Starting phenix.real_space_refine on Thu Feb 5 01:52:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r34_53547/02_2026/9r34_53547.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r34_53547/02_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_53547/02_2026/9r34_53547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r34_53547/02_2026/9r34_53547.map" model { file = "/net/cci-nas-00/data/ceres_data/9r34_53547/02_2026/9r34_53547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r34_53547/02_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-2.0-5952/lib/python3.9/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: 3.73, per 1000 atoms: 0.26 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: 1.20 Conformation dependent library (CDL) restraints added in 807.9 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: 0.35 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: 2.49 Time building geometry restraints manager: 1.63 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=" N ARG A 152 " pdb=" CA ARG A 152 " ideal model delta sigma weight residual 1.454 1.479 -0.025 1.29e-02 6.01e+03 3.80e+00 bond pdb=" N ASP D 64 " pdb=" CA ASP D 64 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.11e+00 bond pdb=" N ASP E 64 " pdb=" CA ASP E 64 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N ASP B 64 " pdb=" CA ASP B 64 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N ASP A 64 " pdb=" CA ASP A 64 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 ... (remaining 14257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 18915 1.67 - 3.33: 366 3.33 - 5.00: 57 5.00 - 6.67: 5 6.67 - 8.33: 1 Bond angle restraints: 19344 Sorted by residual: angle pdb=" CA ARG A 152 " pdb=" C ARG A 152 " pdb=" O ARG A 152 " ideal model delta sigma weight residual 121.44 118.04 3.40 1.17e+00 7.31e-01 8.43e+00 angle pdb=" PA AGS D 401 " pdb=" O3A AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sigma weight residual 119.76 128.09 -8.33 3.00e+00 1.11e-01 7.72e+00 angle pdb=" PA AGS C 401 " pdb=" O3A AGS C 401 " pdb=" PB AGS C 401 " ideal model delta sigma weight residual 119.76 126.02 -6.26 3.00e+00 1.11e-01 4.36e+00 angle pdb=" N VAL D 250 " pdb=" CA VAL D 250 " pdb=" C VAL D 250 " ideal model delta sigma weight residual 109.34 113.62 -4.28 2.08e+00 2.31e-01 4.24e+00 angle pdb=" N VAL B 250 " pdb=" CA VAL B 250 " pdb=" C VAL B 250 " ideal model delta sigma weight residual 109.34 113.51 -4.17 2.08e+00 2.31e-01 4.01e+00 ... (remaining 19339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8278 17.98 - 35.96: 428 35.96 - 53.93: 142 53.93 - 71.91: 26 71.91 - 89.89: 12 Dihedral angle restraints: 8886 sinusoidal: 3684 harmonic: 5202 Sorted by residual: dihedral pdb=" CA PRO E 193 " pdb=" C PRO E 193 " pdb=" N ARG E 194 " pdb=" CA ARG E 194 " ideal model delta harmonic sigma weight residual -180.00 -160.60 -19.40 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA TRP E 211 " pdb=" C TRP E 211 " pdb=" N ASP E 212 " pdb=" CA ASP E 212 " ideal model delta harmonic sigma weight residual 180.00 -162.81 -17.19 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA VAL B 197 " pdb=" C VAL B 197 " pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta harmonic sigma weight residual -180.00 -162.92 -17.08 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 8883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1488 0.034 - 0.068: 528 0.068 - 0.102: 107 0.102 - 0.136: 82 0.136 - 0.170: 9 Chirality restraints: 2214 Sorted by residual: chirality pdb=" CA ILE E 256 " pdb=" N ILE E 256 " pdb=" C ILE E 256 " pdb=" CB ILE E 256 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.25e-01 chirality pdb=" CA ILE B 158 " pdb=" N ILE B 158 " pdb=" C ILE B 158 " pdb=" CB ILE B 158 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA ILE F 158 " pdb=" N ILE F 158 " pdb=" C ILE F 158 " pdb=" CB ILE F 158 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 ... (remaining 2211 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: 1.650 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.320 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14262 Z= 0.179 Angle : 0.586 8.334 19344 Z= 0.305 Chirality : 0.041 0.170 2214 Planarity : 0.006 0.054 2520 Dihedral : 13.008 89.888 5502 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 covalent geometry : bond 0.00416 (14262) covalent geometry : angle 0.58566 (19344) hydrogen bonds : bond 0.12530 ( 832) hydrogen bonds : angle 4.42637 ( 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 : 0.569 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: 0.6247 time to fit residues: 158.2085 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 : 0.440 ------------------------------------------------------------------------------- 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: 0.0070 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: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4038 r_free = 0.4038 target = 0.193790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.145401 restraints weight = 14144.877| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.77 r_work: 0.3057 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14262 Z= 0.127 Angle : 0.567 9.977 19344 Z= 0.291 Chirality : 0.041 0.154 2214 Planarity : 0.005 0.050 2520 Dihedral : 8.461 57.080 2078 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.85 % Favored : 98.10 % 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: 2.52 (0.20), residues: 1788 helix: 2.77 (0.16), residues: 959 sheet: 1.30 (0.35), residues: 197 loop : 0.07 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 152 TYR 0.016 0.002 TYR D 101 PHE 0.009 0.001 PHE E 249 TRP 0.006 0.001 TRP F 200 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00267 (14262) covalent geometry : angle 0.56714 (19344) hydrogen bonds : bond 0.04876 ( 832) hydrogen bonds : angle 3.44158 ( 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 242 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.3201 (mtt) cc_final: 0.0619 (ttt) REVERT: A 245 LYS cc_start: 0.6650 (OUTLIER) cc_final: 0.6208 (mtmt) REVERT: A 327 GLN cc_start: 0.6270 (mm110) cc_final: 0.6030 (mm110) REVERT: A 357 GLN cc_start: 0.7183 (tt0) cc_final: 0.6609 (tt0) REVERT: B 80 MET cc_start: 0.5610 (mpp) cc_final: 0.3663 (mmp) REVERT: B 101 TYR cc_start: 0.6252 (t80) cc_final: 0.4806 (t80) REVERT: E 93 ARG cc_start: 0.6958 (tpt170) cc_final: 0.6677 (tpt-90) REVERT: E 247 MET cc_start: 0.7794 (ttp) cc_final: 0.7006 (ttm) REVERT: E 274 VAL cc_start: 0.8936 (p) cc_final: 0.8622 (t) REVERT: E 329 ASN cc_start: 0.8707 (m-40) cc_final: 0.8503 (m110) outliers start: 36 outliers final: 22 residues processed: 226 average time/residue: 0.5828 time to fit residues: 143.5308 Evaluate side-chains 213 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 87 SER 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 267 ASP Chi-restraints excluded: chain D residue 357 GLN 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 217 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: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN B 348 GLN ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN 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 = 0.4024 r_free = 0.4024 target = 0.192430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.141982 restraints weight = 14213.039| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.25 r_work: 0.3005 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14262 Z= 0.149 Angle : 0.590 7.103 19344 Z= 0.301 Chirality : 0.042 0.159 2214 Planarity : 0.005 0.051 2520 Dihedral : 8.098 53.769 2061 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.68 % Favored : 98.27 % Rotamer: Outliers : 3.03 % Allowed : 11.26 % Favored : 85.70 % 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: 2.39 (0.20), residues: 1788 helix: 2.71 (0.16), residues: 949 sheet: 1.35 (0.35), residues: 196 loop : -0.08 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 344 TYR 0.022 0.002 TYR A 203 PHE 0.010 0.001 PHE C 324 TRP 0.007 0.002 TRP D 211 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00338 (14262) covalent geometry : angle 0.59024 (19344) hydrogen bonds : bond 0.05042 ( 832) hydrogen bonds : angle 3.41384 ( 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 242 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 196 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 80 MET cc_start: 0.2765 (mtt) cc_final: 0.0446 (ttt) REVERT: A 137 MET cc_start: 0.4316 (tmt) cc_final: 0.4041 (tmm) REVERT: A 245 LYS cc_start: 0.6517 (OUTLIER) cc_final: 0.6064 (mtmt) REVERT: A 288 GLU cc_start: 0.7390 (tp30) cc_final: 0.6413 (tt0) REVERT: A 327 GLN cc_start: 0.6132 (mm110) cc_final: 0.5885 (mm110) REVERT: A 357 GLN cc_start: 0.6955 (tt0) cc_final: 0.6373 (tt0) REVERT: A 361 GLN cc_start: 0.7000 (tp-100) cc_final: 0.6744 (tp40) REVERT: B 148 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7037 (pt0) REVERT: B 207 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: B 285 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8327 (m) REVERT: B 316 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8410 (mtm) REVERT: C 342 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8121 (tt) REVERT: D 102 MET cc_start: 0.6922 (mtp) cc_final: 0.6625 (mtp) REVERT: D 358 ASP cc_start: 0.7371 (m-30) cc_final: 0.7130 (m-30) REVERT: D 359 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6837 (mt-10) REVERT: E 93 ARG cc_start: 0.6899 (tpt170) cc_final: 0.6441 (tpt170) REVERT: E 247 MET cc_start: 0.7750 (ttp) cc_final: 0.6918 (ttm) REVERT: E 274 VAL cc_start: 0.8905 (p) cc_final: 0.8579 (t) REVERT: E 329 ASN cc_start: 0.8719 (m-40) cc_final: 0.8503 (m110) outliers start: 46 outliers final: 25 residues processed: 222 average time/residue: 0.6418 time to fit residues: 155.0824 Evaluate side-chains 217 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 92 VAL 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 B residue 316 MET 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 355 GLU 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 137 MET Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 151 SER 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 347 ILE 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: 3.9990 chunk 3 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 170 optimal weight: 0.0980 chunk 161 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 ASN E 327 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 = 0.4066 r_free = 0.4066 target = 0.196868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.168188 restraints weight = 13928.703| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.25 r_work: 0.3467 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14262 Z= 0.111 Angle : 0.520 7.122 19344 Z= 0.268 Chirality : 0.040 0.146 2214 Planarity : 0.005 0.054 2520 Dihedral : 7.813 50.153 2061 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.17 % Favored : 98.77 % Rotamer: Outliers : 3.10 % Allowed : 12.12 % Favored : 84.78 % 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: 2.73 (0.16), residues: 954 sheet: 1.59 (0.36), residues: 196 loop : 0.07 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 344 TYR 0.012 0.002 TYR C 214 PHE 0.007 0.001 PHE E 249 TRP 0.005 0.001 TRP A 200 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00231 (14262) covalent geometry : angle 0.51970 (19344) hydrogen bonds : bond 0.04207 ( 832) hydrogen bonds : angle 3.29630 ( 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 242 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 195 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 80 MET cc_start: 0.3648 (mtt) cc_final: 0.1069 (ttt) REVERT: A 288 GLU cc_start: 0.7313 (tp30) cc_final: 0.6944 (tt0) REVERT: A 357 GLN cc_start: 0.7357 (tt0) cc_final: 0.6984 (tt0) REVERT: B 148 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7318 (pt0) REVERT: B 207 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: B 316 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8436 (mtm) REVERT: C 342 ILE cc_start: 0.8312 (tt) cc_final: 0.8108 (tt) REVERT: E 247 MET cc_start: 0.7842 (ttp) cc_final: 0.7097 (ttm) REVERT: E 274 VAL cc_start: 0.8889 (p) cc_final: 0.8609 (t) outliers start: 47 outliers final: 26 residues processed: 224 average time/residue: 0.6492 time to fit residues: 158.8444 Evaluate side-chains 216 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 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 92 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 316 MET 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 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 355 GLU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 137 MET 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 362 LEU 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: 2.9990 chunk 133 optimal weight: 0.2980 chunk 101 optimal weight: 0.7980 chunk 173 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 ASN C 181 ASN ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN F 146 GLN F 361 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.195153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.145415 restraints weight = 13945.766| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.30 r_work: 0.3092 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14262 Z= 0.139 Angle : 0.575 8.386 19344 Z= 0.294 Chirality : 0.042 0.164 2214 Planarity : 0.005 0.057 2520 Dihedral : 7.812 48.683 2059 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.85 % Favored : 98.10 % Rotamer: Outliers : 3.29 % Allowed : 12.85 % Favored : 83.86 % 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: 2.46 (0.20), residues: 1788 helix: 2.67 (0.16), residues: 955 sheet: 1.59 (0.36), residues: 196 loop : 0.04 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 344 TYR 0.016 0.002 TYR C 214 PHE 0.010 0.001 PHE C 324 TRP 0.006 0.002 TRP D 211 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00313 (14262) covalent geometry : angle 0.57539 (19344) hydrogen bonds : bond 0.04657 ( 832) hydrogen bonds : angle 3.36768 ( 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 237 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 187 time to evaluate : 0.566 Fit side-chains REVERT: A 80 MET cc_start: 0.2370 (mtt) cc_final: 0.0412 (ttt) REVERT: A 179 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7504 (tt) REVERT: A 288 GLU cc_start: 0.7491 (tp30) cc_final: 0.6494 (tt0) REVERT: A 357 GLN cc_start: 0.7056 (tt0) cc_final: 0.6544 (tt0) REVERT: B 148 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7181 (pt0) REVERT: B 195 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7454 (mt-10) REVERT: B 207 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: B 316 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8483 (mtm) REVERT: C 87 SER cc_start: 0.7148 (t) cc_final: 0.6419 (p) REVERT: C 132 ILE cc_start: 0.6015 (OUTLIER) cc_final: 0.5776 (tp) REVERT: C 342 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8135 (tt) REVERT: D 358 ASP cc_start: 0.7383 (m-30) cc_final: 0.7131 (m-30) REVERT: D 359 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6845 (mt-10) REVERT: E 102 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7844 (tpt) REVERT: E 109 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6824 (tt0) REVERT: E 247 MET cc_start: 0.7747 (ttp) cc_final: 0.7071 (ttm) REVERT: E 274 VAL cc_start: 0.8891 (p) cc_final: 0.8561 (t) REVERT: F 279 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6779 (m-30) outliers start: 50 outliers final: 31 residues processed: 217 average time/residue: 0.6101 time to fit residues: 144.8212 Evaluate side-chains 225 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 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 137 MET Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 195 GLU 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 B residue 316 MET Chi-restraints excluded: chain C residue 132 ILE 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 151 SER 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 102 MET 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 150 THR Chi-restraints excluded: chain E residue 151 SER 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 Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 362 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 121 optimal weight: 5.9990 chunk 95 optimal weight: 0.2980 chunk 78 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 ASN C 181 ASN ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN 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 = 0.4043 r_free = 0.4043 target = 0.194335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.147603 restraints weight = 14048.396| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.67 r_work: 0.3079 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14262 Z= 0.119 Angle : 0.543 7.154 19344 Z= 0.281 Chirality : 0.041 0.144 2214 Planarity : 0.005 0.065 2520 Dihedral : 7.670 52.835 2059 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.34 % Favored : 98.60 % Rotamer: Outliers : 3.10 % Allowed : 13.50 % Favored : 83.40 % 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: 2.64 (0.16), residues: 956 sheet: 1.71 (0.36), residues: 196 loop : 0.10 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 344 TYR 0.013 0.002 TYR C 214 PHE 0.008 0.001 PHE F 307 TRP 0.005 0.001 TRP A 200 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00254 (14262) covalent geometry : angle 0.54269 (19344) hydrogen bonds : bond 0.04298 ( 832) hydrogen bonds : angle 3.36316 ( 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 238 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 191 time to evaluate : 0.417 Fit side-chains REVERT: A 80 MET cc_start: 0.3332 (mtt) cc_final: 0.0760 (ttt) REVERT: A 179 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7493 (tt) REVERT: A 288 GLU cc_start: 0.7391 (tp30) cc_final: 0.6564 (tt0) REVERT: A 344 ARG cc_start: 0.7374 (ttm110) cc_final: 0.6570 (mtm180) REVERT: A 357 GLN cc_start: 0.7050 (tt0) cc_final: 0.6589 (tt0) REVERT: A 361 GLN cc_start: 0.6827 (tp-100) cc_final: 0.6607 (mm-40) REVERT: B 148 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7171 (pt0) REVERT: B 207 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7601 (mp0) REVERT: B 316 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8449 (mtm) REVERT: C 87 SER cc_start: 0.7029 (OUTLIER) cc_final: 0.6255 (p) REVERT: C 132 ILE cc_start: 0.6070 (OUTLIER) cc_final: 0.5802 (tp) REVERT: C 342 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.8000 (tt) REVERT: D 102 MET cc_start: 0.6996 (mtp) cc_final: 0.6699 (mtt) REVERT: D 359 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6656 (mt-10) REVERT: E 109 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6915 (tt0) REVERT: E 274 VAL cc_start: 0.8902 (p) cc_final: 0.8582 (t) REVERT: F 279 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6703 (m-30) outliers start: 47 outliers final: 26 residues processed: 221 average time/residue: 0.5748 time to fit residues: 138.9008 Evaluate side-chains 223 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 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 217 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 132 ILE 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 188 LYS 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 151 SER 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 179 LEU Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 362 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 3 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 172 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 32 optimal weight: 0.0980 chunk 159 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.194893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.174899 restraints weight = 14043.362| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.00 r_work: 0.3624 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1564 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= 0.114 Angle : 0.532 6.648 19344 Z= 0.275 Chirality : 0.040 0.191 2214 Planarity : 0.005 0.053 2520 Dihedral : 7.570 59.021 2059 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.45 % Favored : 98.49 % Rotamer: Outliers : 3.49 % Allowed : 13.44 % 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: 2.49 (0.20), residues: 1788 helix: 2.59 (0.16), residues: 960 sheet: 1.76 (0.36), residues: 196 loop : 0.14 (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 0.005 0.001 TRP A 200 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00245 (14262) covalent geometry : angle 0.53173 (19344) hydrogen bonds : bond 0.04175 ( 832) hydrogen bonds : angle 3.31780 ( 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 246 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 193 time to evaluate : 0.562 Fit side-chains REVERT: A 80 MET cc_start: 0.3621 (mtt) cc_final: 0.1225 (ttt) REVERT: A 344 ARG cc_start: 0.6910 (ttm110) cc_final: 0.6634 (mtm180) REVERT: B 148 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7224 (pt0) REVERT: B 207 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: B 316 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8366 (mtm) REVERT: C 342 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8087 (tt) REVERT: D 359 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6486 (mt-10) REVERT: E 191 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8157 (mt) REVERT: E 274 VAL cc_start: 0.8902 (p) cc_final: 0.8609 (t) REVERT: F 279 ASP cc_start: 0.6844 (OUTLIER) cc_final: 0.6512 (m-30) outliers start: 53 outliers final: 30 residues processed: 228 average time/residue: 0.5528 time to fit residues: 138.0162 Evaluate side-chains 226 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 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 217 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain C residue 88 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 342 ILE 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 188 LYS Chi-restraints excluded: chain D residue 267 ASP 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 151 SER 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 Chi-restraints excluded: chain F residue 279 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 65 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 chunk 52 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 158 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 118 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 ASN C 181 ASN ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4042 r_free = 0.4042 target = 0.194195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.145774 restraints weight = 14079.801| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.77 r_work: 0.3086 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14262 Z= 0.126 Angle : 0.561 8.011 19344 Z= 0.287 Chirality : 0.041 0.146 2214 Planarity : 0.005 0.052 2520 Dihedral : 7.476 59.124 2057 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.62 % Favored : 98.32 % Rotamer: Outliers : 2.96 % Allowed : 14.36 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.20), residues: 1788 helix: 2.62 (0.16), residues: 957 sheet: 1.74 (0.36), residues: 196 loop : 0.09 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 344 TYR 0.014 0.002 TYR C 214 PHE 0.009 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 covalent geometry : bond 0.00279 (14262) covalent geometry : angle 0.56076 (19344) hydrogen bonds : bond 0.04335 ( 832) hydrogen bonds : angle 3.33251 ( 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 236 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 0.576 Fit side-chains REVERT: A 80 MET cc_start: 0.3241 (mtt) cc_final: 0.0888 (ttt) REVERT: A 344 ARG cc_start: 0.7381 (ttm110) cc_final: 0.6589 (mtm180) REVERT: B 148 GLU cc_start: 0.7523 (mt-10) cc_final: 0.6969 (pt0) REVERT: B 207 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: B 316 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8395 (mtm) REVERT: C 342 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.8017 (tt) REVERT: D 359 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6638 (mt-10) REVERT: E 191 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8182 (mt) REVERT: E 274 VAL cc_start: 0.8897 (p) cc_final: 0.8563 (t) REVERT: F 279 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6627 (m-30) outliers start: 45 outliers final: 30 residues processed: 218 average time/residue: 0.5521 time to fit residues: 132.1207 Evaluate side-chains 222 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 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 217 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain C residue 88 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 342 ILE 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 267 ASP 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 137 MET Chi-restraints excluded: chain E residue 151 SER 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 Chi-restraints excluded: chain F residue 279 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 17 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 153 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.193380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.140616 restraints weight = 14081.759| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.24 r_work: 0.3030 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14262 Z= 0.140 Angle : 0.594 13.863 19344 Z= 0.302 Chirality : 0.042 0.190 2214 Planarity : 0.005 0.052 2520 Dihedral : 7.562 58.911 2057 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.73 % Favored : 98.21 % Rotamer: Outliers : 2.90 % Allowed : 14.43 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.20), residues: 1788 helix: 2.57 (0.16), residues: 957 sheet: 1.69 (0.36), residues: 196 loop : -0.01 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 344 TYR 0.020 0.002 TYR F 101 PHE 0.011 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 covalent geometry : bond 0.00320 (14262) covalent geometry : angle 0.59372 (19344) hydrogen bonds : bond 0.04618 ( 832) hydrogen bonds : angle 3.37493 ( 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 232 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 0.367 Fit side-chains REVERT: A 80 MET cc_start: 0.3016 (mtt) cc_final: 0.0828 (ttt) REVERT: A 354 MET cc_start: 0.8018 (mmt) cc_final: 0.7744 (tpt) REVERT: B 207 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: B 316 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8427 (mtm) REVERT: C 342 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8118 (tt) REVERT: D 359 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6733 (mt-10) REVERT: E 274 VAL cc_start: 0.8905 (p) cc_final: 0.8563 (t) REVERT: F 279 ASP cc_start: 0.7037 (OUTLIER) cc_final: 0.6674 (m-30) outliers start: 44 outliers final: 35 residues processed: 217 average time/residue: 0.5433 time to fit residues: 129.3412 Evaluate side-chains 226 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 245 LYS Chi-restraints excluded: chain A residue 259 ASN 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 B residue 316 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 132 ILE 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 342 ILE 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 236 THR Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 151 SER 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 91 LEU Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 285 THR 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: 3.9990 chunk 108 optimal weight: 3.9990 chunk 20 optimal weight: 0.0670 chunk 144 optimal weight: 0.0470 chunk 126 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 overall best weight: 1.1420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.193236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.173106 restraints weight = 14100.246| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.02 r_work: 0.3598 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1643 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= 0.135 Angle : 0.589 12.685 19344 Z= 0.301 Chirality : 0.041 0.147 2214 Planarity : 0.005 0.077 2520 Dihedral : 7.552 59.858 2057 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.79 % Favored : 98.15 % Rotamer: Outliers : 2.70 % Allowed : 14.82 % 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: 2.37 (0.20), residues: 1788 helix: 2.57 (0.16), residues: 957 sheet: 1.70 (0.36), residues: 196 loop : -0.03 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG A 344 TYR 0.029 0.002 TYR F 101 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 covalent geometry : bond 0.00304 (14262) covalent geometry : angle 0.58864 (19344) hydrogen bonds : bond 0.04507 ( 832) hydrogen bonds : angle 3.37471 ( 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 227 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 0.557 Fit side-chains REVERT: A 80 MET cc_start: 0.3722 (mtt) cc_final: 0.1543 (ttt) REVERT: A 102 MET cc_start: 0.3697 (ppp) cc_final: 0.3450 (pp-130) REVERT: A 344 ARG cc_start: 0.6984 (ttm110) cc_final: 0.6567 (mtm180) REVERT: B 207 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: B 316 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8359 (mtm) REVERT: C 342 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8236 (tt) REVERT: D 359 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6538 (mt-10) REVERT: E 274 VAL cc_start: 0.8917 (p) cc_final: 0.8605 (t) REVERT: F 279 ASP cc_start: 0.6826 (OUTLIER) cc_final: 0.6506 (m-30) outliers start: 41 outliers final: 32 residues processed: 215 average time/residue: 0.5503 time to fit residues: 129.7751 Evaluate side-chains 221 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 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 217 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 132 ILE 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 342 ILE 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 359 GLU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 151 SER 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 91 LEU Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 285 THR 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: 20.0000 chunk 17 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 120 optimal weight: 30.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 ASN C 181 ASN ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.192750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.171879 restraints weight = 14053.784| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.07 r_work: 0.3573 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14262 Z= 0.149 Angle : 0.611 9.020 19344 Z= 0.313 Chirality : 0.042 0.152 2214 Planarity : 0.005 0.080 2520 Dihedral : 7.627 57.613 2057 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.93 % Rotamer: Outliers : 2.83 % Allowed : 14.95 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.20), residues: 1788 helix: 2.54 (0.16), residues: 957 sheet: 1.32 (0.34), residues: 220 loop : -0.10 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 344 TYR 0.018 0.002 TYR C 214 PHE 0.012 0.001 PHE C 324 TRP 0.007 0.002 TRP F 211 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00344 (14262) covalent geometry : angle 0.61088 (19344) hydrogen bonds : bond 0.04779 ( 832) hydrogen bonds : angle 3.40686 ( 2430) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4250.02 seconds wall clock time: 73 minutes 12.87 seconds (4392.87 seconds total)