Starting phenix.real_space_refine on Sat Sep 12 09:05:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7oug_13076/09_2026/7oug_13076.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oug_13076/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7oug_13076/09_2026/7oug_13076.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oug_13076/09_2026/7oug_13076.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7oug_13076/09_2026/7oug_13076.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7oug_13076/09_2026/7oug_13076.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oug_13076/09_2026/7oug_13076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oug_13076/09_2026/7oug_13076.map" } 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-2.2.1-6174/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: 4.06, per 1000 atoms: 0.27 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: 1.30 Conformation dependent library (CDL) restraints added in 598.7 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: 1.64 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: 2.20 Time building geometry restraints manager: 1.72 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.660 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.170 ------------------------------------------------------------------------------- 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 : 0.818 35.200 21684 Z= 0.413 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 0.71216 / 0.41 (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 : 0.608 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: 0.6889 (mmm) REVERT: E 127 TYR cc_start: 0.7630 (m-10) cc_final: 0.7307 (m-10) REVERT: F 45 LYS cc_start: 0.6338 (mtpt) cc_final: 0.5316 (mtpt) REVERT: F 78 GLU cc_start: 0.6638 (tm-30) cc_final: 0.6432 (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: 0.6800 (ttp80) REVERT: F 287 MET cc_start: 0.6472 (mmm) cc_final: 0.6266 (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: 0.7221 (m-10) REVERT: B 175 ASN cc_start: 0.6739 (m110) cc_final: 0.6471 (m110) REVERT: C 41 LEU cc_start: 0.7835 (tt) cc_final: 0.7523 (tt) REVERT: C 45 LYS cc_start: 0.6260 (mtpt) cc_final: 0.4864 (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: 0.6561 (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: 0.6808 (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: 0.1673 time to fit residues: 109.7544 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 : 0.516 ------------------------------------------------------------------------------- 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 82 HIS ** 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 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.154319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.123426 restraints weight = 22599.091| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.26 r_work: 0.3399 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15688 Z= 0.176 Angle : 0.653 10.333 21684 Z= 0.341 Chirality : 0.045 0.240 2406 Planarity : 0.006 0.127 2466 Dihedral : 20.744 170.720 2698 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.99 % Allowed : 10.37 % Favored : 87.64 % 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: 0.41 (0.20), residues: 1640 helix: 1.16 (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 0.010 0.001 ARG C 143 TYR 0.020 0.002 TYR A 231 PHE 0.014 0.001 PHE F 42 TRP 0.010 0.001 TRP A 229 HIS 0.008 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (15672) covalent geometry : angle 0.65095 / 0.34 (21678) hydrogen bonds : bond 0.05271 / 3.70 ( 689) hydrogen bonds : angle 4.74932 / 3.41 ( 1965) metal coordination : bond 0.01595 / 0.94 ( 16) metal coordination : angle 3.01770 / 1.67 ( 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 464 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 435 time to evaluate : 0.511 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: D 131 GLU cc_start: 0.7539 (tp30) cc_final: 0.7265 (tp30) REVERT: D 274 LYS cc_start: 0.8938 (ttmt) cc_final: 0.8602 (ttmt) REVERT: E 47 MET cc_start: 0.8512 (mmm) cc_final: 0.8183 (mmm) REVERT: E 70 LYS cc_start: 0.8304 (ttpt) cc_final: 0.8103 (tttt) REVERT: E 127 TYR cc_start: 0.8158 (m-10) cc_final: 0.7834 (m-10) REVERT: E 133 GLN cc_start: 0.7478 (mm-40) cc_final: 0.7240 (mm-40) REVERT: F 44 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7932 (mp10) REVERT: F 67 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6543 (tm-30) REVERT: F 76 MET cc_start: 0.7568 (mtp) cc_final: 0.7337 (mtm) REVERT: F 78 GLU cc_start: 0.7290 (tm-30) cc_final: 0.7030 (tm-30) REVERT: F 169 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7547 (tm-30) REVERT: F 210 ARG cc_start: 0.8094 (ttp80) cc_final: 0.7701 (ttp80) REVERT: F 227 ILE cc_start: 0.8640 (mt) cc_final: 0.8354 (tt) REVERT: F 283 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7821 (tm-30) REVERT: F 287 MET cc_start: 0.8109 (mmm) cc_final: 0.7819 (mmm) REVERT: F 300 LYS cc_start: 0.8210 (ttpt) cc_final: 0.7933 (ttpt) REVERT: F 308 LEU cc_start: 0.8346 (mt) cc_final: 0.7930 (tp) REVERT: F 310 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7664 (mm-30) REVERT: A 131 GLU cc_start: 0.7581 (tp30) cc_final: 0.7216 (tp30) REVERT: B 29 LEU cc_start: 0.8248 (mt) cc_final: 0.7978 (mp) REVERT: B 47 MET cc_start: 0.8437 (mmm) cc_final: 0.8137 (mmm) REVERT: B 127 TYR cc_start: 0.8050 (m-10) cc_final: 0.7829 (m-10) REVERT: B 171 TYR cc_start: 0.8944 (m-10) cc_final: 0.8703 (m-10) REVERT: C 41 LEU cc_start: 0.8351 (tt) cc_final: 0.7994 (tt) REVERT: C 67 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6780 (tm-30) REVERT: C 70 ARG cc_start: 0.7893 (ptm-80) cc_final: 0.7508 (ttp80) REVERT: C 75 GLU cc_start: 0.7916 (tt0) cc_final: 0.7661 (tt0) REVERT: C 154 ILE cc_start: 0.8137 (mm) cc_final: 0.7800 (pt) REVERT: C 169 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7525 (tm-30) REVERT: C 190 TYR cc_start: 0.8018 (t80) cc_final: 0.7724 (t80) REVERT: C 201 ARG cc_start: 0.8073 (mtm-85) cc_final: 0.7576 (mtm-85) REVERT: C 227 ILE cc_start: 0.8650 (mt) cc_final: 0.8381 (tt) REVERT: C 241 GLU cc_start: 0.5640 (tm-30) cc_final: 0.5189 (tm-30) REVERT: C 246 PHE cc_start: 0.7728 (t80) cc_final: 0.7362 (t80) REVERT: C 266 GLN cc_start: 0.8470 (mp10) cc_final: 0.8061 (mp10) REVERT: C 283 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7608 (tm-30) REVERT: C 287 MET cc_start: 0.7953 (mmm) cc_final: 0.7611 (mmm) REVERT: C 300 LYS cc_start: 0.8156 (ttpt) cc_final: 0.7951 (ttpt) REVERT: C 310 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7238 (mm-30) outliers start: 29 outliers final: 14 residues processed: 448 average time/residue: 0.1708 time to fit residues: 104.0760 Evaluate side-chains 434 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 419 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 44 GLN Chi-restraints excluded: chain F residue 107 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 182 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 61 optimal weight: 0.0570 chunk 25 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 125 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 139 optimal weight: 0.0470 chunk 62 optimal weight: 0.5980 chunk 73 optimal weight: 0.0980 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN D 238 ASN E 59 ASN E 112 HIS E 161 ASN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 59 ASN C 133 HIS ** C 243 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 = 0.3999 r_free = 0.3999 target = 0.157111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.126605 restraints weight = 22714.821| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.27 r_work: 0.3419 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 15688 Z= 0.121 Angle : 0.569 8.258 21684 Z= 0.296 Chirality : 0.041 0.232 2406 Planarity : 0.005 0.097 2466 Dihedral : 20.795 166.014 2698 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.92 % Allowed : 13.12 % Favored : 84.96 % 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: 0.61 (0.21), residues: 1640 helix: 1.35 (0.19), residues: 758 sheet: 0.44 (0.32), residues: 222 loop : -0.68 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 143 TYR 0.019 0.002 TYR C 158 PHE 0.018 0.001 PHE C 99 TRP 0.009 0.001 TRP D 229 HIS 0.007 0.001 HIS F 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (15672) covalent geometry : angle 0.56595 / 0.30 (21678) hydrogen bonds : bond 0.04150 / 2.91 ( 689) hydrogen bonds : angle 4.41698 / 3.16 ( 1965) metal coordination : bond 0.00463 / 0.28 ( 16) metal coordination : angle 3.78338 / 2.07 ( 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 457 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 429 time to evaluate : 0.652 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: 0.8186 (t0) cc_final: 0.7974 (t0) REVERT: D 131 GLU cc_start: 0.7638 (tp30) cc_final: 0.7240 (tp30) REVERT: D 274 LYS cc_start: 0.8927 (ttmt) cc_final: 0.8591 (ttmt) REVERT: E 47 MET cc_start: 0.8495 (mmm) cc_final: 0.8153 (mmm) REVERT: E 70 LYS cc_start: 0.8338 (ttpt) cc_final: 0.8130 (tttt) REVERT: E 127 TYR cc_start: 0.8141 (m-10) cc_final: 0.7780 (m-10) REVERT: E 133 GLN cc_start: 0.7528 (mm-40) cc_final: 0.7286 (mm-40) REVERT: E 202 LYS cc_start: 0.8432 (mtmm) cc_final: 0.8154 (mtmm) REVERT: F 75 GLU cc_start: 0.7999 (tt0) cc_final: 0.7712 (tt0) REVERT: F 169 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7445 (tm-30) REVERT: F 183 LYS cc_start: 0.8594 (ttpp) cc_final: 0.8315 (ptpp) REVERT: F 210 ARG cc_start: 0.8055 (ttp80) cc_final: 0.7640 (ttp80) REVERT: F 283 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7796 (tm-30) REVERT: F 287 MET cc_start: 0.8117 (mmm) cc_final: 0.7869 (mmm) REVERT: F 300 LYS cc_start: 0.8328 (ttpt) cc_final: 0.8025 (ttpt) REVERT: F 304 PHE cc_start: 0.8637 (m-80) cc_final: 0.8404 (m-80) REVERT: F 308 LEU cc_start: 0.8238 (mt) cc_final: 0.7969 (tp) REVERT: A 131 GLU cc_start: 0.7603 (tp30) cc_final: 0.7307 (tp30) REVERT: A 142 ARG cc_start: 0.7692 (mtt-85) cc_final: 0.7485 (mtt-85) REVERT: B 29 LEU cc_start: 0.8151 (mt) cc_final: 0.7939 (mp) REVERT: B 32 LEU cc_start: 0.8677 (mm) cc_final: 0.8467 (mt) REVERT: B 47 MET cc_start: 0.8450 (mmm) cc_final: 0.8140 (mmm) REVERT: B 175 ASN cc_start: 0.7550 (OUTLIER) cc_final: 0.7340 (t0) REVERT: C 41 LEU cc_start: 0.8285 (tt) cc_final: 0.8029 (tt) REVERT: C 44 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7865 (mp10) REVERT: C 67 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6756 (tm-30) REVERT: C 139 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7407 (tm-30) REVERT: C 169 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7448 (tm-30) REVERT: C 174 GLU cc_start: 0.7934 (pp20) cc_final: 0.7623 (pp20) REVERT: C 190 TYR cc_start: 0.8002 (t80) cc_final: 0.7720 (t80) REVERT: C 201 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7613 (mtm-85) REVERT: C 227 ILE cc_start: 0.8604 (mt) cc_final: 0.8342 (tt) REVERT: C 241 GLU cc_start: 0.5747 (tm-30) cc_final: 0.5241 (tm-30) REVERT: C 263 TYR cc_start: 0.7623 (p90) cc_final: 0.7399 (p90) REVERT: C 266 GLN cc_start: 0.8559 (mp10) cc_final: 0.8089 (mp10) REVERT: C 283 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7519 (tm-30) REVERT: C 287 MET cc_start: 0.7909 (mmm) cc_final: 0.7574 (mmm) REVERT: C 300 LYS cc_start: 0.8288 (ttpt) cc_final: 0.8040 (ttpt) REVERT: C 304 PHE cc_start: 0.8640 (m-80) cc_final: 0.8422 (m-80) REVERT: C 310 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7022 (mm-30) outliers start: 28 outliers final: 17 residues processed: 435 average time/residue: 0.1706 time to fit residues: 100.9442 Evaluate side-chains 440 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 421 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 E residue 175 ASN Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 232 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 119 optimal weight: 0.6980 chunk 78 optimal weight: 0.0570 chunk 56 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 59 ASN D 182 ASN D 238 ASN E 59 ASN F 38 GLN F 203 GLN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 59 ASN B 112 HIS ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.154336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.123838 restraints weight = 22712.117| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.26 r_work: 0.3390 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15688 Z= 0.169 Angle : 0.594 8.067 21684 Z= 0.309 Chirality : 0.043 0.279 2406 Planarity : 0.005 0.078 2466 Dihedral : 20.644 161.897 2698 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.50 % Allowed : 14.01 % Favored : 82.49 % 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: 0.54 (0.20), residues: 1640 helix: 1.24 (0.18), residues: 760 sheet: 0.41 (0.31), residues: 242 loop : -0.67 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 143 TYR 0.025 0.002 TYR C 158 PHE 0.021 0.001 PHE C 99 TRP 0.013 0.001 TRP C 65 HIS 0.006 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (15672) covalent geometry : angle 0.59364 / 0.31 (21678) hydrogen bonds : bond 0.04262 / 2.98 ( 689) hydrogen bonds : angle 4.42969 / 3.16 ( 1965) metal coordination : bond 0.01299 / 0.76 ( 16) metal coordination : angle 1.58470 / 0.89 ( 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 479 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 428 time to evaluate : 0.542 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: 0.8254 (t0) cc_final: 0.8047 (t0) REVERT: D 131 GLU cc_start: 0.7736 (tp30) cc_final: 0.7228 (tp30) REVERT: D 274 LYS cc_start: 0.8890 (ttmt) cc_final: 0.8543 (ttmt) REVERT: E 32 LEU cc_start: 0.8665 (mm) cc_final: 0.8394 (mt) REVERT: E 47 MET cc_start: 0.8502 (mmm) cc_final: 0.8155 (mmm) REVERT: F 87 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7477 (mm) REVERT: F 165 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7417 (mm) REVERT: F 169 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7544 (tm-30) REVERT: F 177 ARG cc_start: 0.8287 (mpp80) cc_final: 0.7731 (mpp80) REVERT: F 183 LYS cc_start: 0.8630 (ttpp) cc_final: 0.8366 (ptpp) REVERT: F 210 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7774 (ttp80) REVERT: F 283 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7858 (tm-30) REVERT: F 287 MET cc_start: 0.8131 (mmm) cc_final: 0.7888 (mmm) REVERT: F 300 LYS cc_start: 0.8274 (ttpt) cc_final: 0.7942 (ttpt) REVERT: F 304 PHE cc_start: 0.8691 (m-80) cc_final: 0.8262 (m-80) REVERT: F 308 LEU cc_start: 0.8150 (mt) cc_final: 0.7641 (mt) REVERT: A 131 GLU cc_start: 0.7750 (tp30) cc_final: 0.7357 (tp30) REVERT: B 29 LEU cc_start: 0.8252 (mt) cc_final: 0.8018 (mp) REVERT: B 47 MET cc_start: 0.8480 (mmm) cc_final: 0.8139 (mmm) REVERT: B 175 ASN cc_start: 0.7671 (OUTLIER) cc_final: 0.7411 (t0) REVERT: C 67 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6892 (tm-30) REVERT: C 75 GLU cc_start: 0.8077 (tt0) cc_final: 0.7801 (tt0) REVERT: C 83 ASN cc_start: 0.8170 (m-40) cc_final: 0.7913 (m-40) REVERT: C 94 GLU cc_start: 0.7248 (pm20) cc_final: 0.6921 (mm-30) REVERT: C 139 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7430 (tm-30) REVERT: C 154 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7670 (tp) REVERT: C 169 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7532 (tm-30) REVERT: C 174 GLU cc_start: 0.8023 (pp20) cc_final: 0.7742 (pp20) REVERT: C 201 ARG cc_start: 0.8137 (mtm-85) cc_final: 0.7560 (mtm-85) REVERT: C 210 ARG cc_start: 0.8015 (mtm-85) cc_final: 0.7533 (mtm-85) REVERT: C 227 ILE cc_start: 0.8648 (mt) cc_final: 0.8307 (tt) REVERT: C 241 GLU cc_start: 0.5803 (tm-30) cc_final: 0.5281 (tm-30) REVERT: C 283 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7679 (tm-30) REVERT: C 287 MET cc_start: 0.7957 (mmm) cc_final: 0.7618 (mmm) REVERT: C 300 LYS cc_start: 0.8208 (ttpt) cc_final: 0.8001 (ttpt) REVERT: C 310 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7038 (mm-30) outliers start: 51 outliers final: 29 residues processed: 442 average time/residue: 0.1595 time to fit residues: 96.5483 Evaluate side-chains 450 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 417 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 177 ASN 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 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 134 HIS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 275 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 61 optimal weight: 0.2980 chunk 74 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 59 ASN D 238 ASN E 59 ASN E 112 HIS E 118 HIS E 134 HIS F 38 GLN ** 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 ** 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 = 0.3956 r_free = 0.3956 target = 0.153289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.122729 restraints weight = 22636.305| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.27 r_work: 0.3371 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15688 Z= 0.161 Angle : 0.592 8.787 21684 Z= 0.307 Chirality : 0.043 0.267 2406 Planarity : 0.005 0.074 2466 Dihedral : 20.603 159.668 2698 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.30 % Allowed : 16.41 % Favored : 80.29 % 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: 1.26 (0.18), residues: 756 sheet: 0.47 (0.31), residues: 242 loop : -0.73 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 142 TYR 0.025 0.002 TYR F 269 PHE 0.015 0.001 PHE C 99 TRP 0.009 0.001 TRP F 65 HIS 0.007 0.001 HIS E 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (15672) covalent geometry : angle 0.59132 / 0.31 (21678) hydrogen bonds : bond 0.04087 / 2.85 ( 689) hydrogen bonds : angle 4.41669 / 3.15 ( 1965) metal coordination : bond 0.01084 / 0.62 ( 16) metal coordination : angle 1.66305 / 0.94 ( 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 472 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 424 time to evaluate : 0.550 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: 0.7270 (tp30) REVERT: D 212 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7840 (mtt90) REVERT: D 274 LYS cc_start: 0.8881 (ttmt) cc_final: 0.8529 (ttmt) REVERT: E 47 MET cc_start: 0.8506 (mmm) cc_final: 0.8173 (mmm) REVERT: F 87 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7554 (mm) REVERT: F 165 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7539 (mm) REVERT: F 169 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7507 (tm-30) REVERT: F 283 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7812 (tm-30) REVERT: F 287 MET cc_start: 0.8108 (mmm) cc_final: 0.7856 (mmm) REVERT: F 300 LYS cc_start: 0.8288 (ttpt) cc_final: 0.8061 (ttpt) REVERT: F 304 PHE cc_start: 0.8669 (m-80) cc_final: 0.8350 (m-80) REVERT: F 308 LEU cc_start: 0.8130 (mt) cc_final: 0.7593 (mt) REVERT: A 131 GLU cc_start: 0.7792 (tp30) cc_final: 0.7373 (tp30) REVERT: B 29 LEU cc_start: 0.8242 (mt) cc_final: 0.8026 (mp) REVERT: B 47 MET cc_start: 0.8480 (mmm) cc_final: 0.8156 (mmm) REVERT: B 175 ASN cc_start: 0.7707 (OUTLIER) cc_final: 0.7469 (t0) REVERT: B 202 LYS cc_start: 0.8488 (mtmm) cc_final: 0.8272 (mtmm) REVERT: C 67 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6955 (tm-30) REVERT: C 83 ASN cc_start: 0.8197 (m-40) cc_final: 0.7934 (m-40) REVERT: C 139 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7488 (tm-30) REVERT: C 154 ILE cc_start: 0.8134 (tp) cc_final: 0.7792 (tp) REVERT: C 169 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7518 (tm-30) REVERT: C 174 GLU cc_start: 0.8051 (pp20) cc_final: 0.7722 (pp20) REVERT: C 177 ARG cc_start: 0.8333 (mpp80) cc_final: 0.7618 (mpp80) REVERT: C 201 ARG cc_start: 0.8112 (mtm-85) cc_final: 0.7570 (mtm-85) REVERT: C 210 ARG cc_start: 0.7920 (mtm-85) cc_final: 0.7537 (mtm-85) REVERT: C 241 GLU cc_start: 0.5935 (tm-30) cc_final: 0.5384 (tm-30) REVERT: C 283 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7618 (tm-30) REVERT: C 287 MET cc_start: 0.7947 (mmm) cc_final: 0.7600 (mmm) REVERT: C 310 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7060 (mm-30) outliers start: 48 outliers final: 32 residues processed: 439 average time/residue: 0.1665 time to fit residues: 99.4806 Evaluate side-chains 452 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 416 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 THR 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 212 ARG 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 175 ASN 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 165 LEU Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 260 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 15 GLN Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 275 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 70 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 159 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 164 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN D 182 ASN D 206 GLN E 59 ASN E 112 HIS 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 206 GLN A 238 ASN B 59 ASN B 112 HIS ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.152660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122445 restraints weight = 22541.679| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.25 r_work: 0.3380 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15688 Z= 0.165 Angle : 0.603 11.225 21684 Z= 0.313 Chirality : 0.042 0.165 2406 Planarity : 0.005 0.070 2466 Dihedral : 20.559 157.996 2698 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.23 % Allowed : 17.10 % Favored : 79.67 % 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: 0.50 (0.20), residues: 1640 helix: 1.20 (0.18), residues: 760 sheet: 0.54 (0.31), residues: 242 loop : -0.76 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 142 TYR 0.027 0.002 TYR F 269 PHE 0.012 0.001 PHE C 141 TRP 0.009 0.001 TRP C 65 HIS 0.005 0.001 HIS B 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (15672) covalent geometry : angle 0.60269 / 0.31 (21678) hydrogen bonds : bond 0.04025 / 2.81 ( 689) hydrogen bonds : angle 4.39116 / 3.14 ( 1965) metal coordination : bond 0.01153 / 0.66 ( 16) metal coordination : angle 1.55263 / 0.88 ( 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 480 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 433 time to evaluate : 0.545 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: D 131 GLU cc_start: 0.7863 (tp30) cc_final: 0.7265 (tp30) REVERT: D 212 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7868 (mtt90) REVERT: D 274 LYS cc_start: 0.8867 (ttmt) cc_final: 0.8520 (ttmt) REVERT: E 47 MET cc_start: 0.8492 (mmm) cc_final: 0.8153 (mmm) REVERT: F 44 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7835 (mp10) REVERT: F 87 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7610 (mm) REVERT: F 164 VAL cc_start: 0.8596 (t) cc_final: 0.8215 (m) REVERT: F 165 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7408 (mm) REVERT: F 169 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7514 (tm-30) REVERT: F 183 LYS cc_start: 0.8617 (ttpp) cc_final: 0.8369 (ptpp) REVERT: F 254 LEU cc_start: 0.7479 (tp) cc_final: 0.6840 (tt) REVERT: F 267 LEU cc_start: 0.8403 (tt) cc_final: 0.8126 (tp) REVERT: F 283 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7794 (tm-30) REVERT: F 287 MET cc_start: 0.8091 (mmm) cc_final: 0.7836 (mmm) REVERT: F 300 LYS cc_start: 0.8282 (ttpt) cc_final: 0.8037 (ttpt) REVERT: F 308 LEU cc_start: 0.8097 (mt) cc_final: 0.7544 (mt) REVERT: A 131 GLU cc_start: 0.7791 (tp30) cc_final: 0.7386 (tp30) REVERT: B 29 LEU cc_start: 0.8289 (mt) cc_final: 0.8074 (mp) REVERT: B 47 MET cc_start: 0.8475 (mmm) cc_final: 0.8137 (mmm) REVERT: C 67 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6944 (tm-30) REVERT: C 75 GLU cc_start: 0.8067 (tt0) cc_final: 0.7815 (tt0) REVERT: C 77 VAL cc_start: 0.7756 (p) cc_final: 0.7554 (p) REVERT: C 83 ASN cc_start: 0.8196 (m-40) cc_final: 0.7924 (m-40) REVERT: C 95 VAL cc_start: 0.8283 (t) cc_final: 0.8017 (p) REVERT: C 139 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7412 (tm-30) REVERT: C 154 ILE cc_start: 0.8181 (tp) cc_final: 0.7851 (tp) REVERT: C 169 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7556 (tm-30) REVERT: C 174 GLU cc_start: 0.8079 (pp20) cc_final: 0.7755 (pp20) REVERT: C 201 ARG cc_start: 0.8087 (mtm-85) cc_final: 0.7537 (mtm-85) REVERT: C 210 ARG cc_start: 0.7944 (mtm-85) cc_final: 0.7652 (mtm-85) REVERT: C 223 GLU cc_start: 0.7499 (mp0) cc_final: 0.7186 (mp0) REVERT: C 227 ILE cc_start: 0.8583 (mt) cc_final: 0.8229 (tt) REVERT: C 258 LYS cc_start: 0.7806 (tptp) cc_final: 0.7529 (tptp) REVERT: C 283 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7633 (tm-30) REVERT: C 287 MET cc_start: 0.7982 (mmm) cc_final: 0.7619 (mmm) REVERT: C 310 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7119 (mm-30) outliers start: 47 outliers final: 32 residues processed: 447 average time/residue: 0.1628 time to fit residues: 99.7117 Evaluate side-chains 462 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 426 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 212 ARG 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 175 ASN Chi-restraints excluded: chain E residue 177 ASN 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 88 THR Chi-restraints excluded: chain F residue 107 LEU 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 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 15 GLN Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 275 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 131 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN E 59 ASN E 112 HIS E 130 GLN E 134 HIS ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 HIS A 59 ASN A 238 ASN B 59 ASN B 112 HIS ** B 134 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 = 0.3915 r_free = 0.3915 target = 0.150139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.119933 restraints weight = 22522.898| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.24 r_work: 0.3327 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15688 Z= 0.239 Angle : 0.637 11.124 21684 Z= 0.335 Chirality : 0.045 0.191 2406 Planarity : 0.005 0.068 2466 Dihedral : 20.582 157.232 2698 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.02 % Allowed : 18.54 % Favored : 78.43 % 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: 0.37 (0.20), residues: 1640 helix: 1.09 (0.18), residues: 762 sheet: 0.64 (0.32), residues: 242 loop : -0.91 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 142 TYR 0.025 0.002 TYR F 269 PHE 0.012 0.001 PHE F 42 TRP 0.010 0.002 TRP A 62 HIS 0.008 0.001 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.24 (15672) covalent geometry : angle 0.63656 / 0.33 (21678) hydrogen bonds : bond 0.04606 / 3.22 ( 689) hydrogen bonds : angle 4.51364 / 3.23 ( 1965) metal coordination : bond 0.01998 / 1.20 ( 16) metal coordination : angle 1.96310 / 1.11 ( 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 483 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 439 time to evaluate : 0.538 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: 0.7903 (tp30) cc_final: 0.7316 (tp30) REVERT: D 212 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7854 (mtt90) REVERT: D 274 LYS cc_start: 0.8806 (ttmt) cc_final: 0.8459 (ttmt) REVERT: E 47 MET cc_start: 0.8602 (mmm) cc_final: 0.8279 (mmm) REVERT: E 54 ARG cc_start: 0.8204 (mtp85) cc_final: 0.7986 (mmt180) REVERT: E 161 ASN cc_start: 0.8091 (m-40) cc_final: 0.7858 (m-40) REVERT: E 246 GLN cc_start: 0.8067 (mm110) cc_final: 0.7590 (mt0) REVERT: F 44 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7719 (mp10) REVERT: F 87 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7803 (mm) REVERT: F 164 VAL cc_start: 0.8671 (t) cc_final: 0.8330 (m) REVERT: F 165 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7506 (mm) REVERT: F 169 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7500 (tm-30) REVERT: F 183 LYS cc_start: 0.8628 (ttpp) cc_final: 0.8365 (ptpp) REVERT: F 233 ASN cc_start: 0.8409 (t0) cc_final: 0.8202 (t0) REVERT: F 254 LEU cc_start: 0.7666 (tp) cc_final: 0.6980 (tt) REVERT: F 267 LEU cc_start: 0.8431 (tt) cc_final: 0.8193 (tp) REVERT: F 283 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7894 (tm-30) REVERT: F 287 MET cc_start: 0.8091 (mmm) cc_final: 0.7844 (mmm) REVERT: F 300 LYS cc_start: 0.8304 (ttpt) cc_final: 0.8023 (ttpt) REVERT: F 308 LEU cc_start: 0.8141 (mt) cc_final: 0.7671 (mt) REVERT: A 131 GLU cc_start: 0.7862 (tp30) cc_final: 0.7467 (tp30) REVERT: B 29 LEU cc_start: 0.8266 (mt) cc_final: 0.8033 (mp) REVERT: B 47 MET cc_start: 0.8547 (mmm) cc_final: 0.8193 (mmm) REVERT: B 134 HIS cc_start: 0.8255 (m-70) cc_final: 0.7955 (m-70) REVERT: B 246 GLN cc_start: 0.8058 (mm110) cc_final: 0.7526 (mt0) REVERT: C 44 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7766 (mp10) REVERT: C 67 GLU cc_start: 0.7339 (mm-30) cc_final: 0.6989 (tm-30) REVERT: C 75 GLU cc_start: 0.8089 (tt0) cc_final: 0.7850 (tt0) REVERT: C 83 ASN cc_start: 0.8233 (m-40) cc_final: 0.7955 (m-40) REVERT: C 92 TYR cc_start: 0.7530 (m-80) cc_final: 0.7044 (m-80) REVERT: C 95 VAL cc_start: 0.8471 (t) cc_final: 0.8215 (p) REVERT: C 139 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7461 (tm-30) REVERT: C 154 ILE cc_start: 0.8308 (tp) cc_final: 0.7956 (tp) REVERT: C 169 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7617 (tm-30) REVERT: C 174 GLU cc_start: 0.8094 (pp20) cc_final: 0.7733 (pp20) REVERT: C 177 ARG cc_start: 0.8293 (mpp80) cc_final: 0.7590 (mpp80) REVERT: C 201 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7576 (mtm-85) REVERT: C 210 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7628 (mtm-85) REVERT: C 227 ILE cc_start: 0.8592 (mt) cc_final: 0.8253 (tt) REVERT: C 283 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7657 (tm-30) REVERT: C 287 MET cc_start: 0.7973 (mmm) cc_final: 0.7599 (mmm) REVERT: C 291 LYS cc_start: 0.8437 (ttpp) cc_final: 0.8116 (ttpp) REVERT: C 310 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7185 (mm-30) outliers start: 44 outliers final: 30 residues processed: 452 average time/residue: 0.1640 time to fit residues: 101.5911 Evaluate side-chains 452 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 417 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 212 ARG 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 65 ASP Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 177 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 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 15 GLN Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 275 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 166 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 33 HIS D 238 ASN E 59 ASN E 112 HIS F 203 GLN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 ASN A 238 ASN B 59 ASN B 112 HIS B 134 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 = 0.3931 r_free = 0.3931 target = 0.151329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.121295 restraints weight = 22593.952| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.24 r_work: 0.3357 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15688 Z= 0.160 Angle : 0.606 8.724 21684 Z= 0.317 Chirality : 0.042 0.182 2406 Planarity : 0.005 0.070 2466 Dihedral : 20.548 155.964 2698 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.54 % Allowed : 19.99 % Favored : 77.47 % 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: 0.46 (0.20), residues: 1640 helix: 1.20 (0.18), residues: 760 sheet: 0.60 (0.32), residues: 242 loop : -0.86 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 142 TYR 0.025 0.002 TYR F 269 PHE 0.016 0.001 PHE F 42 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 0.00345 / 0.16 (15672) covalent geometry : angle 0.60527 / 0.32 (21678) hydrogen bonds : bond 0.04014 / 2.79 ( 689) hydrogen bonds : angle 4.47264 / 3.20 ( 1965) metal coordination : bond 0.00845 / 0.50 ( 16) metal coordination : angle 1.96247 / 1.11 ( 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 470 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 433 time to evaluate : 0.519 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: 0.7880 (tp30) cc_final: 0.7292 (tp30) REVERT: D 212 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7837 (mtt90) REVERT: D 274 LYS cc_start: 0.8797 (ttmt) cc_final: 0.8490 (ttmt) REVERT: E 47 MET cc_start: 0.8546 (mmm) cc_final: 0.8244 (mmm) REVERT: E 161 ASN cc_start: 0.8029 (m-40) cc_final: 0.7812 (m-40) REVERT: F 44 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7781 (mp10) REVERT: F 95 VAL cc_start: 0.8386 (t) cc_final: 0.8005 (p) REVERT: F 139 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7504 (tm-30) REVERT: F 164 VAL cc_start: 0.8589 (t) cc_final: 0.8225 (m) REVERT: F 165 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7441 (mm) REVERT: F 169 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7474 (tm-30) REVERT: F 183 LYS cc_start: 0.8622 (ttpp) cc_final: 0.8347 (ptpp) REVERT: F 254 LEU cc_start: 0.7587 (tp) cc_final: 0.6915 (tt) REVERT: F 267 LEU cc_start: 0.8415 (tt) cc_final: 0.8180 (tp) REVERT: F 300 LYS cc_start: 0.8297 (ttpt) cc_final: 0.8054 (ttpt) REVERT: A 131 GLU cc_start: 0.7798 (tp30) cc_final: 0.7427 (tp30) REVERT: B 29 LEU cc_start: 0.8230 (mt) cc_final: 0.8019 (mp) REVERT: B 47 MET cc_start: 0.8519 (mmm) cc_final: 0.8202 (mmm) REVERT: C 44 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7743 (mp10) REVERT: C 67 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7010 (tm-30) REVERT: C 70 ARG cc_start: 0.7890 (ptm-80) cc_final: 0.7666 (ptm-80) REVERT: C 75 GLU cc_start: 0.8086 (tt0) cc_final: 0.7860 (tt0) REVERT: C 83 ASN cc_start: 0.8198 (m-40) cc_final: 0.7886 (m-40) REVERT: C 95 VAL cc_start: 0.8479 (t) cc_final: 0.8237 (p) REVERT: C 139 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7446 (tm-30) REVERT: C 154 ILE cc_start: 0.8292 (tp) cc_final: 0.8067 (tp) REVERT: C 167 LEU cc_start: 0.8330 (tt) cc_final: 0.8111 (tp) REVERT: C 169 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7575 (tm-30) REVERT: C 201 ARG cc_start: 0.8085 (mtm-85) cc_final: 0.7532 (mtm-85) REVERT: C 227 ILE cc_start: 0.8574 (mt) cc_final: 0.8291 (tt) REVERT: C 283 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7588 (tm-30) REVERT: C 287 MET cc_start: 0.7973 (mmm) cc_final: 0.7598 (mmm) REVERT: C 291 LYS cc_start: 0.8367 (ttpp) cc_final: 0.8135 (ttpp) REVERT: C 310 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7234 (mm-30) outliers start: 37 outliers final: 25 residues processed: 443 average time/residue: 0.1645 time to fit residues: 99.3972 Evaluate side-chains 463 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 433 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 212 ARG 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 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 260 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 177 ASN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 275 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 43 optimal weight: 0.5980 chunk 127 optimal weight: 0.5980 chunk 153 optimal weight: 0.8980 chunk 161 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 238 ASN E 59 ASN E 112 HIS E 134 HIS ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 59 ASN B 112 HIS B 134 HIS ** 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 = 0.3928 r_free = 0.3928 target = 0.151168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.121062 restraints weight = 22490.303| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.23 r_work: 0.3366 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15688 Z= 0.154 Angle : 0.613 9.316 21684 Z= 0.320 Chirality : 0.042 0.169 2406 Planarity : 0.005 0.067 2466 Dihedral : 20.497 156.049 2698 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.47 % Allowed : 20.88 % Favored : 76.65 % 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: 0.49 (0.20), residues: 1640 helix: 1.18 (0.18), residues: 760 sheet: 0.62 (0.32), residues: 242 loop : -0.78 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 142 TYR 0.025 0.002 TYR F 269 PHE 0.010 0.001 PHE F 141 TRP 0.008 0.001 TRP C 65 HIS 0.009 0.001 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (15672) covalent geometry : angle 0.61273 / 0.32 (21678) hydrogen bonds : bond 0.03943 / 2.75 ( 689) hydrogen bonds : angle 4.47052 / 3.19 ( 1965) metal coordination : bond 0.00843 / 0.50 ( 16) metal coordination : angle 1.65026 / 0.95 ( 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 476 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 440 time to evaluate : 0.552 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: 0.7889 (tp30) cc_final: 0.7297 (tp30) REVERT: D 212 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7892 (mtt90) REVERT: D 274 LYS cc_start: 0.8798 (ttmt) cc_final: 0.8481 (ttmt) REVERT: E 47 MET cc_start: 0.8552 (mmm) cc_final: 0.8251 (mmm) REVERT: E 161 ASN cc_start: 0.7974 (m-40) cc_final: 0.7752 (m-40) REVERT: F 44 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7795 (mp10) REVERT: F 77 VAL cc_start: 0.7507 (p) cc_final: 0.7166 (p) REVERT: F 94 GLU cc_start: 0.7823 (pm20) cc_final: 0.7235 (mm-30) REVERT: F 95 VAL cc_start: 0.8347 (t) cc_final: 0.7912 (p) REVERT: F 139 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: F 164 VAL cc_start: 0.8635 (t) cc_final: 0.8331 (m) REVERT: F 165 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7546 (mm) REVERT: F 169 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7509 (tm-30) REVERT: F 254 LEU cc_start: 0.7609 (tp) cc_final: 0.6935 (tt) REVERT: F 300 LYS cc_start: 0.8297 (ttpt) cc_final: 0.8051 (ttpt) REVERT: F 308 LEU cc_start: 0.7922 (mt) cc_final: 0.7583 (mt) REVERT: A 131 GLU cc_start: 0.7795 (tp30) cc_final: 0.7420 (tp30) REVERT: B 29 LEU cc_start: 0.8254 (mt) cc_final: 0.8041 (mp) REVERT: B 47 MET cc_start: 0.8511 (mmm) cc_final: 0.8192 (mmm) REVERT: C 44 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7737 (mp10) REVERT: C 67 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7004 (tm-30) REVERT: C 70 ARG cc_start: 0.7875 (ptm-80) cc_final: 0.7632 (ptm-80) REVERT: C 75 GLU cc_start: 0.8060 (tt0) cc_final: 0.7856 (tt0) REVERT: C 77 VAL cc_start: 0.7775 (p) cc_final: 0.7549 (p) REVERT: C 83 ASN cc_start: 0.8172 (m-40) cc_final: 0.7850 (m-40) REVERT: C 95 VAL cc_start: 0.8501 (t) cc_final: 0.8255 (p) REVERT: C 139 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7398 (tm-30) REVERT: C 154 ILE cc_start: 0.8311 (tp) cc_final: 0.8091 (tp) REVERT: C 167 LEU cc_start: 0.8314 (tt) cc_final: 0.8099 (tp) REVERT: C 169 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7591 (tm-30) REVERT: C 201 ARG cc_start: 0.8071 (mtm-85) cc_final: 0.7531 (mtm-85) REVERT: C 223 GLU cc_start: 0.7519 (mp0) cc_final: 0.7136 (mp0) REVERT: C 227 ILE cc_start: 0.8588 (mt) cc_final: 0.8331 (tt) REVERT: C 258 LYS cc_start: 0.7760 (tptp) cc_final: 0.7498 (tptp) REVERT: C 283 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7630 (tm-30) REVERT: C 287 MET cc_start: 0.7988 (mmm) cc_final: 0.7612 (mmm) REVERT: C 291 LYS cc_start: 0.8399 (ttpp) cc_final: 0.8142 (ttpp) REVERT: C 308 LEU cc_start: 0.8170 (tt) cc_final: 0.7709 (pp) REVERT: C 310 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7295 (mm-30) outliers start: 36 outliers final: 22 residues processed: 452 average time/residue: 0.1602 time to fit residues: 98.7818 Evaluate side-chains 459 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 432 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 212 ARG 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 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 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 175 ASN Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 228 LEU 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 130 optimal weight: 3.9990 chunk 65 optimal weight: 0.0870 chunk 143 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 51 optimal weight: 0.0970 chunk 26 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 73 optimal weight: 0.0970 chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 238 ASN E 59 ASN E 112 HIS E 134 HIS ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 59 ASN B 112 HIS B 130 GLN B 134 HIS ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.151959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.121766 restraints weight = 22563.254| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.24 r_work: 0.3372 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15688 Z= 0.132 Angle : 0.620 9.591 21684 Z= 0.322 Chirality : 0.041 0.187 2406 Planarity : 0.005 0.064 2466 Dihedral : 20.442 156.125 2698 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.13 % Allowed : 21.43 % Favored : 76.44 % 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: 0.51 (0.20), residues: 1640 helix: 1.15 (0.18), residues: 758 sheet: 0.59 (0.32), residues: 242 loop : -0.69 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 142 TYR 0.029 0.002 TYR F 269 PHE 0.012 0.001 PHE C 141 TRP 0.009 0.001 TRP F 65 HIS 0.009 0.001 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (15672) covalent geometry : angle 0.61878 / 0.32 (21678) hydrogen bonds : bond 0.03691 / 2.58 ( 689) hydrogen bonds : angle 4.47528 / 3.20 ( 1965) metal coordination : bond 0.00407 / 0.25 ( 16) metal coordination : angle 1.99757 / 1.13 ( 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 468 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 437 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: symmetry clash REVERT: D 131 GLU cc_start: 0.7877 (tp30) cc_final: 0.7295 (tp30) REVERT: D 212 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7947 (mtt90) REVERT: D 274 LYS cc_start: 0.8792 (ttmt) cc_final: 0.8484 (ttmt) REVERT: E 47 MET cc_start: 0.8527 (mmm) cc_final: 0.8238 (mmm) REVERT: E 202 LYS cc_start: 0.8496 (mtmm) cc_final: 0.8209 (mtmm) REVERT: F 44 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7820 (mp10) REVERT: F 77 VAL cc_start: 0.7533 (p) cc_final: 0.7284 (p) REVERT: F 94 GLU cc_start: 0.7851 (pm20) cc_final: 0.7608 (mm-30) REVERT: F 95 VAL cc_start: 0.8391 (t) cc_final: 0.7899 (p) REVERT: F 103 MET cc_start: 0.7734 (mmp) cc_final: 0.7467 (mmm) REVERT: F 139 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7454 (tm-30) REVERT: F 164 VAL cc_start: 0.8565 (t) cc_final: 0.8215 (m) REVERT: F 165 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7529 (mm) REVERT: F 169 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7424 (tm-30) REVERT: F 183 LYS cc_start: 0.8678 (ttpp) cc_final: 0.8455 (ptpp) REVERT: F 201 ARG cc_start: 0.8079 (mtm-85) cc_final: 0.7529 (mtm-85) REVERT: F 210 ARG cc_start: 0.8117 (ttp80) cc_final: 0.7707 (ttp80) REVERT: F 254 LEU cc_start: 0.7589 (tp) cc_final: 0.6953 (tt) REVERT: F 300 LYS cc_start: 0.8279 (ttpt) cc_final: 0.8027 (ttpt) REVERT: F 308 LEU cc_start: 0.7922 (mt) cc_final: 0.7424 (pp) REVERT: A 131 GLU cc_start: 0.7785 (tp30) cc_final: 0.7399 (tp30) REVERT: B 29 LEU cc_start: 0.8203 (mt) cc_final: 0.7997 (mp) REVERT: B 47 MET cc_start: 0.8516 (mmm) cc_final: 0.8206 (mmm) REVERT: C 44 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7733 (mp10) REVERT: C 67 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7018 (tm-30) REVERT: C 70 ARG cc_start: 0.7860 (ptm-80) cc_final: 0.7607 (ptm-80) REVERT: C 76 MET cc_start: 0.7772 (ptp) cc_final: 0.7433 (ptp) REVERT: C 95 VAL cc_start: 0.8549 (t) cc_final: 0.8299 (p) REVERT: C 152 PRO cc_start: 0.8320 (Cg_endo) cc_final: 0.8116 (Cg_exo) REVERT: C 154 ILE cc_start: 0.8284 (tp) cc_final: 0.8062 (tp) REVERT: C 167 LEU cc_start: 0.8226 (tt) cc_final: 0.8011 (tp) REVERT: C 169 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7474 (tm-30) REVERT: C 201 ARG cc_start: 0.8069 (mtm-85) cc_final: 0.7530 (mtm-85) REVERT: C 227 ILE cc_start: 0.8684 (mt) cc_final: 0.8317 (tt) REVERT: C 252 LEU cc_start: 0.8451 (mt) cc_final: 0.8243 (pp) REVERT: C 258 LYS cc_start: 0.7770 (tptp) cc_final: 0.7522 (tptp) REVERT: C 283 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7573 (tm-30) REVERT: C 287 MET cc_start: 0.7931 (mmm) cc_final: 0.7551 (mmm) REVERT: C 291 LYS cc_start: 0.8338 (ttpp) cc_final: 0.8075 (ttpp) REVERT: C 310 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7380 (mm-30) outliers start: 31 outliers final: 21 residues processed: 447 average time/residue: 0.1599 time to fit residues: 97.5182 Evaluate side-chains 459 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 433 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 212 ARG Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 263 THR 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 260 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 263 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 228 LEU 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: 0.8980 chunk 85 optimal weight: 0.0040 chunk 95 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 238 ASN E 41 ASN E 59 ASN E 112 HIS E 134 HIS F 203 GLN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3933 r_free = 0.3933 target = 0.151567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.121544 restraints weight = 22558.135| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.22 r_work: 0.3372 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15688 Z= 0.161 Angle : 0.640 10.200 21684 Z= 0.330 Chirality : 0.042 0.183 2406 Planarity : 0.005 0.073 2466 Dihedral : 20.435 156.651 2698 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.27 % Allowed : 21.77 % Favored : 75.96 % 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: 0.41 (0.20), residues: 1640 helix: 1.04 (0.18), residues: 770 sheet: 0.64 (0.32), residues: 242 loop : -0.77 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 177 TYR 0.027 0.002 TYR F 269 PHE 0.013 0.001 PHE C 99 TRP 0.013 0.001 TRP F 131 HIS 0.006 0.001 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (15672) covalent geometry : angle 0.63949 / 0.33 (21678) hydrogen bonds : bond 0.03825 / 2.67 ( 689) hydrogen bonds : angle 4.49319 / 3.21 ( 1965) metal coordination : bond 0.00900 / 0.53 ( 16) metal coordination : angle 1.69152 / 0.97 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4945.83 seconds wall clock time: 85 minutes 14.44 seconds (5114.44 seconds total)