Starting phenix.real_space_refine on Fri Jul 3 15:54:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7oug_13076/07_2026/7oug_13076.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oug_13076/07_2026/7oug_13076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oug_13076/07_2026/7oug_13076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oug_13076/07_2026/7oug_13076.map" model { file = "/net/cci-nas-00/data/ceres_data/7oug_13076/07_2026/7oug_13076.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oug_13076/07_2026/7oug_13076.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7oug_13076/07_2026/7oug_13076.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7oug_13076/07_2026/7oug_13076.cif" } resolution = 3.1 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= 0.021 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: 8 Type Number sf(0) Gaussians Zn 4 6.06 5 P 76 5.49 5 Mg 4 5.21 5 S 46 5.16 5 C 9424 2.51 5 N 2710 2.21 5 O 2824 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15090 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2057 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 17, 'TRANS': 240} Chain breaks: 2 Chain: "E" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2212 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 257} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2423 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "I" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 422 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "J" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 2, ' ZN': 1, 'RLT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 239 SG CYS D 35 105.427 119.943 25.979 1.00 64.43 S ATOM 260 SG CYS D 38 103.330 122.249 27.523 1.00 61.41 S ATOM 2296 SG CYS E 35 73.195 55.648 38.011 1.00 18.21 S ATOM 2317 SG CYS E 38 70.364 57.662 38.953 1.00 8.92 S Restraints were copied for chains: A, B, C, K, L Time building chain proxies: 3.75, per 1000 atoms: 0.25 Number of scatterers: 15090 At special positions: 0 Unit cell: (128.7, 166.1, 92.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 S 46 16.00 P 76 15.00 Mg 4 11.99 F 2 9.00 O 2824 8.00 N 2710 7.00 C 9424 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: 1.26 Conformation dependent library (CDL) restraints added in 588.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" ND1 HIS A 12 " pdb="ZN ZN A1000 " - pdb=" NE2 HIS A 8 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 38 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 35 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 8 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 12 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 35 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 38 " pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" ND1 HIS D 12 " pdb="ZN ZN D1000 " - pdb=" NE2 HIS D 8 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 38 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 35 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 8 " pdb="ZN ZN E 301 " - pdb=" ND1 HIS E 12 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 35 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 38 " Number of angles added : 6 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3212 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 12 sheets defined 51.6% alpha, 10.9% beta 20 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'D' and resid 3 through 12 Processing helix chain 'D' and resid 14 through 21 removed outlier: 3.502A pdb=" N LEU D 18 " --> pdb=" O GLY D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 35 Processing helix chain 'D' and resid 98 through 113 Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.565A pdb=" N LEU D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 175 Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 203 through 210 Processing helix chain 'E' and resid 4 through 12 Processing helix chain 'E' and resid 14 through 21 removed outlier: 3.645A pdb=" N HIS E 21 " --> pdb=" O ALA E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 35 Processing helix chain 'E' and resid 35 through 42 removed outlier: 3.584A pdb=" N ARG E 39 " --> pdb=" O CYS E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 113 Processing helix chain 'E' and resid 129 through 139 removed outlier: 3.511A pdb=" N LEU E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 153 Processing helix chain 'E' and resid 154 through 175 removed outlier: 3.915A pdb=" N ASP E 174 " --> pdb=" O LYS E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 194 Processing helix chain 'E' and resid 203 through 209 Processing helix chain 'F' and resid 29 through 33 removed outlier: 3.886A pdb=" N VAL F 33 " --> pdb=" O ILE F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 49 Processing helix chain 'F' and resid 62 through 81 removed outlier: 3.579A pdb=" N THR F 81 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 91 through 103 removed outlier: 3.723A pdb=" N VAL F 95 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL F 96 " --> pdb=" O TYR F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 146 Processing helix chain 'F' and resid 154 through 158 removed outlier: 3.739A pdb=" N LYS F 157 " --> pdb=" O ILE F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 169 Processing helix chain 'F' and resid 170 through 173 Processing helix chain 'F' and resid 175 through 193 removed outlier: 3.885A pdb=" N ARG F 188 " --> pdb=" O THR F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 213 removed outlier: 3.588A pdb=" N ILE F 200 " --> pdb=" O LEU F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 234 removed outlier: 3.825A pdb=" N LEU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 250 removed outlier: 3.589A pdb=" N LYS F 244 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 262 removed outlier: 3.830A pdb=" N VAL F 257 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LYS F 258 " --> pdb=" O HIS F 255 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER F 259 " --> pdb=" O LYS F 256 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER F 261 " --> pdb=" O LYS F 258 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL F 262 " --> pdb=" O SER F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 276 removed outlier: 3.636A pdb=" N LEU F 267 " --> pdb=" O TYR F 263 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU F 276 " --> pdb=" O VAL F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 281 No H-bonds generated for 'chain 'F' and resid 279 through 281' Processing helix chain 'F' and resid 282 through 292 Processing helix chain 'F' and resid 300 through 316 removed outlier: 4.029A pdb=" N PHE F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 333 removed outlier: 3.598A pdb=" N LYS F 333 " --> pdb=" O ARG F 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 12 Processing helix chain 'A' and resid 14 through 21 removed outlier: 3.503A pdb=" N LEU A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 35 Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.565A pdb=" N LEU A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 175 Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 203 through 210 Processing helix chain 'B' and resid 4 through 12 Processing helix chain 'B' and resid 14 through 21 removed outlier: 3.645A pdb=" N HIS B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 35 Processing helix chain 'B' and resid 35 through 42 removed outlier: 3.584A pdb=" N ARG B 39 " --> pdb=" O CYS B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 113 Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.511A pdb=" N LEU B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 153 Processing helix chain 'B' and resid 154 through 175 removed outlier: 3.915A pdb=" N ASP B 174 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 203 through 209 Processing helix chain 'C' and resid 29 through 33 removed outlier: 3.887A pdb=" N VAL C 33 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 49 Processing helix chain 'C' and resid 62 through 81 removed outlier: 3.579A pdb=" N THR C 81 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 91 through 103 removed outlier: 3.722A pdb=" N VAL C 95 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 96 " --> pdb=" O TYR C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 146 Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.738A pdb=" N LYS C 157 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 169 Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 175 through 193 removed outlier: 3.885A pdb=" N ARG C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 213 removed outlier: 3.588A pdb=" N ILE C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 234 removed outlier: 3.826A pdb=" N LEU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY C 234 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 250 removed outlier: 3.588A pdb=" N LYS C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.830A pdb=" N VAL C 257 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LYS C 258 " --> pdb=" O HIS C 255 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER C 259 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER C 261 " --> pdb=" O LYS C 258 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C 262 " --> pdb=" O SER C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 removed outlier: 3.636A pdb=" N LEU C 267 " --> pdb=" O TYR C 263 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU C 276 " --> pdb=" O VAL C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 281 No H-bonds generated for 'chain 'C' and resid 279 through 281' Processing helix chain 'C' and resid 282 through 292 Processing helix chain 'C' and resid 300 through 316 removed outlier: 4.030A pdb=" N PHE C 304 " --> pdb=" O LYS C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 333 removed outlier: 3.599A pdb=" N LYS C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 89 through 94 removed outlier: 4.559A pdb=" N ASP D 122 " --> pdb=" O GLY D 64 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N ILE D 66 " --> pdb=" O ASP D 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 245 through 247 Processing sheet with id=AA3, first strand: chain 'D' and resid 250 through 251 removed outlier: 3.856A pdb=" N GLN D 250 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 89 through 94 removed outlier: 6.183A pdb=" N TRP E 62 " --> pdb=" O ASN E 120 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 243 through 247 removed outlier: 5.348A pdb=" N GLY E 244 " --> pdb=" O PHE E 232 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N PHE E 232 " --> pdb=" O GLY E 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 255 through 259 Processing sheet with id=AA7, first strand: chain 'A' and resid 89 through 94 removed outlier: 4.559A pdb=" N ASP A 122 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ILE A 66 " --> pdb=" O ASP A 122 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 245 through 247 Processing sheet with id=AA9, first strand: chain 'A' and resid 250 through 251 removed outlier: 3.856A pdb=" N GLN A 250 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 89 through 94 removed outlier: 6.183A pdb=" N TRP B 62 " --> pdb=" O ASN B 120 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 243 through 247 removed outlier: 5.348A pdb=" N GLY B 244 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE B 232 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 255 through 259 641 hydrogen bonds defined for protein. 1869 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3564 1.33 - 1.45: 3583 1.45 - 1.57: 8311 1.57 - 1.69: 152 1.69 - 1.81: 62 Bond restraints: 15672 Sorted by residual: bond pdb=" CAZ RLT B 304 " pdb=" CBB RLT B 304 " ideal model delta sigma weight residual 1.357 1.476 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" CAZ RLT E 304 " pdb=" CBB RLT E 304 " ideal model delta sigma weight residual 1.357 1.475 -0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" CBC RLT E 304 " pdb=" NBE RLT E 304 " ideal model delta sigma weight residual 1.376 1.458 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" CBC RLT B 304 " pdb=" NAQ RLT B 304 " ideal model delta sigma weight residual 1.281 1.363 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" CBC RLT E 304 " pdb=" NAQ RLT E 304 " ideal model delta sigma weight residual 1.281 1.362 -0.081 2.00e-02 2.50e+03 1.66e+01 ... (remaining 15667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.02: 21654 5.02 - 10.04: 16 10.04 - 15.06: 2 15.06 - 20.08: 2 20.08 - 25.09: 4 Bond angle restraints: 21678 Sorted by residual: angle pdb=" CBC RLT B 304 " pdb=" CBF RLT B 304 " pdb=" NAS RLT B 304 " ideal model delta sigma weight residual 107.02 81.93 25.09 3.00e+00 1.11e-01 7.00e+01 angle pdb=" CBC RLT E 304 " pdb=" CBF RLT E 304 " pdb=" NAS RLT E 304 " ideal model delta sigma weight residual 107.02 82.19 24.83 3.00e+00 1.11e-01 6.85e+01 angle pdb=" CAD RLT E 304 " pdb=" CBF RLT E 304 " pdb=" CBC RLT E 304 " ideal model delta sigma weight residual 109.99 89.52 20.47 3.00e+00 1.11e-01 4.66e+01 angle pdb=" CAD RLT B 304 " pdb=" CBF RLT B 304 " pdb=" CBC RLT B 304 " ideal model delta sigma weight residual 109.99 89.57 20.42 3.00e+00 1.11e-01 4.63e+01 angle pdb=" CAD RLT B 304 " pdb=" CBF RLT B 304 " pdb=" NAS RLT B 304 " ideal model delta sigma weight residual 108.80 127.67 -18.87 3.00e+00 1.11e-01 3.96e+01 ... (remaining 21673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 8650 35.20 - 70.41: 462 70.41 - 105.61: 16 105.61 - 140.81: 0 140.81 - 176.01: 8 Dihedral angle restraints: 9136 sinusoidal: 4220 harmonic: 4916 Sorted by residual: dihedral pdb=" CA TYR E 230 " pdb=" C TYR E 230 " pdb=" N TYR E 231 " pdb=" CA TYR E 231 " ideal model delta harmonic sigma weight residual 180.00 156.17 23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA TYR B 230 " pdb=" C TYR B 230 " pdb=" N TYR B 231 " pdb=" CA TYR B 231 " ideal model delta harmonic sigma weight residual 180.00 156.18 23.82 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA TYR D 230 " pdb=" C TYR D 230 " pdb=" N TYR D 231 " pdb=" CA TYR D 231 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 9133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1697 0.037 - 0.074: 466 0.074 - 0.110: 195 0.110 - 0.147: 46 0.147 - 0.184: 2 Chirality restraints: 2406 Sorted by residual: chirality pdb=" CG LEU B 257 " pdb=" CB LEU B 257 " pdb=" CD1 LEU B 257 " pdb=" CD2 LEU B 257 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.46e-01 chirality pdb=" CG LEU E 257 " pdb=" CB LEU E 257 " pdb=" CD1 LEU E 257 " pdb=" CD2 LEU E 257 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.22e-01 chirality pdb=" CA ILE E 147 " pdb=" N ILE E 147 " pdb=" C ILE E 147 " pdb=" CB ILE E 147 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 2403 not shown) Planarity restraints: 2466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAV RLT E 304 " 0.081 2.00e-02 2.50e+03 2.61e-01 8.52e+02 pdb=" CBA RLT E 304 " -0.176 2.00e-02 2.50e+03 pdb=" CBF RLT E 304 " -0.307 2.00e-02 2.50e+03 pdb=" NAS RLT E 304 " 0.455 2.00e-02 2.50e+03 pdb=" OAF RLT E 304 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAV RLT B 304 " 0.080 2.00e-02 2.50e+03 2.60e-01 8.44e+02 pdb=" CBA RLT B 304 " -0.175 2.00e-02 2.50e+03 pdb=" CBF RLT B 304 " -0.305 2.00e-02 2.50e+03 pdb=" NAS RLT B 304 " 0.452 2.00e-02 2.50e+03 pdb=" OAF RLT B 304 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAN RLT B 304 " -0.158 2.00e-02 2.50e+03 1.30e-01 2.10e+02 pdb=" CAU RLT B 304 " 0.052 2.00e-02 2.50e+03 pdb=" CBB RLT B 304 " -0.120 2.00e-02 2.50e+03 pdb=" NAR RLT B 304 " 0.204 2.00e-02 2.50e+03 pdb=" OAE RLT B 304 " 0.022 2.00e-02 2.50e+03 ... (remaining 2463 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 51 2.39 - 3.02: 8121 3.02 - 3.65: 22380 3.65 - 4.27: 33986 4.27 - 4.90: 55555 Nonbonded interactions: 120093 Sorted by model distance: nonbonded pdb="MG MG B 303 " pdb=" OAE RLT B 304 " model vdw 1.769 2.170 nonbonded pdb=" OE2 GLU B 158 " pdb="MG MG B 303 " model vdw 1.777 2.170 nonbonded pdb=" OE2 GLU E 158 " pdb="MG MG E 303 " model vdw 1.785 2.170 nonbonded pdb="MG MG E 303 " pdb=" OAE RLT E 304 " model vdw 1.786 2.170 nonbonded pdb=" OE1 GLU E 158 " pdb="MG MG E 303 " model vdw 1.833 2.170 ... (remaining 120088 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: 0.03 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'A' } ncs_group { reference = chain 'E' selection = chain 'B' } ncs_group { reference = chain 'F' selection = chain 'C' } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.270 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 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 0.119 15688 Z= 0.297 Angle : 0.817 35.200 21684 Z= 0.412 Chirality : 0.042 0.184 2406 Planarity : 0.009 0.261 2466 Dihedral : 18.715 176.015 5924 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.14 % Allowed : 0.07 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.20), residues: 1640 helix: 1.16 (0.19), residues: 742 sheet: 0.36 (0.31), residues: 222 loop : -0.94 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 240 TYR 0.013 0.001 TYR F 138 PHE 0.019 0.001 PHE C 274 TRP 0.011 0.001 TRP C 131 HIS 0.004 0.001 HIS D 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.30 (15672) covalent geometry : angle 0.71121 / 0.40 (21678) hydrogen bonds : bond 0.16919 / 11.43 ( 689) hydrogen bonds : angle 6.25417 / 4.58 ( 1965) metal coordination : bond 0.02060 / 1.39 ( 16) metal coordination : angle 24.18352 / 13.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 477 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.7182 (mmm) cc_final: 0.6886 (mmm) REVERT: E 127 TYR cc_start: 0.7630 (m-10) cc_final: 0.7309 (m-10) REVERT: F 45 LYS cc_start: 0.6338 (mtpt) cc_final: 0.5315 (mtpt) REVERT: F 78 GLU cc_start: 0.6638 (tm-30) cc_final: 0.6431 (tm-30) REVERT: F 174 GLU cc_start: 0.6874 (pp20) cc_final: 0.6650 (pp20) REVERT: F 201 ARG cc_start: 0.7267 (mtm-85) cc_final: 0.6937 (mtm-85) REVERT: F 210 ARG cc_start: 0.7050 (ttp80) cc_final: 0.6801 (ttp80) REVERT: F 287 MET cc_start: 0.6472 (mmm) cc_final: 0.6265 (mmm) REVERT: F 308 LEU cc_start: 0.8349 (mt) cc_final: 0.8041 (mt) REVERT: F 310 GLU cc_start: 0.7260 (mm-30) cc_final: 0.7004 (mm-30) REVERT: B 47 MET cc_start: 0.7127 (mmm) cc_final: 0.6823 (mmm) REVERT: B 127 TYR cc_start: 0.7441 (m-10) cc_final: 0.7224 (m-10) REVERT: B 175 ASN cc_start: 0.6739 (m110) cc_final: 0.6475 (m110) REVERT: C 41 LEU cc_start: 0.7835 (tt) cc_final: 0.7524 (tt) REVERT: C 45 LYS cc_start: 0.6260 (mtpt) cc_final: 0.4862 (mtpt) REVERT: C 92 TYR cc_start: 0.5749 (m-80) cc_final: 0.5427 (m-80) REVERT: C 139 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6562 (tm-30) REVERT: C 154 ILE cc_start: 0.7912 (mm) cc_final: 0.7695 (pt) REVERT: C 174 GLU cc_start: 0.6887 (pp20) cc_final: 0.6619 (pp20) REVERT: C 201 ARG cc_start: 0.7051 (mtm-85) cc_final: 0.6809 (mtm-85) REVERT: C 241 GLU cc_start: 0.4459 (tm-30) cc_final: 0.4008 (tm-30) REVERT: C 245 ILE cc_start: 0.6937 (mt) cc_final: 0.6410 (mt) REVERT: C 308 LEU cc_start: 0.8335 (mt) cc_final: 0.8061 (mt) outliers start: 2 outliers final: 0 residues processed: 477 average time/residue: 0.1553 time to fit residues: 101.7725 Evaluate side-chains 430 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 430 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN D 118 HIS D 195 ASN D 206 GLN D 238 ASN E 21 HIS E 59 ASN E 93 HIS E 133 GLN E 161 ASN E 201 GLN E 241 GLN ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 HIS A 134 HIS A 195 ASN A 238 ASN B 59 ASN B 133 GLN B 195 ASN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.154180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.123470 restraints weight = 22622.695| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.26 r_work: 0.3398 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15688 Z= 0.181 Angle : 0.647 9.938 21684 Z= 0.338 Chirality : 0.045 0.215 2406 Planarity : 0.006 0.134 2466 Dihedral : 20.745 170.992 2698 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.06 % Allowed : 10.23 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.20), residues: 1640 helix: 1.19 (0.18), residues: 756 sheet: 0.22 (0.30), residues: 242 loop : -0.71 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 70 TYR 0.019 0.002 TYR A 231 PHE 0.015 0.001 PHE F 42 TRP 0.010 0.001 TRP C 293 HIS 0.008 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (15672) covalent geometry : angle 0.64458 / 0.34 (21678) hydrogen bonds : bond 0.05294 / 3.72 ( 689) hydrogen bonds : angle 4.75667 / 3.42 ( 1965) metal coordination : bond 0.01240 / 0.74 ( 16) metal coordination : angle 3.39485 / 1.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 438 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 GLU cc_start: 0.7505 (tp30) cc_final: 0.7269 (tp30) REVERT: D 213 LEU cc_start: 0.9160 (mt) cc_final: 0.8922 (mt) REVERT: D 274 LYS cc_start: 0.8926 (ttmt) cc_final: 0.8610 (ttmt) REVERT: E 47 MET cc_start: 0.8520 (mmm) cc_final: 0.8189 (mmm) REVERT: E 70 LYS cc_start: 0.8312 (ttpt) cc_final: 0.8095 (tttt) REVERT: E 127 TYR cc_start: 0.8157 (m-10) cc_final: 0.7833 (m-10) REVERT: E 133 GLN cc_start: 0.7450 (mm-40) cc_final: 0.7213 (mm-40) REVERT: F 67 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6569 (tm-30) REVERT: F 76 MET cc_start: 0.7512 (mtp) cc_final: 0.7289 (mtm) REVERT: F 78 GLU cc_start: 0.7374 (tm-30) cc_final: 0.7078 (tm-30) REVERT: F 165 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7474 (mm) REVERT: F 169 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7527 (tm-30) REVERT: F 210 ARG cc_start: 0.8086 (ttp80) cc_final: 0.7695 (ttp80) REVERT: F 227 ILE cc_start: 0.8635 (mt) cc_final: 0.8343 (tt) REVERT: F 283 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7843 (tm-30) REVERT: F 287 MET cc_start: 0.8094 (mmm) cc_final: 0.7819 (mmm) REVERT: F 300 LYS cc_start: 0.8203 (ttpt) cc_final: 0.7992 (ttpt) REVERT: F 308 LEU cc_start: 0.8353 (mt) cc_final: 0.7936 (tp) REVERT: F 310 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7673 (mm-30) REVERT: A 131 GLU cc_start: 0.7579 (tp30) cc_final: 0.7211 (tp30) REVERT: B 29 LEU cc_start: 0.8262 (mt) cc_final: 0.8001 (mp) REVERT: B 47 MET cc_start: 0.8441 (mmm) cc_final: 0.8140 (mmm) REVERT: B 161 ASN cc_start: 0.8290 (m110) cc_final: 0.8081 (m-40) REVERT: B 171 TYR cc_start: 0.8931 (m-10) cc_final: 0.8693 (m-10) REVERT: C 41 LEU cc_start: 0.8393 (tt) cc_final: 0.7992 (tt) REVERT: C 44 GLN cc_start: 0.8113 (mt0) cc_final: 0.7808 (mp10) REVERT: C 67 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6789 (tm-30) REVERT: C 70 ARG cc_start: 0.7894 (ptm-80) cc_final: 0.7505 (ttp80) REVERT: C 75 GLU cc_start: 0.7894 (tt0) cc_final: 0.7670 (tt0) REVERT: C 154 ILE cc_start: 0.8144 (mm) cc_final: 0.7803 (pt) REVERT: C 169 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7518 (tm-30) REVERT: C 201 ARG cc_start: 0.8084 (mtm-85) cc_final: 0.7588 (mtm-85) REVERT: C 227 ILE cc_start: 0.8648 (mt) cc_final: 0.8373 (tt) REVERT: C 241 GLU cc_start: 0.5639 (tm-30) cc_final: 0.4945 (tm-30) REVERT: C 245 ILE cc_start: 0.7733 (mt) cc_final: 0.7192 (mt) REVERT: C 246 PHE cc_start: 0.7729 (t80) cc_final: 0.7385 (t80) REVERT: C 266 GLN cc_start: 0.8478 (mp10) cc_final: 0.8055 (mp10) REVERT: C 283 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7598 (tm-30) REVERT: C 287 MET cc_start: 0.7920 (mmm) cc_final: 0.7586 (mmm) REVERT: C 310 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7261 (mm-30) outliers start: 30 outliers final: 15 residues processed: 452 average time/residue: 0.1472 time to fit residues: 90.4479 Evaluate side-chains 439 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 423 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 182 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 61 optimal weight: 0.0870 chunk 25 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN D 182 ASN D 238 ASN E 59 ASN E 112 HIS E 161 ASN F 82 HIS ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 59 ASN ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.154493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123941 restraints weight = 22668.665| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.26 r_work: 0.3390 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15688 Z= 0.166 Angle : 0.591 8.208 21684 Z= 0.311 Chirality : 0.043 0.248 2406 Planarity : 0.005 0.103 2466 Dihedral : 20.821 163.408 2698 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.34 % Allowed : 13.12 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.20), residues: 1640 helix: 1.28 (0.19), residues: 758 sheet: 0.37 (0.31), residues: 242 loop : -0.73 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 143 TYR 0.021 0.002 TYR D 231 PHE 0.018 0.001 PHE C 99 TRP 0.011 0.001 TRP D 229 HIS 0.006 0.001 HIS F 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (15672) covalent geometry : angle 0.58949 / 0.31 (21678) hydrogen bonds : bond 0.04606 / 3.22 ( 689) hydrogen bonds : angle 4.51812 / 3.24 ( 1965) metal coordination : bond 0.01176 / 0.66 ( 16) metal coordination : angle 2.59023 / 1.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 433 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 120 ASN cc_start: 0.8263 (t0) cc_final: 0.8013 (t0) REVERT: D 131 GLU cc_start: 0.7656 (tp30) cc_final: 0.7203 (tp30) REVERT: D 274 LYS cc_start: 0.8909 (ttmt) cc_final: 0.8556 (ttmt) REVERT: E 47 MET cc_start: 0.8507 (mmm) cc_final: 0.8193 (mmm) REVERT: E 54 ARG cc_start: 0.8193 (mtp85) cc_final: 0.7955 (mmt180) REVERT: E 70 LYS cc_start: 0.8330 (ttpt) cc_final: 0.8125 (tttt) REVERT: F 67 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6614 (tm-30) REVERT: F 151 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7932 (tm-30) REVERT: F 165 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7491 (mm) REVERT: F 169 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7495 (tm-30) REVERT: F 183 LYS cc_start: 0.8639 (ttpp) cc_final: 0.8373 (ptpp) REVERT: F 210 ARG cc_start: 0.8094 (ttp80) cc_final: 0.7698 (ttp80) REVERT: F 223 GLU cc_start: 0.7385 (mp0) cc_final: 0.7128 (mp0) REVERT: F 283 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7782 (tm-30) REVERT: F 287 MET cc_start: 0.8101 (mmm) cc_final: 0.7850 (mmm) REVERT: F 300 LYS cc_start: 0.8349 (ttpt) cc_final: 0.8086 (ttpt) REVERT: F 308 LEU cc_start: 0.8284 (mt) cc_final: 0.8015 (tp) REVERT: A 131 GLU cc_start: 0.7656 (tp30) cc_final: 0.7291 (tp30) REVERT: A 142 ARG cc_start: 0.7653 (mtt-85) cc_final: 0.7438 (mtt-85) REVERT: B 29 LEU cc_start: 0.8249 (mt) cc_final: 0.8018 (mp) REVERT: B 32 LEU cc_start: 0.8701 (mm) cc_final: 0.8472 (mt) REVERT: B 47 MET cc_start: 0.8463 (mmm) cc_final: 0.8108 (mmm) REVERT: B 133 GLN cc_start: 0.7546 (mm-40) cc_final: 0.7300 (mm-40) REVERT: C 41 LEU cc_start: 0.8435 (tt) cc_final: 0.8187 (tt) REVERT: C 67 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6769 (tm-30) REVERT: C 83 ASN cc_start: 0.8181 (m-40) cc_final: 0.7855 (m-40) REVERT: C 94 GLU cc_start: 0.7044 (pm20) cc_final: 0.6515 (tp30) REVERT: C 95 VAL cc_start: 0.7864 (t) cc_final: 0.7583 (t) REVERT: C 139 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7463 (tm-30) REVERT: C 169 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7545 (tm-30) REVERT: C 174 GLU cc_start: 0.8009 (pp20) cc_final: 0.7680 (pp20) REVERT: C 201 ARG cc_start: 0.8164 (mtm-85) cc_final: 0.7686 (mtm-85) REVERT: C 227 ILE cc_start: 0.8592 (mt) cc_final: 0.8345 (tt) REVERT: C 241 GLU cc_start: 0.5775 (tm-30) cc_final: 0.5275 (tm-30) REVERT: C 246 PHE cc_start: 0.7748 (t80) cc_final: 0.7436 (t80) REVERT: C 266 GLN cc_start: 0.8578 (mp10) cc_final: 0.8086 (mp10) REVERT: C 283 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7604 (tm-30) REVERT: C 287 MET cc_start: 0.7929 (mmm) cc_final: 0.7604 (mmm) REVERT: C 308 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8072 (tt) REVERT: C 310 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7114 (mm-30) outliers start: 34 outliers final: 17 residues processed: 441 average time/residue: 0.1620 time to fit residues: 97.4059 Evaluate side-chains 445 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 426 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 119 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 59 ASN D 238 ASN E 59 ASN E 118 HIS E 250 GLN F 203 GLN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 59 ASN B 112 HIS B 238 ASN ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.152178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.122058 restraints weight = 22705.114| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.27 r_work: 0.3360 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15688 Z= 0.225 Angle : 0.617 6.683 21684 Z= 0.325 Chirality : 0.045 0.227 2406 Planarity : 0.005 0.088 2466 Dihedral : 20.738 159.587 2698 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.64 % Allowed : 14.08 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.20), residues: 1640 helix: 1.12 (0.18), residues: 756 sheet: 0.47 (0.31), residues: 242 loop : -0.90 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 143 TYR 0.022 0.002 TYR F 269 PHE 0.021 0.002 PHE C 99 TRP 0.019 0.002 TRP C 65 HIS 0.007 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.23 (15672) covalent geometry : angle 0.61613 / 0.32 (21678) hydrogen bonds : bond 0.04761 / 3.33 ( 689) hydrogen bonds : angle 4.58037 / 3.27 ( 1965) metal coordination : bond 0.01809 / 1.07 ( 16) metal coordination : angle 1.85030 / 1.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 438 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 120 ASN cc_start: 0.8323 (t0) cc_final: 0.8063 (t0) REVERT: D 131 GLU cc_start: 0.7802 (tp30) cc_final: 0.7230 (tp30) REVERT: D 274 LYS cc_start: 0.8842 (ttmt) cc_final: 0.8493 (ttmt) REVERT: E 29 LEU cc_start: 0.8299 (mp) cc_final: 0.8096 (mm) REVERT: E 47 MET cc_start: 0.8520 (mmm) cc_final: 0.8190 (mmm) REVERT: E 54 ARG cc_start: 0.8209 (mtp85) cc_final: 0.8005 (mmt180) REVERT: E 70 LYS cc_start: 0.8370 (ttpt) cc_final: 0.8169 (tttt) REVERT: E 257 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8314 (tt) REVERT: F 44 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7877 (mp10) REVERT: F 67 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6686 (tm-30) REVERT: F 75 GLU cc_start: 0.8047 (tt0) cc_final: 0.7800 (tt0) REVERT: F 87 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7622 (mm) REVERT: F 164 VAL cc_start: 0.8565 (t) cc_final: 0.8179 (m) REVERT: F 165 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7522 (mm) REVERT: F 169 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7560 (tm-30) REVERT: F 183 LYS cc_start: 0.8656 (ttpp) cc_final: 0.8383 (ptpp) REVERT: F 210 ARG cc_start: 0.8191 (ttp80) cc_final: 0.7806 (ttp80) REVERT: F 223 GLU cc_start: 0.7535 (mp0) cc_final: 0.7238 (mp0) REVERT: F 251 LEU cc_start: 0.7818 (tp) cc_final: 0.7533 (tt) REVERT: F 283 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7852 (tm-30) REVERT: F 287 MET cc_start: 0.8131 (mmm) cc_final: 0.7872 (mmm) REVERT: F 300 LYS cc_start: 0.8330 (ttpt) cc_final: 0.8053 (ttpt) REVERT: F 308 LEU cc_start: 0.8206 (mt) cc_final: 0.7943 (tt) REVERT: A 131 GLU cc_start: 0.7775 (tp30) cc_final: 0.7403 (tp30) REVERT: B 29 LEU cc_start: 0.8326 (mt) cc_final: 0.8109 (mp) REVERT: B 47 MET cc_start: 0.8492 (mmm) cc_final: 0.8166 (mmm) REVERT: B 202 LYS cc_start: 0.8520 (mtmm) cc_final: 0.8315 (mtmm) REVERT: C 41 LEU cc_start: 0.8486 (tt) cc_final: 0.8279 (tt) REVERT: C 67 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6940 (tm-30) REVERT: C 75 GLU cc_start: 0.8100 (tt0) cc_final: 0.7840 (tt0) REVERT: C 83 ASN cc_start: 0.8251 (m-40) cc_final: 0.7941 (m-40) REVERT: C 94 GLU cc_start: 0.7430 (pm20) cc_final: 0.7150 (mm-30) REVERT: C 95 VAL cc_start: 0.8197 (t) cc_final: 0.7907 (t) REVERT: C 139 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7476 (tm-30) REVERT: C 154 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7771 (tp) REVERT: C 169 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7604 (tm-30) REVERT: C 174 GLU cc_start: 0.8085 (pp20) cc_final: 0.7788 (pp20) REVERT: C 201 ARG cc_start: 0.8139 (mtm-85) cc_final: 0.7560 (mtm-85) REVERT: C 210 ARG cc_start: 0.8054 (mtm-85) cc_final: 0.7586 (mtm-85) REVERT: C 227 ILE cc_start: 0.8608 (mt) cc_final: 0.8383 (tt) REVERT: C 241 GLU cc_start: 0.5809 (tm-30) cc_final: 0.5301 (tm-30) REVERT: C 246 PHE cc_start: 0.7780 (t80) cc_final: 0.7438 (t80) REVERT: C 283 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7680 (tm-30) REVERT: C 287 MET cc_start: 0.7959 (mmm) cc_final: 0.7609 (mmm) REVERT: C 310 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7198 (mm-30) outliers start: 53 outliers final: 28 residues processed: 453 average time/residue: 0.1559 time to fit residues: 96.4895 Evaluate side-chains 455 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 422 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 177 ASN Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 300 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 61 optimal weight: 0.0370 chunk 74 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN D 238 ASN E 59 ASN ** E 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 59 ASN B 112 HIS ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.152800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122778 restraints weight = 22672.391| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.24 r_work: 0.3367 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 15688 Z= 0.166 Angle : 0.597 10.638 21684 Z= 0.312 Chirality : 0.043 0.242 2406 Planarity : 0.005 0.076 2466 Dihedral : 20.690 157.658 2698 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.95 % Allowed : 17.51 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.20), residues: 1640 helix: 1.19 (0.18), residues: 756 sheet: 0.50 (0.32), residues: 242 loop : -0.86 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 247 TYR 0.025 0.002 TYR F 269 PHE 0.017 0.001 PHE C 99 TRP 0.010 0.001 TRP C 65 HIS 0.006 0.001 HIS F 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (15672) covalent geometry : angle 0.59661 / 0.31 (21678) hydrogen bonds : bond 0.04296 / 3.00 ( 689) hydrogen bonds : angle 4.48587 / 3.21 ( 1965) metal coordination : bond 0.01049 / 0.61 ( 16) metal coordination : angle 1.79556 / 1.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 431 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 120 ASN cc_start: 0.8312 (t0) cc_final: 0.8082 (t0) REVERT: D 131 GLU cc_start: 0.7838 (tp30) cc_final: 0.7223 (tp30) REVERT: D 274 LYS cc_start: 0.8840 (ttmt) cc_final: 0.8493 (ttmt) REVERT: E 47 MET cc_start: 0.8493 (mmm) cc_final: 0.8186 (mmm) REVERT: E 70 LYS cc_start: 0.8390 (ttpt) cc_final: 0.8178 (tttt) REVERT: F 44 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7858 (mp10) REVERT: F 67 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6735 (tm-30) REVERT: F 75 GLU cc_start: 0.8068 (tt0) cc_final: 0.7862 (tt0) REVERT: F 87 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7614 (mm) REVERT: F 164 VAL cc_start: 0.8557 (t) cc_final: 0.8174 (m) REVERT: F 165 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7490 (mm) REVERT: F 169 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7538 (tm-30) REVERT: F 223 GLU cc_start: 0.7388 (mp0) cc_final: 0.7017 (mp0) REVERT: F 254 LEU cc_start: 0.7392 (tp) cc_final: 0.6826 (tt) REVERT: F 283 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7788 (tm-30) REVERT: F 287 MET cc_start: 0.8104 (mmm) cc_final: 0.7857 (mmm) REVERT: F 300 LYS cc_start: 0.8289 (ttpt) cc_final: 0.8039 (ttpt) REVERT: F 308 LEU cc_start: 0.8160 (mt) cc_final: 0.7623 (mt) REVERT: A 131 GLU cc_start: 0.7813 (tp30) cc_final: 0.7417 (tp30) REVERT: B 29 LEU cc_start: 0.8281 (mt) cc_final: 0.8057 (mp) REVERT: B 47 MET cc_start: 0.8476 (mmm) cc_final: 0.8118 (mmm) REVERT: C 41 LEU cc_start: 0.8500 (tt) cc_final: 0.8267 (tt) REVERT: C 67 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6936 (tm-30) REVERT: C 75 GLU cc_start: 0.8113 (tt0) cc_final: 0.7855 (tt0) REVERT: C 83 ASN cc_start: 0.8221 (m-40) cc_final: 0.7901 (m-40) REVERT: C 95 VAL cc_start: 0.8285 (t) cc_final: 0.8021 (t) REVERT: C 139 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7484 (tm-30) REVERT: C 154 ILE cc_start: 0.8239 (tp) cc_final: 0.7888 (tp) REVERT: C 169 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7572 (tm-30) REVERT: C 174 GLU cc_start: 0.8078 (pp20) cc_final: 0.7742 (pp20) REVERT: C 201 ARG cc_start: 0.8108 (mtm-85) cc_final: 0.7534 (mtm-85) REVERT: C 210 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7563 (mtm-85) REVERT: C 227 ILE cc_start: 0.8629 (mt) cc_final: 0.8353 (tt) REVERT: C 283 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7640 (tm-30) REVERT: C 287 MET cc_start: 0.7965 (mmm) cc_final: 0.7603 (mmm) REVERT: C 310 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7190 (mm-30) outliers start: 43 outliers final: 30 residues processed: 447 average time/residue: 0.1540 time to fit residues: 93.9798 Evaluate side-chains 447 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 414 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 300 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 70 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 159 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 164 optimal weight: 0.0370 chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 33 HIS D 59 ASN D 238 ASN E 59 ASN E 134 HIS F 203 GLN F 243 HIS ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 59 ASN B 112 HIS B 130 GLN B 134 HIS ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.152234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.121685 restraints weight = 22333.419| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.24 r_work: 0.3372 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15688 Z= 0.137 Angle : 0.576 7.689 21684 Z= 0.302 Chirality : 0.042 0.263 2406 Planarity : 0.005 0.074 2466 Dihedral : 20.608 156.974 2698 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.95 % Allowed : 18.27 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.20), residues: 1640 helix: 1.31 (0.18), residues: 756 sheet: 0.51 (0.32), residues: 242 loop : -0.78 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 142 TYR 0.026 0.002 TYR F 269 PHE 0.013 0.001 PHE C 141 TRP 0.009 0.001 TRP C 65 HIS 0.006 0.001 HIS F 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (15672) covalent geometry : angle 0.57566 / 0.30 (21678) hydrogen bonds : bond 0.03955 / 2.77 ( 689) hydrogen bonds : angle 4.43202 / 3.17 ( 1965) metal coordination : bond 0.00678 / 0.39 ( 16) metal coordination : angle 1.81029 / 1.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 435 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 GLU cc_start: 0.7825 (tp30) cc_final: 0.7224 (tp30) REVERT: D 274 LYS cc_start: 0.8856 (ttmt) cc_final: 0.8514 (ttmt) REVERT: E 47 MET cc_start: 0.8457 (mmm) cc_final: 0.8100 (mmm) REVERT: E 70 LYS cc_start: 0.8403 (ttpt) cc_final: 0.8185 (tttt) REVERT: F 44 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7864 (mp10) REVERT: F 67 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6750 (tm-30) REVERT: F 87 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7612 (mm) REVERT: F 164 VAL cc_start: 0.8547 (t) cc_final: 0.8172 (m) REVERT: F 165 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7495 (mm) REVERT: F 169 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7489 (tm-30) REVERT: F 183 LYS cc_start: 0.8538 (ttpp) cc_final: 0.8273 (ptpp) REVERT: F 210 ARG cc_start: 0.8143 (ttp80) cc_final: 0.7751 (ttp80) REVERT: F 223 GLU cc_start: 0.7367 (mp0) cc_final: 0.7062 (mp0) REVERT: F 254 LEU cc_start: 0.7396 (tp) cc_final: 0.6896 (tt) REVERT: F 267 LEU cc_start: 0.8422 (tt) cc_final: 0.8204 (tp) REVERT: F 283 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7711 (tm-30) REVERT: F 287 MET cc_start: 0.8091 (mmm) cc_final: 0.7842 (mmm) REVERT: F 300 LYS cc_start: 0.8275 (ttpt) cc_final: 0.7997 (ttpt) REVERT: F 308 LEU cc_start: 0.8079 (mt) cc_final: 0.7634 (mt) REVERT: A 131 GLU cc_start: 0.7792 (tp30) cc_final: 0.7389 (tp30) REVERT: B 29 LEU cc_start: 0.8269 (mt) cc_final: 0.8049 (mp) REVERT: B 47 MET cc_start: 0.8430 (mmm) cc_final: 0.8097 (mmm) REVERT: C 41 LEU cc_start: 0.8474 (tt) cc_final: 0.8241 (tt) REVERT: C 67 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6910 (tm-30) REVERT: C 75 GLU cc_start: 0.8048 (tt0) cc_final: 0.7806 (tt0) REVERT: C 77 VAL cc_start: 0.7725 (p) cc_final: 0.7521 (p) REVERT: C 95 VAL cc_start: 0.8225 (t) cc_final: 0.7961 (p) REVERT: C 139 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7448 (tm-30) REVERT: C 154 ILE cc_start: 0.8200 (tp) cc_final: 0.7869 (tp) REVERT: C 169 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7512 (tm-30) REVERT: C 174 GLU cc_start: 0.8087 (pp20) cc_final: 0.7739 (pp20) REVERT: C 177 ARG cc_start: 0.8230 (mpp80) cc_final: 0.7567 (mpp80) REVERT: C 201 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7493 (mtm-85) REVERT: C 210 ARG cc_start: 0.7897 (mtm-85) cc_final: 0.7602 (mtm-85) REVERT: C 227 ILE cc_start: 0.8585 (mt) cc_final: 0.8292 (tt) REVERT: C 283 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7530 (tm-30) REVERT: C 287 MET cc_start: 0.7916 (mmm) cc_final: 0.7561 (mmm) REVERT: C 291 LYS cc_start: 0.8422 (ttpp) cc_final: 0.8087 (ttpp) REVERT: C 310 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7213 (mm-30) outliers start: 43 outliers final: 29 residues processed: 450 average time/residue: 0.1553 time to fit residues: 95.3497 Evaluate side-chains 457 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 425 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 300 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 76 optimal weight: 0.0170 chunk 29 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 0.1980 chunk 3 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 167 optimal weight: 9.9990 chunk 165 optimal weight: 3.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 238 ASN E 59 ASN E 134 HIS ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 HIS A 238 ASN B 59 ASN B 112 HIS B 134 HIS ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.152574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122331 restraints weight = 22581.937| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.25 r_work: 0.3374 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15688 Z= 0.141 Angle : 0.569 7.851 21684 Z= 0.299 Chirality : 0.042 0.194 2406 Planarity : 0.005 0.069 2466 Dihedral : 20.536 156.443 2698 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.82 % Allowed : 19.44 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.20), residues: 1640 helix: 1.28 (0.18), residues: 758 sheet: 0.55 (0.32), residues: 242 loop : -0.76 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 142 TYR 0.029 0.002 TYR F 158 PHE 0.012 0.001 PHE F 141 TRP 0.009 0.001 TRP C 65 HIS 0.006 0.001 HIS F 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (15672) covalent geometry : angle 0.56808 / 0.30 (21678) hydrogen bonds : bond 0.03858 / 2.70 ( 689) hydrogen bonds : angle 4.39734 / 3.14 ( 1965) metal coordination : bond 0.00766 / 0.44 ( 16) metal coordination : angle 1.62583 / 0.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 428 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 GLU cc_start: 0.7842 (tp30) cc_final: 0.7242 (tp30) REVERT: D 142 ARG cc_start: 0.7755 (mtt-85) cc_final: 0.7546 (mtt-85) REVERT: D 274 LYS cc_start: 0.8832 (ttmt) cc_final: 0.8520 (ttmt) REVERT: E 47 MET cc_start: 0.8488 (mmm) cc_final: 0.8155 (mmm) REVERT: E 70 LYS cc_start: 0.8376 (ttpt) cc_final: 0.8165 (tttt) REVERT: E 131 GLU cc_start: 0.8191 (pt0) cc_final: 0.7898 (pt0) REVERT: E 161 ASN cc_start: 0.7978 (m-40) cc_final: 0.7763 (m-40) REVERT: F 44 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7877 (mp10) REVERT: F 67 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6823 (tm-30) REVERT: F 87 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7668 (mm) REVERT: F 95 VAL cc_start: 0.8200 (t) cc_final: 0.7942 (p) REVERT: F 164 VAL cc_start: 0.8536 (t) cc_final: 0.8161 (m) REVERT: F 165 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7534 (mm) REVERT: F 169 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7493 (tm-30) REVERT: F 254 LEU cc_start: 0.7445 (tp) cc_final: 0.6950 (tt) REVERT: F 267 LEU cc_start: 0.8434 (tt) cc_final: 0.8214 (tp) REVERT: F 283 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7792 (tm-30) REVERT: F 287 MET cc_start: 0.8074 (mmm) cc_final: 0.7818 (mmm) REVERT: F 300 LYS cc_start: 0.8306 (ttpt) cc_final: 0.8037 (ttpt) REVERT: A 131 GLU cc_start: 0.7826 (tp30) cc_final: 0.7404 (tp30) REVERT: A 206 GLN cc_start: 0.8244 (tt0) cc_final: 0.8024 (tt0) REVERT: B 29 LEU cc_start: 0.8219 (mt) cc_final: 0.8001 (mp) REVERT: B 47 MET cc_start: 0.8474 (mmm) cc_final: 0.8151 (mmm) REVERT: C 41 LEU cc_start: 0.8479 (tt) cc_final: 0.8092 (tt) REVERT: C 44 GLN cc_start: 0.8035 (mt0) cc_final: 0.7629 (mp10) REVERT: C 67 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6972 (tm-30) REVERT: C 75 GLU cc_start: 0.8094 (tt0) cc_final: 0.7869 (tt0) REVERT: C 77 VAL cc_start: 0.7761 (p) cc_final: 0.7538 (p) REVERT: C 95 VAL cc_start: 0.8363 (t) cc_final: 0.8102 (p) REVERT: C 139 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7461 (tm-30) REVERT: C 154 ILE cc_start: 0.8221 (tp) cc_final: 0.7607 (pt) REVERT: C 169 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7556 (tm-30) REVERT: C 174 GLU cc_start: 0.8068 (pp20) cc_final: 0.7732 (pp20) REVERT: C 182 LEU cc_start: 0.8741 (mt) cc_final: 0.8410 (mt) REVERT: C 201 ARG cc_start: 0.8105 (mtm-85) cc_final: 0.7554 (mtm-85) REVERT: C 210 ARG cc_start: 0.7929 (mtm-85) cc_final: 0.7613 (mtm-85) REVERT: C 227 ILE cc_start: 0.8633 (mt) cc_final: 0.8397 (tt) REVERT: C 283 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7650 (tm-30) REVERT: C 287 MET cc_start: 0.7925 (mmm) cc_final: 0.7543 (mmm) REVERT: C 291 LYS cc_start: 0.8416 (ttpp) cc_final: 0.8130 (ttpp) REVERT: C 310 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7285 (mm-30) outliers start: 41 outliers final: 29 residues processed: 442 average time/residue: 0.1604 time to fit residues: 96.3493 Evaluate side-chains 447 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 415 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 300 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 166 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 93 optimal weight: 0.0060 chunk 116 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 99 optimal weight: 0.5980 chunk 159 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 238 ASN E 59 ASN F 203 GLN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 59 ASN B 112 HIS B 134 HIS C 133 HIS ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.153150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.122892 restraints weight = 22664.394| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.26 r_work: 0.3381 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15688 Z= 0.128 Angle : 0.560 7.859 21684 Z= 0.295 Chirality : 0.041 0.172 2406 Planarity : 0.005 0.062 2466 Dihedral : 20.443 156.119 2698 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.75 % Allowed : 19.85 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.21), residues: 1640 helix: 1.34 (0.19), residues: 762 sheet: 0.54 (0.32), residues: 242 loop : -0.67 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 142 TYR 0.027 0.002 TYR F 269 PHE 0.012 0.001 PHE F 141 TRP 0.008 0.001 TRP C 65 HIS 0.006 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (15672) covalent geometry : angle 0.55919 / 0.29 (21678) hydrogen bonds : bond 0.03678 / 2.57 ( 689) hydrogen bonds : angle 4.33544 / 3.09 ( 1965) metal coordination : bond 0.00525 / 0.31 ( 16) metal coordination : angle 1.84871 / 1.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 432 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 GLU cc_start: 0.7831 (tp30) cc_final: 0.7204 (tp30) REVERT: D 142 ARG cc_start: 0.7748 (mtt-85) cc_final: 0.7540 (mtt-85) REVERT: D 274 LYS cc_start: 0.8830 (ttmt) cc_final: 0.8521 (ttmt) REVERT: E 47 MET cc_start: 0.8536 (mmm) cc_final: 0.8224 (mmm) REVERT: E 70 LYS cc_start: 0.8376 (ttpt) cc_final: 0.8152 (tttt) REVERT: F 44 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7880 (mp10) REVERT: F 67 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6906 (tm-30) REVERT: F 94 GLU cc_start: 0.7874 (pm20) cc_final: 0.7611 (mm-30) REVERT: F 95 VAL cc_start: 0.8390 (t) cc_final: 0.8017 (p) REVERT: F 103 MET cc_start: 0.7830 (mmt) cc_final: 0.7577 (mmm) REVERT: F 139 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7506 (tm-30) REVERT: F 164 VAL cc_start: 0.8551 (t) cc_final: 0.8141 (m) REVERT: F 165 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7497 (mm) REVERT: F 169 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7456 (tm-30) REVERT: F 183 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8356 (ptpp) REVERT: F 223 GLU cc_start: 0.7367 (mp0) cc_final: 0.7012 (mp0) REVERT: F 254 LEU cc_start: 0.7475 (tp) cc_final: 0.6842 (tt) REVERT: F 283 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7625 (tm-30) REVERT: F 287 MET cc_start: 0.8048 (mmm) cc_final: 0.7642 (mmm) REVERT: F 300 LYS cc_start: 0.8307 (ttpt) cc_final: 0.8018 (ttpt) REVERT: F 308 LEU cc_start: 0.7940 (mt) cc_final: 0.7432 (pp) REVERT: A 131 GLU cc_start: 0.7793 (tp30) cc_final: 0.7419 (tp30) REVERT: A 206 GLN cc_start: 0.8247 (tt0) cc_final: 0.8043 (tt0) REVERT: B 29 LEU cc_start: 0.8219 (mt) cc_final: 0.8015 (mp) REVERT: B 47 MET cc_start: 0.8457 (mmm) cc_final: 0.8145 (mmm) REVERT: C 41 LEU cc_start: 0.8452 (tt) cc_final: 0.8215 (tt) REVERT: C 67 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6988 (tm-30) REVERT: C 70 ARG cc_start: 0.7857 (ptm-80) cc_final: 0.7602 (ptm-80) REVERT: C 95 VAL cc_start: 0.8467 (t) cc_final: 0.8233 (p) REVERT: C 143 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7668 (tpp80) REVERT: C 154 ILE cc_start: 0.8243 (tp) cc_final: 0.7655 (pt) REVERT: C 169 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7520 (tm-30) REVERT: C 174 GLU cc_start: 0.8092 (pp20) cc_final: 0.7746 (pp20) REVERT: C 201 ARG cc_start: 0.8068 (mtm-85) cc_final: 0.7549 (mtm-85) REVERT: C 221 ILE cc_start: 0.8594 (tp) cc_final: 0.8376 (tp) REVERT: C 223 GLU cc_start: 0.7378 (mp0) cc_final: 0.6993 (mp0) REVERT: C 227 ILE cc_start: 0.8627 (mt) cc_final: 0.8418 (tt) REVERT: C 283 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7609 (tm-30) REVERT: C 287 MET cc_start: 0.7932 (mmm) cc_final: 0.7540 (mmm) REVERT: C 291 LYS cc_start: 0.8374 (ttpp) cc_final: 0.8137 (ttpp) REVERT: C 310 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7386 (mm-30) outliers start: 40 outliers final: 29 residues processed: 444 average time/residue: 0.1453 time to fit residues: 88.2027 Evaluate side-chains 460 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 427 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 300 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 13 optimal weight: 6.9990 chunk 18 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 127 optimal weight: 0.9990 chunk 153 optimal weight: 0.6980 chunk 161 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 238 ASN E 59 ASN E 130 GLN E 134 HIS F 203 GLN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN A 238 ASN B 30 ASN B 59 ASN B 112 HIS ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.152104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.121906 restraints weight = 22533.836| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.24 r_work: 0.3371 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15688 Z= 0.152 Angle : 0.577 8.590 21684 Z= 0.303 Chirality : 0.041 0.157 2406 Planarity : 0.005 0.062 2466 Dihedral : 20.437 156.425 2698 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.54 % Allowed : 19.78 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.21), residues: 1640 helix: 1.32 (0.18), residues: 762 sheet: 0.61 (0.32), residues: 242 loop : -0.69 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 142 TYR 0.027 0.002 TYR F 269 PHE 0.013 0.001 PHE F 141 TRP 0.007 0.001 TRP C 65 HIS 0.006 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (15672) covalent geometry : angle 0.57634 / 0.30 (21678) hydrogen bonds : bond 0.03776 / 2.63 ( 689) hydrogen bonds : angle 4.35681 / 3.11 ( 1965) metal coordination : bond 0.00931 / 0.54 ( 16) metal coordination : angle 1.52153 / 0.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 431 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 GLU cc_start: 0.7836 (tp30) cc_final: 0.7329 (tp30) REVERT: D 142 ARG cc_start: 0.7776 (mtt-85) cc_final: 0.7571 (mtt-85) REVERT: D 274 LYS cc_start: 0.8800 (ttmt) cc_final: 0.8489 (ttmt) REVERT: E 47 MET cc_start: 0.8543 (mmm) cc_final: 0.8249 (mmm) REVERT: E 70 LYS cc_start: 0.8370 (ttpt) cc_final: 0.8160 (tttt) REVERT: F 44 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7858 (mp10) REVERT: F 67 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6893 (tm-30) REVERT: F 77 VAL cc_start: 0.7474 (p) cc_final: 0.7150 (p) REVERT: F 94 GLU cc_start: 0.8001 (pm20) cc_final: 0.7630 (mm-30) REVERT: F 95 VAL cc_start: 0.8412 (t) cc_final: 0.8029 (p) REVERT: F 103 MET cc_start: 0.7739 (mmt) cc_final: 0.7486 (mmm) REVERT: F 139 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7473 (tm-30) REVERT: F 164 VAL cc_start: 0.8581 (t) cc_final: 0.8165 (m) REVERT: F 165 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7584 (mm) REVERT: F 169 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7455 (tm-30) REVERT: F 183 LYS cc_start: 0.8608 (ttpp) cc_final: 0.8363 (ptpp) REVERT: F 201 ARG cc_start: 0.8144 (mtm-85) cc_final: 0.7607 (mtm-85) REVERT: F 223 GLU cc_start: 0.7397 (mp0) cc_final: 0.7036 (mp0) REVERT: F 254 LEU cc_start: 0.7515 (tp) cc_final: 0.6869 (tt) REVERT: F 283 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7661 (tm-30) REVERT: F 287 MET cc_start: 0.8061 (mmm) cc_final: 0.7664 (mmm) REVERT: F 300 LYS cc_start: 0.8296 (ttpt) cc_final: 0.8001 (ttpt) REVERT: F 308 LEU cc_start: 0.7931 (mt) cc_final: 0.7439 (pp) REVERT: A 131 GLU cc_start: 0.7803 (tp30) cc_final: 0.7436 (tp30) REVERT: A 206 GLN cc_start: 0.8244 (tt0) cc_final: 0.8043 (tt0) REVERT: B 29 LEU cc_start: 0.8208 (mt) cc_final: 0.8003 (mp) REVERT: B 47 MET cc_start: 0.8524 (mmm) cc_final: 0.8207 (mmm) REVERT: C 41 LEU cc_start: 0.8463 (tt) cc_final: 0.8096 (tt) REVERT: C 44 GLN cc_start: 0.8048 (mt0) cc_final: 0.7628 (mp10) REVERT: C 67 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7030 (tm-30) REVERT: C 70 ARG cc_start: 0.7895 (ptm-80) cc_final: 0.7633 (ptm-80) REVERT: C 95 VAL cc_start: 0.8516 (t) cc_final: 0.8281 (p) REVERT: C 143 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7665 (tpp80) REVERT: C 154 ILE cc_start: 0.8297 (tp) cc_final: 0.7696 (pt) REVERT: C 169 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7550 (tm-30) REVERT: C 174 GLU cc_start: 0.8102 (pp20) cc_final: 0.7757 (pp20) REVERT: C 201 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7570 (mtm-85) REVERT: C 227 ILE cc_start: 0.8671 (mt) cc_final: 0.8393 (tt) REVERT: C 283 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7591 (tm-30) REVERT: C 287 MET cc_start: 0.7946 (mmm) cc_final: 0.7555 (mmm) REVERT: C 291 LYS cc_start: 0.8381 (ttpp) cc_final: 0.8138 (ttpp) outliers start: 37 outliers final: 29 residues processed: 441 average time/residue: 0.1391 time to fit residues: 84.4519 Evaluate side-chains 457 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 424 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 275 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 130 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 121 optimal weight: 0.2980 chunk 73 optimal weight: 0.0570 chunk 150 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 96 optimal weight: 0.4980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 238 ASN E 41 ASN E 59 ASN E 134 HIS F 203 GLN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN A 238 ASN B 41 ASN B 59 ASN B 112 HIS B 134 HIS ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.152741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.122550 restraints weight = 22557.014| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.24 r_work: 0.3389 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15688 Z= 0.133 Angle : 0.577 7.209 21684 Z= 0.303 Chirality : 0.041 0.161 2406 Planarity : 0.005 0.066 2466 Dihedral : 20.432 156.425 2698 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.61 % Allowed : 20.19 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.21), residues: 1640 helix: 1.33 (0.18), residues: 762 sheet: 0.60 (0.32), residues: 242 loop : -0.68 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 177 TYR 0.026 0.002 TYR F 269 PHE 0.013 0.001 PHE F 141 TRP 0.012 0.001 TRP C 131 HIS 0.006 0.001 HIS F 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (15672) covalent geometry : angle 0.57682 / 0.30 (21678) hydrogen bonds : bond 0.03642 / 2.54 ( 689) hydrogen bonds : angle 4.35885 / 3.11 ( 1965) metal coordination : bond 0.00575 / 0.34 ( 16) metal coordination : angle 1.59479 / 0.92 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 427 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 GLU cc_start: 0.7823 (tp30) cc_final: 0.7247 (tp30) REVERT: D 142 ARG cc_start: 0.7735 (mtt-85) cc_final: 0.7527 (mtt-85) REVERT: D 274 LYS cc_start: 0.8813 (ttmt) cc_final: 0.8503 (ttmt) REVERT: E 47 MET cc_start: 0.8537 (mmm) cc_final: 0.8225 (mmm) REVERT: E 70 LYS cc_start: 0.8374 (ttpt) cc_final: 0.8157 (tttt) REVERT: F 44 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7809 (mp10) REVERT: F 67 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6908 (tm-30) REVERT: F 77 VAL cc_start: 0.7516 (p) cc_final: 0.7254 (p) REVERT: F 94 GLU cc_start: 0.7957 (pm20) cc_final: 0.7704 (mm-30) REVERT: F 95 VAL cc_start: 0.8432 (t) cc_final: 0.8053 (p) REVERT: F 103 MET cc_start: 0.7721 (mmt) cc_final: 0.7516 (mmm) REVERT: F 139 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7445 (tm-30) REVERT: F 164 VAL cc_start: 0.8567 (t) cc_final: 0.8183 (m) REVERT: F 165 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7476 (mm) REVERT: F 169 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7478 (tm-30) REVERT: F 201 ARG cc_start: 0.8102 (mtm-85) cc_final: 0.7579 (mtm-85) REVERT: F 210 ARG cc_start: 0.8149 (ttp80) cc_final: 0.7747 (ttp80) REVERT: F 223 GLU cc_start: 0.7387 (mp0) cc_final: 0.7007 (mp0) REVERT: F 228 LEU cc_start: 0.8512 (mt) cc_final: 0.8145 (mm) REVERT: F 254 LEU cc_start: 0.7502 (tp) cc_final: 0.6860 (tt) REVERT: F 283 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7659 (tm-30) REVERT: F 287 MET cc_start: 0.8043 (mmm) cc_final: 0.7673 (mmm) REVERT: F 291 LYS cc_start: 0.8600 (ttpp) cc_final: 0.8164 (ttpp) REVERT: F 300 LYS cc_start: 0.8288 (ttpt) cc_final: 0.7994 (ttpt) REVERT: F 308 LEU cc_start: 0.7886 (mt) cc_final: 0.7390 (pp) REVERT: A 131 GLU cc_start: 0.7773 (tp30) cc_final: 0.7406 (tp30) REVERT: A 206 GLN cc_start: 0.8262 (tt0) cc_final: 0.8061 (tt0) REVERT: B 47 MET cc_start: 0.8508 (mmm) cc_final: 0.8214 (mmm) REVERT: C 41 LEU cc_start: 0.8459 (tt) cc_final: 0.8089 (tt) REVERT: C 44 GLN cc_start: 0.8059 (mt0) cc_final: 0.7627 (mp10) REVERT: C 67 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6963 (tm-30) REVERT: C 76 MET cc_start: 0.7708 (ptp) cc_final: 0.7443 (ptp) REVERT: C 95 VAL cc_start: 0.8526 (t) cc_final: 0.8289 (p) REVERT: C 143 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7646 (tpp80) REVERT: C 154 ILE cc_start: 0.8300 (tp) cc_final: 0.7716 (pt) REVERT: C 167 LEU cc_start: 0.8256 (tt) cc_final: 0.8034 (tp) REVERT: C 169 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7529 (tm-30) REVERT: C 174 GLU cc_start: 0.8094 (pp20) cc_final: 0.7755 (pp20) REVERT: C 201 ARG cc_start: 0.8108 (mtm-85) cc_final: 0.7574 (mtm-85) REVERT: C 227 ILE cc_start: 0.8664 (mt) cc_final: 0.8316 (tt) REVERT: C 283 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7546 (tm-30) REVERT: C 287 MET cc_start: 0.7954 (mmm) cc_final: 0.7562 (mmm) REVERT: C 291 LYS cc_start: 0.8383 (ttpp) cc_final: 0.8133 (ttpp) outliers start: 38 outliers final: 30 residues processed: 438 average time/residue: 0.1633 time to fit residues: 97.0165 Evaluate side-chains 455 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 421 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 275 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 144 optimal weight: 0.0040 chunk 85 optimal weight: 0.1980 chunk 95 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 133 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 140 optimal weight: 0.9980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 238 ASN E 59 ASN E 134 HIS ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 HIS A 238 ASN B 59 ASN B 112 HIS C 203 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.152834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.122641 restraints weight = 22548.718| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.24 r_work: 0.3376 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.254 15688 Z= 0.227 Angle : 0.810 59.167 21684 Z= 0.475 Chirality : 0.043 0.702 2406 Planarity : 0.006 0.155 2466 Dihedral : 20.431 156.429 2698 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.40 % Allowed : 20.19 % Favored : 77.40 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.21), residues: 1640 helix: 1.32 (0.19), residues: 762 sheet: 0.60 (0.32), residues: 242 loop : -0.68 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 177 TYR 0.023 0.002 TYR F 269 PHE 0.012 0.001 PHE F 141 TRP 0.015 0.001 TRP F 131 HIS 0.008 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.23 (15672) covalent geometry : angle 0.80985 / 0.47 (21678) hydrogen bonds : bond 0.03643 / 2.54 ( 689) hydrogen bonds : angle 4.36519 / 3.11 ( 1965) metal coordination : bond 0.00571 / 0.34 ( 16) metal coordination : angle 1.58937 / 0.91 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4674.24 seconds wall clock time: 80 minutes 28.88 seconds (4828.88 seconds total)