Starting phenix.real_space_refine on Fri Jul 3 14:03:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r34_53547/07_2026/9r34_53547.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r34_53547/07_2026/9r34_53547.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9r34_53547/07_2026/9r34_53547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r34_53547/07_2026/9r34_53547.map" model { file = "/net/cci-nas-00/data/ceres_data/9r34_53547/07_2026/9r34_53547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r34_53547/07_2026/9r34_53547.cif" } 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= 0.001 sd= 0.032 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 18 5.49 5 Mg 6 5.21 5 S 120 5.16 5 C 8664 2.51 5 N 2484 2.21 5 O 2940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 14232 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2306 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 282} Chain: "B" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2306 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 282} Chain: "C" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2306 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 282} Chain: "D" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2306 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 282} Chain: "E" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2306 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 282} Chain: "F" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2306 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 282} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "E" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 3.42, per 1000 atoms: 0.24 Number of scatterers: 14232 At special positions: 0 Unit cell: (96.3, 117.9, 113.4, 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 120 16.00 P 18 15.00 Mg 6 11.99 O 2940 8.00 N 2484 7.00 C 8664 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: 1.19 Conformation dependent library (CDL) restraints added in 666.3 milliseconds 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 14 sheets defined 55.7% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 64 through 87 Processing helix chain 'A' and resid 87 through 94 Processing helix chain 'A' and resid 94 through 119 Processing helix chain 'A' and resid 121 through 149 Processing helix chain 'A' and resid 167 through 184 Processing helix chain 'A' and resid 218 through 230 Processing helix chain 'A' and resid 270 through 277 removed outlier: 3.728A pdb=" N ARG A 277 " --> pdb=" O PRO A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 Processing helix chain 'A' and resid 299 through 305 Processing helix chain 'A' and resid 341 through 363 Processing helix chain 'B' and resid 65 through 86 removed outlier: 3.698A pdb=" N THR B 86 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 94 through 119 Processing helix chain 'B' and resid 121 through 148 removed outlier: 3.583A pdb=" N VAL B 125 " --> pdb=" O ASP B 121 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 148 " --> pdb=" O LYS B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 184 Processing helix chain 'B' and resid 218 through 230 Processing helix chain 'B' and resid 241 through 245 Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'B' and resid 286 through 296 Processing helix chain 'B' and resid 299 through 305 Processing helix chain 'B' and resid 341 through 363 Processing helix chain 'C' and resid 65 through 87 removed outlier: 3.684A pdb=" N THR C 69 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'C' and resid 94 through 119 Processing helix chain 'C' and resid 121 through 148 Processing helix chain 'C' and resid 167 through 184 Processing helix chain 'C' and resid 218 through 230 Processing helix chain 'C' and resid 241 through 245 Processing helix chain 'C' and resid 270 through 276 Processing helix chain 'C' and resid 286 through 296 Processing helix chain 'C' and resid 299 through 307 removed outlier: 3.972A pdb=" N LEU C 303 " --> pdb=" O ASP C 299 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 363 Processing helix chain 'D' and resid 65 through 87 removed outlier: 3.561A pdb=" N SER D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 93 Processing helix chain 'D' and resid 94 through 119 removed outlier: 3.526A pdb=" N ASN D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 148 removed outlier: 3.530A pdb=" N GLU D 148 " --> pdb=" O LYS D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 184 Processing helix chain 'D' and resid 218 through 230 Processing helix chain 'D' and resid 270 through 276 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 299 through 305 removed outlier: 3.824A pdb=" N LEU D 303 " --> pdb=" O ASP D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 363 Processing helix chain 'E' and resid 65 through 94 removed outlier: 6.744A pdb=" N THR E 89 " --> pdb=" O SER E 85 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 119 Processing helix chain 'E' and resid 121 through 148 Processing helix chain 'E' and resid 167 through 184 Processing helix chain 'E' and resid 218 through 230 Processing helix chain 'E' and resid 270 through 276 Processing helix chain 'E' and resid 286 through 296 Processing helix chain 'E' and resid 299 through 307 removed outlier: 3.546A pdb=" N LEU E 303 " --> pdb=" O ASP E 299 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE E 307 " --> pdb=" O LEU E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 362 Processing helix chain 'F' and resid 65 through 86 Processing helix chain 'F' and resid 87 through 94 Processing helix chain 'F' and resid 94 through 119 removed outlier: 3.643A pdb=" N ALA F 98 " --> pdb=" O ASP F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 148 Processing helix chain 'F' and resid 167 through 184 Processing helix chain 'F' and resid 218 through 230 Processing helix chain 'F' and resid 241 through 245 removed outlier: 3.564A pdb=" N LYS F 245 " --> pdb=" O ILE F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 277 removed outlier: 3.951A pdb=" N ARG F 277 " --> pdb=" O PRO F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 Processing helix chain 'F' and resid 299 through 307 removed outlier: 3.589A pdb=" N PHE F 307 " --> pdb=" O LEU F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 363 Processing sheet with id=AA1, first strand: chain 'A' and resid 189 through 191 removed outlier: 6.561A pdb=" N MET A 209 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N THR A 257 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TRP A 211 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 156 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE A 256 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE A 158 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N THR A 258 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N MET A 160 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL A 157 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL A 282 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET A 159 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N CYS A 284 " --> pdb=" O MET A 159 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N CYS A 161 " --> pdb=" O CYS A 284 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N MET A 316 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 237 removed outlier: 4.506A pdb=" N MET A 247 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA4, first strand: chain 'B' and resid 189 through 191 removed outlier: 6.441A pdb=" N MET B 209 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N THR B 257 " --> pdb=" O MET B 209 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N TRP B 211 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL B 156 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE B 256 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE B 158 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N THR B 258 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N MET B 160 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL B 157 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL B 282 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N MET B 159 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N CYS B 284 " --> pdb=" O MET B 159 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N CYS B 161 " --> pdb=" O CYS B 284 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N MET B 316 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 236 through 237 removed outlier: 4.599A pdb=" N MET B 247 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 329 through 330 Processing sheet with id=AA7, first strand: chain 'C' and resid 189 through 191 removed outlier: 6.705A pdb=" N GLY C 190 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N MET C 209 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N THR C 257 " --> pdb=" O MET C 209 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TRP C 211 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL C 157 " --> pdb=" O PHE C 280 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL C 282 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N MET C 159 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N CYS C 284 " --> pdb=" O MET C 159 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N CYS C 161 " --> pdb=" O CYS C 284 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET C 316 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 236 through 237 removed outlier: 4.295A pdb=" N MET C 247 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 189 through 191 removed outlier: 6.577A pdb=" N GLY D 190 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ASP D 212 " --> pdb=" O GLY D 190 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N MET D 209 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N THR D 257 " --> pdb=" O MET D 209 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TRP D 211 " --> pdb=" O THR D 257 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET D 316 " --> pdb=" O THR D 340 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 236 through 237 removed outlier: 4.326A pdb=" N MET D 247 " --> pdb=" O LEU D 237 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 189 through 191 removed outlier: 6.322A pdb=" N MET E 209 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N THR E 257 " --> pdb=" O MET E 209 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TRP E 211 " --> pdb=" O THR E 257 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N MET E 316 " --> pdb=" O THR E 340 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 236 through 237 removed outlier: 4.272A pdb=" N MET E 247 " --> pdb=" O LEU E 237 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 189 through 191 removed outlier: 6.181A pdb=" N VAL F 156 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE F 256 " --> pdb=" O VAL F 156 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE F 158 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N THR F 258 " --> pdb=" O ILE F 158 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N MET F 160 " --> pdb=" O THR F 258 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N MET F 316 " --> pdb=" O THR F 340 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 236 through 237 removed outlier: 4.385A pdb=" N MET F 247 " --> pdb=" O LEU F 237 " (cutoff:3.500A) 832 hydrogen bonds defined for protein. 2430 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: 2.29 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 4895 1.37 - 1.51: 3924 1.51 - 1.66: 5245 1.66 - 1.80: 150 1.80 - 1.95: 48 Bond restraints: 14262 Sorted by residual: bond pdb=" O3B AGS E 401 " pdb=" PB AGS E 401 " ideal model delta sigma weight residual 1.673 1.576 0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" O3B AGS C 401 " pdb=" PB AGS C 401 " ideal model delta sigma weight residual 1.673 1.578 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" O3B AGS F 401 " pdb=" PB AGS F 401 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" O3B AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sigma weight residual 1.673 1.584 0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" O3A AGS B 401 " pdb=" PA AGS B 401 " ideal model delta sigma weight residual 1.664 1.577 0.087 2.00e-02 2.50e+03 1.91e+01 ... (remaining 14257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 18948 1.93 - 3.86: 307 3.86 - 5.79: 52 5.79 - 7.72: 21 7.72 - 9.65: 16 Bond angle restraints: 19344 Sorted by residual: angle pdb=" O3A AGS E 401 " pdb=" PB AGS E 401 " pdb=" O3B AGS E 401 " ideal model delta sigma weight residual 100.38 110.03 -9.65 3.00e+00 1.11e-01 1.04e+01 angle pdb=" O1A AGS D 401 " pdb=" PA AGS D 401 " pdb=" O2A AGS D 401 " ideal model delta sigma weight residual 122.09 112.52 9.57 3.00e+00 1.11e-01 1.02e+01 angle pdb=" O3A AGS A 401 " pdb=" PB AGS A 401 " pdb=" O3B AGS A 401 " ideal model delta sigma weight residual 100.38 109.79 -9.41 3.00e+00 1.11e-01 9.84e+00 angle pdb=" O3A AGS F 401 " pdb=" PB AGS F 401 " pdb=" O3B AGS F 401 " ideal model delta sigma weight residual 100.38 109.50 -9.12 3.00e+00 1.11e-01 9.24e+00 angle pdb=" O1B AGS A 401 " pdb=" PB AGS A 401 " pdb=" O2B AGS A 401 " ideal model delta sigma weight residual 121.53 112.45 9.08 3.00e+00 1.11e-01 9.16e+00 ... (remaining 19339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.19: 8736 31.19 - 62.38: 229 62.38 - 93.57: 17 93.57 - 124.76: 5 124.76 - 155.95: 7 Dihedral angle restraints: 8994 sinusoidal: 3792 harmonic: 5202 Sorted by residual: dihedral pdb=" O2A AGS A 401 " pdb=" O3A AGS A 401 " pdb=" PA AGS A 401 " pdb=" PB AGS A 401 " ideal model delta sinusoidal sigma weight residual -52.28 103.67 -155.95 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" O2A AGS D 401 " pdb=" O3A AGS D 401 " pdb=" PA AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sinusoidal sigma weight residual -52.28 100.99 -153.27 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" O2A AGS E 401 " pdb=" O3A AGS E 401 " pdb=" PA AGS E 401 " pdb=" PB AGS E 401 " ideal model delta sinusoidal sigma weight residual -52.28 92.86 -145.14 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 8991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1820 0.052 - 0.103: 291 0.103 - 0.155: 84 0.155 - 0.206: 3 0.206 - 0.258: 4 Chirality restraints: 2202 Sorted by residual: chirality pdb=" C3' AGS F 401 " pdb=" C2' AGS F 401 " pdb=" C4' AGS F 401 " pdb=" O3' AGS F 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" C3' AGS D 401 " pdb=" C2' AGS D 401 " pdb=" C4' AGS D 401 " pdb=" O3' AGS D 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C3' AGS E 401 " pdb=" C2' AGS E 401 " pdb=" C4' AGS E 401 " pdb=" O3' AGS E 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.60 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 2199 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 272 " -0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO D 273 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 338 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO F 339 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO F 339 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 339 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 272 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO E 273 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO E 273 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 273 " -0.030 5.00e-02 4.00e+02 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 84 2.38 - 3.01: 8445 3.01 - 3.64: 20964 3.64 - 4.27: 31908 4.27 - 4.90: 53986 Nonbonded interactions: 115387 Sorted by model distance: nonbonded pdb=" O3G AGS F 401 " pdb="MG MG F 402 " model vdw 1.751 2.170 nonbonded pdb=" O2B AGS A 401 " pdb="MG MG A 402 " model vdw 1.830 2.170 nonbonded pdb=" O3G AGS E 401 " pdb="MG MG E 402 " model vdw 1.851 2.170 nonbonded pdb=" O HOH B 526 " pdb=" O HOH B 537 " model vdw 1.874 3.040 nonbonded pdb=" OG SER C 232 " pdb=" O HOH C 501 " model vdw 1.877 3.040 ... (remaining 115382 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.00 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: 2.100 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: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.040 Find NCS groups from input model: 0.310 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 23.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 14262 Z= 0.255 Angle : 0.700 9.654 19344 Z= 0.330 Chirality : 0.043 0.258 2202 Planarity : 0.006 0.054 2520 Dihedral : 14.503 155.953 5610 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.84 % Allowed : 5.14 % Favored : 93.02 % 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: 2.13 (0.20), residues: 1788 helix: 2.66 (0.16), residues: 946 sheet: 1.19 (0.35), residues: 194 loop : -0.44 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 152 TYR 0.014 0.002 TYR C 214 PHE 0.012 0.002 PHE B 324 TRP 0.008 0.002 TRP D 211 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.25 (14262) covalent geometry : angle 0.70012 / 0.33 (19344) hydrogen bonds : bond 0.12530 / 8.56 ( 832) hydrogen bonds : angle 4.42637 / 3.18 ( 2430) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.3744 (mtt) cc_final: 0.1089 (ttt) REVERT: A 245 LYS cc_start: 0.6903 (OUTLIER) cc_final: 0.6446 (mtmt) REVERT: A 327 GLN cc_start: 0.6171 (mm110) cc_final: 0.5955 (mm110) REVERT: A 357 GLN cc_start: 0.7126 (tt0) cc_final: 0.6758 (tt0) REVERT: B 80 MET cc_start: 0.4857 (mpp) cc_final: 0.3215 (mmp) REVERT: C 132 ILE cc_start: 0.5971 (OUTLIER) cc_final: 0.5718 (tp) REVERT: C 195 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6020 (pm20) REVERT: D 94 ASP cc_start: 0.7371 (t0) cc_final: 0.7078 (t0) REVERT: D 142 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8261 (tt) REVERT: D 359 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6660 (mt-10) REVERT: E 93 ARG cc_start: 0.7215 (tpt170) cc_final: 0.7014 (tpt-90) REVERT: E 247 MET cc_start: 0.7628 (ttp) cc_final: 0.7117 (ttm) REVERT: E 274 VAL cc_start: 0.8998 (p) cc_final: 0.8578 (t) REVERT: F 247 MET cc_start: 0.6999 (ttp) cc_final: 0.6512 (ttm) REVERT: F 279 ASP cc_start: 0.6837 (OUTLIER) cc_final: 0.6495 (m-30) outliers start: 28 outliers final: 12 residues processed: 233 average time/residue: 0.6551 time to fit residues: 166.2925 Evaluate side-chains 206 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 362 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 96 GLN ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 GLN F 146 GLN F 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.194018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.175948 restraints weight = 14116.162| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 0.86 r_work: 0.3649 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14262 Z= 0.128 Angle : 0.554 9.592 19344 Z= 0.287 Chirality : 0.041 0.155 2202 Planarity : 0.005 0.051 2520 Dihedral : 13.304 150.958 2186 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.57 % Favored : 98.38 % Rotamer: Outliers : 2.37 % Allowed : 9.82 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.49 (0.20), residues: 1788 helix: 2.80 (0.16), residues: 953 sheet: 1.25 (0.35), residues: 196 loop : 0.01 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 293 TYR 0.018 0.002 TYR D 101 PHE 0.008 0.001 PHE F 307 TRP 0.006 0.001 TRP A 200 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (14262) covalent geometry : angle 0.55399 / 0.29 (19344) hydrogen bonds : bond 0.04614 / 3.22 ( 832) hydrogen bonds : angle 3.41679 / 2.44 ( 2430) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 80 MET cc_start: 0.3556 (mtt) cc_final: 0.1248 (ttt) REVERT: A 245 LYS cc_start: 0.7081 (OUTLIER) cc_final: 0.6835 (mtmt) REVERT: A 357 GLN cc_start: 0.7129 (tt0) cc_final: 0.6867 (tt0) REVERT: E 247 MET cc_start: 0.7829 (ttp) cc_final: 0.7008 (ttm) REVERT: E 274 VAL cc_start: 0.8902 (p) cc_final: 0.8618 (t) outliers start: 36 outliers final: 18 residues processed: 224 average time/residue: 0.6161 time to fit residues: 151.3443 Evaluate side-chains 209 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain F residue 362 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 100 optimal weight: 0.1980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 83 optimal weight: 0.0270 chunk 68 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 181 ASN ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN F 146 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.196100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.178125 restraints weight = 14257.864| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 0.89 r_work: 0.3669 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14262 Z= 0.104 Angle : 0.491 6.552 19344 Z= 0.255 Chirality : 0.039 0.144 2202 Planarity : 0.005 0.051 2520 Dihedral : 12.841 150.047 2168 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.29 % Favored : 98.66 % Rotamer: Outliers : 2.24 % Allowed : 11.79 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.20), residues: 1788 helix: 2.87 (0.16), residues: 951 sheet: 1.51 (0.35), residues: 196 loop : 0.11 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 344 TYR 0.018 0.001 TYR A 203 PHE 0.007 0.001 PHE E 249 TRP 0.005 0.001 TRP E 200 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (14262) covalent geometry : angle 0.49119 / 0.26 (19344) hydrogen bonds : bond 0.03953 / 2.76 ( 832) hydrogen bonds : angle 3.23626 / 2.32 ( 2430) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 0.580 Fit side-chains REVERT: A 80 MET cc_start: 0.3517 (mtt) cc_final: 0.1159 (ttt) REVERT: B 148 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7145 (pt0) REVERT: B 195 GLU cc_start: 0.7165 (pt0) cc_final: 0.6918 (mt-10) REVERT: B 207 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: C 342 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7977 (tt) REVERT: E 247 MET cc_start: 0.7849 (ttp) cc_final: 0.7026 (ttm) REVERT: E 274 VAL cc_start: 0.8885 (p) cc_final: 0.8605 (t) REVERT: F 362 LEU cc_start: 0.4450 (OUTLIER) cc_final: 0.4141 (pt) outliers start: 34 outliers final: 18 residues processed: 217 average time/residue: 0.6392 time to fit residues: 151.2871 Evaluate side-chains 212 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 357 GLN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain F residue 362 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 70 optimal weight: 0.1980 chunk 155 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 46 optimal weight: 0.2980 chunk 97 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 329 ASN C 181 ASN E 327 GLN E 329 ASN F 146 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.195688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.161134 restraints weight = 14015.960| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 0.86 r_work: 0.3452 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14262 Z= 0.106 Angle : 0.501 7.005 19344 Z= 0.259 Chirality : 0.039 0.142 2202 Planarity : 0.005 0.051 2520 Dihedral : 12.734 149.281 2165 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.29 % Favored : 98.66 % Rotamer: Outliers : 2.70 % Allowed : 12.32 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.20), residues: 1788 helix: 2.76 (0.16), residues: 963 sheet: 1.69 (0.35), residues: 196 loop : 0.26 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 93 TYR 0.015 0.002 TYR A 203 PHE 0.006 0.001 PHE C 324 TRP 0.004 0.001 TRP F 200 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (14262) covalent geometry : angle 0.50062 / 0.26 (19344) hydrogen bonds : bond 0.03930 / 2.75 ( 832) hydrogen bonds : angle 3.22414 / 2.32 ( 2430) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 80 MET cc_start: 0.3690 (mtt) cc_final: 0.1142 (ttt) REVERT: B 195 GLU cc_start: 0.7293 (pt0) cc_final: 0.7027 (mt-10) REVERT: B 207 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: D 359 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6566 (mt-10) REVERT: E 247 MET cc_start: 0.7866 (ttp) cc_final: 0.7002 (ttm) REVERT: E 274 VAL cc_start: 0.8889 (p) cc_final: 0.8627 (t) REVERT: E 279 ASP cc_start: 0.7761 (m-30) cc_final: 0.7451 (m-30) outliers start: 41 outliers final: 19 residues processed: 216 average time/residue: 0.6165 time to fit residues: 146.0211 Evaluate side-chains 212 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain E residue 358 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 85 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 133 optimal weight: 0.1980 chunk 101 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 162 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 329 ASN C 181 ASN ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN E 329 ASN F 146 GLN F 259 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.194532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.176179 restraints weight = 14181.674| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 0.83 r_work: 0.3657 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14262 Z= 0.127 Angle : 0.544 6.952 19344 Z= 0.281 Chirality : 0.041 0.149 2202 Planarity : 0.005 0.059 2520 Dihedral : 12.686 151.616 2160 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.62 % Favored : 98.32 % Rotamer: Outliers : 2.90 % Allowed : 12.98 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.20), residues: 1788 helix: 2.73 (0.16), residues: 959 sheet: 1.70 (0.36), residues: 196 loop : 0.18 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 344 TYR 0.015 0.002 TYR C 214 PHE 0.010 0.001 PHE C 324 TRP 0.005 0.001 TRP D 211 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (14262) covalent geometry : angle 0.54424 / 0.28 (19344) hydrogen bonds : bond 0.04367 / 3.07 ( 832) hydrogen bonds : angle 3.29664 / 2.38 ( 2430) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 80 MET cc_start: 0.3491 (mtt) cc_final: 0.1235 (ttt) REVERT: A 179 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7817 (tt) REVERT: B 195 GLU cc_start: 0.7102 (pt0) cc_final: 0.6841 (mt-10) REVERT: B 207 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: C 342 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8110 (tt) REVERT: D 359 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6504 (mt-10) REVERT: E 109 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.6058 (tt0) REVERT: E 247 MET cc_start: 0.7846 (ttp) cc_final: 0.7113 (ttm) REVERT: E 274 VAL cc_start: 0.8893 (p) cc_final: 0.8629 (t) REVERT: E 279 ASP cc_start: 0.7665 (m-30) cc_final: 0.7369 (m-30) outliers start: 44 outliers final: 25 residues processed: 216 average time/residue: 0.6230 time to fit residues: 147.3714 Evaluate side-chains 215 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 178 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 121 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 78 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 177 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 329 ASN C 181 ASN ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN E 329 ASN F 146 GLN F 259 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.194866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.142091 restraints weight = 14092.018| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.78 r_work: 0.3079 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14262 Z= 0.110 Angle : 0.508 6.728 19344 Z= 0.264 Chirality : 0.040 0.141 2202 Planarity : 0.005 0.051 2520 Dihedral : 12.606 150.895 2160 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.29 % Favored : 98.66 % Rotamer: Outliers : 2.44 % Allowed : 14.10 % Favored : 83.47 % 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: 2.63 (0.20), residues: 1788 helix: 2.73 (0.16), residues: 960 sheet: 1.78 (0.36), residues: 196 loop : 0.19 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 344 TYR 0.013 0.002 TYR C 214 PHE 0.007 0.001 PHE C 324 TRP 0.004 0.001 TRP A 200 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (14262) covalent geometry : angle 0.50758 / 0.26 (19344) hydrogen bonds : bond 0.03997 / 2.80 ( 832) hydrogen bonds : angle 3.25336 / 2.35 ( 2430) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 0.591 Fit side-chains REVERT: A 179 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7453 (tt) REVERT: A 344 ARG cc_start: 0.7067 (ttm110) cc_final: 0.6476 (mtm180) REVERT: A 354 MET cc_start: 0.7872 (mmt) cc_final: 0.7627 (tpt) REVERT: B 185 PRO cc_start: 0.8166 (Cg_exo) cc_final: 0.7959 (Cg_endo) REVERT: B 195 GLU cc_start: 0.7328 (pt0) cc_final: 0.7097 (mt-10) REVERT: B 207 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: D 358 ASP cc_start: 0.7231 (m-30) cc_final: 0.7014 (m-30) REVERT: D 359 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6708 (mt-10) REVERT: E 109 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7204 (tp30) REVERT: E 191 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8167 (mt) REVERT: E 274 VAL cc_start: 0.8867 (p) cc_final: 0.8564 (t) REVERT: E 279 ASP cc_start: 0.7836 (m-30) cc_final: 0.7505 (m-30) outliers start: 37 outliers final: 22 residues processed: 207 average time/residue: 0.6005 time to fit residues: 136.3188 Evaluate side-chains 214 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 179 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 3 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 329 ASN C 181 ASN ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN E 329 ASN F 259 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.195239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.147088 restraints weight = 14078.844| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.82 r_work: 0.3088 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14262 Z= 0.111 Angle : 0.513 6.970 19344 Z= 0.266 Chirality : 0.040 0.141 2202 Planarity : 0.005 0.051 2520 Dihedral : 12.540 150.802 2156 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.51 % Favored : 98.43 % Rotamer: Outliers : 2.90 % Allowed : 14.03 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.63 (0.20), residues: 1788 helix: 2.73 (0.16), residues: 962 sheet: 1.82 (0.36), residues: 196 loop : 0.16 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 344 TYR 0.014 0.002 TYR C 214 PHE 0.008 0.001 PHE C 324 TRP 0.004 0.001 TRP A 200 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (14262) covalent geometry : angle 0.51290 / 0.27 (19344) hydrogen bonds : bond 0.04023 / 2.83 ( 832) hydrogen bonds : angle 3.25201 / 2.35 ( 2430) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 179 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7433 (tt) REVERT: A 344 ARG cc_start: 0.7053 (ttm110) cc_final: 0.6542 (mtm180) REVERT: A 354 MET cc_start: 0.7815 (mmt) cc_final: 0.7567 (tpt) REVERT: B 195 GLU cc_start: 0.7293 (pt0) cc_final: 0.7075 (mt-10) REVERT: B 207 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: C 304 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8605 (mtpm) REVERT: D 359 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6681 (mt-10) REVERT: E 109 GLU cc_start: 0.7403 (tt0) cc_final: 0.7148 (tp30) REVERT: E 191 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8172 (mt) REVERT: E 274 VAL cc_start: 0.8871 (p) cc_final: 0.8546 (t) REVERT: F 315 LYS cc_start: 0.6119 (mptt) cc_final: 0.5875 (mmmt) REVERT: F 354 MET cc_start: 0.7903 (mmp) cc_final: 0.7154 (tpt) outliers start: 44 outliers final: 28 residues processed: 218 average time/residue: 0.5791 time to fit residues: 138.6726 Evaluate side-chains 219 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 357 GLN Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain F residue 179 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 65 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 158 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 329 ASN C 181 ASN ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN E 329 ASN F 146 GLN F 259 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.195439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.176673 restraints weight = 14062.395| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 0.85 r_work: 0.3658 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14262 Z= 0.128 Angle : 0.549 6.928 19344 Z= 0.283 Chirality : 0.041 0.146 2202 Planarity : 0.005 0.051 2520 Dihedral : 12.612 151.188 2156 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.57 % Favored : 98.38 % Rotamer: Outliers : 2.77 % Allowed : 14.43 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.20), residues: 1788 helix: 2.69 (0.16), residues: 962 sheet: 1.74 (0.36), residues: 196 loop : 0.08 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 344 TYR 0.016 0.002 TYR C 214 PHE 0.010 0.001 PHE C 324 TRP 0.006 0.001 TRP F 211 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (14262) covalent geometry : angle 0.54870 / 0.28 (19344) hydrogen bonds : bond 0.04373 / 3.08 ( 832) hydrogen bonds : angle 3.30036 / 2.39 ( 2430) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7829 (tt) REVERT: B 195 GLU cc_start: 0.7111 (pt0) cc_final: 0.6844 (mt-10) REVERT: B 207 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: C 304 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8286 (mtpm) REVERT: D 359 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6544 (mt-10) REVERT: E 274 VAL cc_start: 0.8909 (p) cc_final: 0.8631 (t) REVERT: E 279 ASP cc_start: 0.7712 (m-30) cc_final: 0.7401 (m-30) REVERT: F 354 MET cc_start: 0.7913 (mmp) cc_final: 0.7567 (tpt) outliers start: 42 outliers final: 27 residues processed: 215 average time/residue: 0.5759 time to fit residues: 135.7510 Evaluate side-chains 216 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 357 GLN Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain F residue 179 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 17 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 chunk 172 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 GLN C 181 ASN ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN E 329 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.194965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.144670 restraints weight = 14117.204| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.32 r_work: 0.3089 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14262 Z= 0.110 Angle : 0.524 8.280 19344 Z= 0.270 Chirality : 0.040 0.139 2202 Planarity : 0.004 0.051 2520 Dihedral : 12.532 151.032 2156 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.40 % Favored : 98.55 % Rotamer: Outliers : 2.24 % Allowed : 15.28 % Favored : 82.48 % 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: 2.61 (0.20), residues: 1788 helix: 2.70 (0.16), residues: 962 sheet: 1.83 (0.36), residues: 196 loop : 0.17 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 194 TYR 0.013 0.002 TYR C 214 PHE 0.007 0.001 PHE C 324 TRP 0.005 0.001 TRP A 200 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (14262) covalent geometry : angle 0.52396 / 0.27 (19344) hydrogen bonds : bond 0.03958 / 2.78 ( 832) hydrogen bonds : angle 3.25815 / 2.35 ( 2430) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 179 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7431 (tt) REVERT: A 245 LYS cc_start: 0.6571 (OUTLIER) cc_final: 0.6048 (mtmt) REVERT: B 195 GLU cc_start: 0.7253 (pt0) cc_final: 0.7017 (mt-10) REVERT: B 207 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: C 304 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8600 (mtpm) REVERT: D 359 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6640 (mt-10) REVERT: E 80 MET cc_start: 0.7016 (mmt) cc_final: 0.6620 (mtp) REVERT: E 274 VAL cc_start: 0.8839 (p) cc_final: 0.8533 (t) REVERT: E 279 ASP cc_start: 0.7842 (m-30) cc_final: 0.7537 (m-30) REVERT: F 354 MET cc_start: 0.7814 (mmp) cc_final: 0.7109 (tpt) outliers start: 34 outliers final: 22 residues processed: 209 average time/residue: 0.5889 time to fit residues: 134.9866 Evaluate side-chains 210 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 178 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 91 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 20 optimal weight: 0.0670 chunk 144 optimal weight: 0.9980 chunk 126 optimal weight: 8.9990 chunk 80 optimal weight: 0.0170 chunk 94 optimal weight: 0.6980 chunk 168 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 329 ASN C 181 ASN ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN E 329 ASN F 259 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.198729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.179125 restraints weight = 14069.426| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 0.89 r_work: 0.3673 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14262 Z= 0.101 Angle : 0.509 8.749 19344 Z= 0.262 Chirality : 0.039 0.134 2202 Planarity : 0.004 0.051 2520 Dihedral : 12.417 149.883 2156 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.12 % Favored : 98.83 % Rotamer: Outliers : 1.58 % Allowed : 15.81 % Favored : 82.61 % 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: 2.67 (0.20), residues: 1788 helix: 2.73 (0.16), residues: 962 sheet: 1.85 (0.36), residues: 197 loop : 0.24 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 194 TYR 0.011 0.001 TYR A 203 PHE 0.006 0.001 PHE C 324 TRP 0.005 0.001 TRP F 200 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (14262) covalent geometry : angle 0.50903 / 0.26 (19344) hydrogen bonds : bond 0.03617 / 2.56 ( 832) hydrogen bonds : angle 3.20522 / 2.31 ( 2430) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.545 Fit side-chains REVERT: B 207 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: C 304 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8268 (mtpm) REVERT: D 160 MET cc_start: 0.7837 (mtm) cc_final: 0.7425 (mtp) REVERT: D 359 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6467 (mt-10) REVERT: E 80 MET cc_start: 0.5034 (mmt) cc_final: 0.4738 (mtp) REVERT: E 274 VAL cc_start: 0.8859 (p) cc_final: 0.8596 (t) REVERT: E 279 ASP cc_start: 0.7647 (m-30) cc_final: 0.7334 (m-30) REVERT: F 354 MET cc_start: 0.7924 (mmp) cc_final: 0.7545 (tpt) outliers start: 24 outliers final: 15 residues processed: 210 average time/residue: 0.5904 time to fit residues: 135.3765 Evaluate side-chains 207 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain F residue 91 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 169 optimal weight: 9.9990 chunk 31 optimal weight: 30.0000 chunk 17 optimal weight: 0.0270 chunk 43 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 120 optimal weight: 30.0000 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 181 ASN ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN E 329 ASN F 146 GLN F 259 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.192786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.140149 restraints weight = 14045.561| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.80 r_work: 0.3119 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14262 Z= 0.147 Angle : 0.587 8.913 19344 Z= 0.301 Chirality : 0.042 0.148 2202 Planarity : 0.005 0.052 2520 Dihedral : 12.599 151.385 2154 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.96 % Favored : 97.99 % Rotamer: Outliers : 2.04 % Allowed : 15.94 % Favored : 82.02 % 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: 2.53 (0.20), residues: 1788 helix: 2.67 (0.16), residues: 960 sheet: 1.77 (0.36), residues: 196 loop : 0.08 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 99 TYR 0.017 0.002 TYR C 214 PHE 0.011 0.001 PHE C 324 TRP 0.007 0.002 TRP D 211 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (14262) covalent geometry : angle 0.58741 / 0.30 (19344) hydrogen bonds : bond 0.04561 / 3.22 ( 832) hydrogen bonds : angle 3.30274 / 2.39 ( 2430) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4392.34 seconds wall clock time: 75 minutes 52.39 seconds (4552.39 seconds total)