 0.006 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (10374) covalent geometry : angle 0.46006 / 0.26 (14010) hydrogen bonds : bond 0.05224 / 3.51 ( 544) hydrogen bonds : angle 3.49563 / 2.54 ( 1575) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 196 time to evaluate : 0.523 Fit side-chains REVERT: A 114 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7983 (mm-30) REVERT: A 139 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8100 (tt0) REVERT: A 230 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.6965 (tmm160) REVERT: A 278 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8273 (mtt-85) REVERT: A 287 LYS cc_start: 0.7193 (tppt) cc_final: 0.6795 (tptp) REVERT: A 310 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7393 (mt-10) REVERT: B 114 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7928 (mm-30) REVERT: C 114 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7903 (mm-30) REVERT: C 252 LYS cc_start: 0.8335 (mtmt) cc_final: 0.8092 (mttm) REVERT: D 114 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7998 (mm-30) REVERT: D 230 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7086 (tmm160) REVERT: E 223 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7467 (p0) REVERT: E 230 ARG cc_start: 0.7757 (tmm160) cc_final: 0.7549 (tmm160) REVERT: E 252 LYS cc_start: 0.8607 (mtpt) cc_final: 0.8131 (mttt) REVERT: F 252 LYS cc_start: 0.8503 (mtpt) cc_final: 0.8180 (mttt) outliers start: 8 outliers final: 1 residues processed: 199 average time/residue: 0.7565 time to fit residues: 158.3599 Evaluate side-chains 200 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 193 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain E residue 223 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 114 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 HIS B 308 ASN C 308 ASN D 117 HIS D 151 HIS D 308 ASN E 151 HIS E 308 ASN F 151 HIS F 308 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.131614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.107106 restraints weight = 9867.249| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.49 r_work: 0.2978 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10374 Z= 0.125 Angle : 0.498 6.908 14010 Z= 0.274 Chirality : 0.037 0.127 1542 Planarity : 0.003 0.023 1782 Dihedral : 4.062 55.506 1394 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.54 % Allowed : 10.87 % Favored : 88.59 % 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: 1.94 (0.23), residues: 1242 helix: 1.97 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.13 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 243 TYR 0.012 0.001 TYR F 255 PHE 0.006 0.001 PHE D 306 HIS 0.006 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (10374) covalent geometry : angle 0.49848 / 0.27 (14010) hydrogen bonds : bond 0.05596 / 3.76 ( 544) hydrogen bonds : angle 3.54067 / 2.57 ( 1575) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4217.96 seconds wall clock time: 72 minutes 30.30 seconds (4350.30 seconds total)