Starting phenix.real_space_refine on Tue Nov 18 14:50:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oug_13076/11_2025/7oug_13076.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oug_13076/11_2025/7oug_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_13076/11_2025/7oug_13076.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oug_13076/11_2025/7oug_13076.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oug_13076/11_2025/7oug_13076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oug_13076/11_2025/7oug_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-2.0-5881/lib/python3.9/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: 4.67, per 1000 atoms: 0.31 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: 1.29 Conformation dependent library (CDL) restraints added in 605.3 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: 1.86 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: 2.54 Time building geometry restraints manager: 1.81 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: 1790 0.037 - 0.074: 432 0.074 - 0.110: 142 0.110 - 0.147: 40 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: 0.02 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: 2.670 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.950 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 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= 0.183 Angle : 0.788 35.200 21684 Z= 0.329 Chirality : 0.039 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 covalent geometry : bond 0.00379 (15672) covalent geometry : angle 0.67825 (21678) hydrogen bonds : bond 0.16919 ( 689) hydrogen bonds : angle 6.25417 ( 1965) metal coordination : bond 0.02060 ( 16) metal coordination : angle 24.18352 ( 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 : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.7182 (mmm) cc_final: 0.6886 (mmm) REVERT: E 127 TYR cc_start: 0.7630 (m-10) cc_final: 0.7309 (m-10) REVERT: F 45 LYS cc_start: 0.6338 (mtpt) cc_final: 0.5315 (mtpt) REVERT: F 78 GLU cc_start: 0.6638 (tm-30) cc_final: 0.6431 (tm-30) REVERT: F 174 GLU cc_start: 0.6874 (pp20) cc_final: 0.6650 (pp20) REVERT: F 201 ARG cc_start: 0.7267 (mtm-85) cc_final: 0.6937 (mtm-85) REVERT: F 210 ARG cc_start: 0.7050 (ttp80) cc_final: 0.6801 (ttp80) REVERT: F 287 MET cc_start: 0.6472 (mmm) cc_final: 0.6265 (mmm) REVERT: F 308 LEU cc_start: 0.8349 (mt) cc_final: 0.8041 (mt) REVERT: F 310 GLU cc_start: 0.7260 (mm-30) cc_final: 0.7004 (mm-30) REVERT: B 47 MET cc_start: 0.7127 (mmm) cc_final: 0.6823 (mmm) REVERT: B 127 TYR cc_start: 0.7441 (m-10) cc_final: 0.7224 (m-10) REVERT: B 175 ASN cc_start: 0.6739 (m110) cc_final: 0.6475 (m110) REVERT: C 41 LEU cc_start: 0.7835 (tt) cc_final: 0.7524 (tt) REVERT: C 45 LYS cc_start: 0.6260 (mtpt) cc_final: 0.4862 (mtpt) REVERT: C 92 TYR cc_start: 0.5749 (m-80) cc_final: 0.5427 (m-80) REVERT: C 139 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6562 (tm-30) REVERT: C 154 ILE cc_start: 0.7912 (mm) cc_final: 0.7695 (pt) REVERT: C 174 GLU cc_start: 0.6887 (pp20) cc_final: 0.6619 (pp20) REVERT: C 201 ARG cc_start: 0.7051 (mtm-85) cc_final: 0.6809 (mtm-85) REVERT: C 241 GLU cc_start: 0.4459 (tm-30) cc_final: 0.4008 (tm-30) REVERT: C 245 ILE cc_start: 0.6937 (mt) cc_final: 0.6410 (mt) REVERT: C 308 LEU cc_start: 0.8335 (mt) cc_final: 0.8061 (mt) outliers start: 2 outliers final: 0 residues processed: 477 average time/residue: 0.1666 time to fit residues: 107.7073 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 : 0.539 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.153998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.123136 restraints weight = 22619.286| |-----------------------------------------------------------------------------| 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: 0.3244 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15688 Z= 0.180 Angle : 0.601 9.838 21684 Z= 0.317 Chirality : 0.043 0.184 2406 Planarity : 0.006 0.134 2466 Dihedral : 20.599 166.521 2698 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.58 % Allowed : 10.92 % Favored : 87.50 % 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: 1.28 (0.19), residues: 756 sheet: 0.25 (0.30), residues: 242 loop : -0.71 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 143 TYR 0.019 0.002 TYR D 231 PHE 0.009 0.001 PHE C 193 TRP 0.011 0.002 TRP A 229 HIS 0.006 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00395 (15672) covalent geometry : angle 0.59986 (21678) hydrogen bonds : bond 0.04934 ( 689) hydrogen bonds : angle 4.62583 ( 1965) metal coordination : bond 0.00993 ( 16) metal coordination : angle 2.43381 ( 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 458 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 435 time to evaluate : 0.495 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: 0.7599 (tp30) cc_final: 0.7265 (tp30) REVERT: D 274 LYS cc_start: 0.8917 (ttmt) cc_final: 0.8572 (ttmt) REVERT: E 47 MET cc_start: 0.8503 (mmm) cc_final: 0.8182 (mmm) REVERT: E 70 LYS cc_start: 0.8316 (ttpt) cc_final: 0.8110 (tttt) REVERT: E 127 TYR cc_start: 0.8161 (m-10) cc_final: 0.7869 (m-10) REVERT: E 133 GLN cc_start: 0.7516 (mm-40) cc_final: 0.7270 (mm-40) REVERT: F 44 GLN cc_start: 0.8099 (mt0) cc_final: 0.7824 (mp10) REVERT: F 67 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6534 (tm-30) REVERT: F 76 MET cc_start: 0.7572 (mtp) cc_final: 0.7370 (mtm) REVERT: F 78 GLU cc_start: 0.7271 (tm-30) cc_final: 0.7009 (tm-30) REVERT: F 169 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7532 (tm-30) REVERT: F 210 ARG cc_start: 0.8083 (ttp80) cc_final: 0.7682 (ttp80) REVERT: F 287 MET cc_start: 0.8113 (mmm) cc_final: 0.7895 (mmm) REVERT: F 300 LYS cc_start: 0.8269 (ttpt) cc_final: 0.8049 (ttpt) REVERT: F 308 LEU cc_start: 0.8297 (mt) cc_final: 0.7898 (tp) REVERT: F 310 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7611 (mm-30) REVERT: A 131 GLU cc_start: 0.7641 (tp30) cc_final: 0.7295 (tp30) REVERT: B 29 LEU cc_start: 0.8238 (mt) cc_final: 0.7974 (mp) REVERT: B 47 MET cc_start: 0.8442 (mmm) cc_final: 0.8112 (mmm) REVERT: B 161 ASN cc_start: 0.8257 (m110) cc_final: 0.7966 (m-40) REVERT: B 171 TYR cc_start: 0.8910 (m-10) cc_final: 0.8707 (m-10) REVERT: C 41 LEU cc_start: 0.8351 (tt) cc_final: 0.8128 (tt) REVERT: C 67 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6759 (tm-30) REVERT: C 70 ARG cc_start: 0.7941 (ptm-80) cc_final: 0.7624 (ttp80) REVERT: C 83 ASN cc_start: 0.8152 (m-40) cc_final: 0.7856 (m-40) REVERT: C 139 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7334 (tm-30) REVERT: C 143 ARG cc_start: 0.8661 (tpp80) cc_final: 0.8381 (tpp80) REVERT: C 154 ILE cc_start: 0.8129 (mm) cc_final: 0.7795 (pt) REVERT: C 169 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7515 (tm-30) REVERT: C 201 ARG cc_start: 0.8096 (mtm-85) cc_final: 0.7605 (mtm-85) REVERT: C 223 GLU cc_start: 0.7275 (mp0) cc_final: 0.7045 (mp0) REVERT: C 227 ILE cc_start: 0.8601 (mt) cc_final: 0.8325 (tt) REVERT: C 241 GLU cc_start: 0.5646 (tm-30) cc_final: 0.5203 (tm-30) REVERT: C 246 PHE cc_start: 0.7656 (t80) cc_final: 0.7320 (t80) REVERT: C 283 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7779 (tm-30) REVERT: C 287 MET cc_start: 0.7934 (mmm) cc_final: 0.7617 (mmm) REVERT: C 310 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7143 (mm-30) outliers start: 23 outliers final: 12 residues processed: 444 average time/residue: 0.1668 time to fit residues: 99.2966 Evaluate side-chains 428 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 416 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 243 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain F residue 107 LEU 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: 0.0040 chunk 25 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 162 optimal weight: 0.0470 chunk 120 optimal weight: 1.9990 chunk 125 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 73 optimal weight: 0.0670 overall best weight: 0.2428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN D 182 ASN D 195 ASN D 238 ASN E 59 ASN E 112 HIS E 161 ASN E 250 GLN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 59 ASN C 133 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.156320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.125987 restraints weight = 22770.450| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.26 r_work: 0.3426 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15688 Z= 0.118 Angle : 0.534 7.266 21684 Z= 0.277 Chirality : 0.039 0.198 2406 Planarity : 0.005 0.090 2466 Dihedral : 20.405 163.393 2698 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.72 % Allowed : 13.46 % Favored : 84.82 % 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: 0.67 (0.21), residues: 1640 helix: 1.44 (0.19), residues: 756 sheet: 0.47 (0.32), residues: 222 loop : -0.69 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 143 TYR 0.018 0.002 TYR A 231 PHE 0.014 0.001 PHE F 141 TRP 0.008 0.001 TRP D 229 HIS 0.006 0.001 HIS F 187 Details of bonding type rmsd covalent geometry : bond 0.00252 (15672) covalent geometry : angle 0.53140 (21678) hydrogen bonds : bond 0.03839 ( 689) hydrogen bonds : angle 4.31678 ( 1965) metal coordination : bond 0.00331 ( 16) metal coordination : angle 3.31050 ( 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 449 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 424 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 120 ASN cc_start: 0.8158 (t0) cc_final: 0.7929 (t0) REVERT: D 131 GLU cc_start: 0.7642 (tp30) cc_final: 0.7255 (tp30) REVERT: D 274 LYS cc_start: 0.8917 (ttmt) cc_final: 0.8583 (ttmt) REVERT: E 47 MET cc_start: 0.8498 (mmm) cc_final: 0.8173 (mmm) REVERT: E 54 ARG cc_start: 0.8159 (mtp85) cc_final: 0.7907 (mmt180) REVERT: E 70 LYS cc_start: 0.8346 (ttpt) cc_final: 0.8140 (tttt) REVERT: E 171 TYR cc_start: 0.8815 (m-10) cc_final: 0.8145 (m-10) REVERT: E 202 LYS cc_start: 0.8443 (mtmm) cc_final: 0.8146 (mtmm) REVERT: F 64 LYS cc_start: 0.7154 (pptt) cc_final: 0.6951 (pttm) REVERT: F 76 MET cc_start: 0.7592 (mtp) cc_final: 0.7357 (mtm) REVERT: F 78 GLU cc_start: 0.7269 (tm-30) cc_final: 0.7000 (tm-30) REVERT: F 169 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7448 (tm-30) REVERT: F 183 LYS cc_start: 0.8621 (ttpp) cc_final: 0.8319 (ptpp) REVERT: F 210 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7655 (ttp80) REVERT: F 287 MET cc_start: 0.8084 (mmm) cc_final: 0.7875 (mmm) REVERT: F 300 LYS cc_start: 0.8309 (ttpt) cc_final: 0.8055 (ttpt) REVERT: F 304 PHE cc_start: 0.8627 (m-80) cc_final: 0.8391 (m-80) REVERT: F 308 LEU cc_start: 0.8173 (mt) cc_final: 0.7926 (tt) REVERT: F 310 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7611 (mm-30) REVERT: A 131 GLU cc_start: 0.7666 (tp30) cc_final: 0.7347 (tp30) REVERT: A 142 ARG cc_start: 0.7688 (mtt-85) cc_final: 0.7483 (mtt-85) REVERT: A 206 GLN cc_start: 0.8209 (tt0) cc_final: 0.7999 (tt0) REVERT: B 29 LEU cc_start: 0.8167 (mt) cc_final: 0.7966 (mp) REVERT: B 34 SER cc_start: 0.8378 (m) cc_final: 0.8032 (p) REVERT: B 47 MET cc_start: 0.8438 (mmm) cc_final: 0.8142 (mmm) REVERT: B 133 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7284 (mm-40) REVERT: B 175 ASN cc_start: 0.7536 (OUTLIER) cc_final: 0.7334 (t0) REVERT: C 41 LEU cc_start: 0.8303 (tt) cc_final: 0.8091 (tt) REVERT: C 67 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6766 (tm-30) REVERT: C 83 ASN cc_start: 0.8127 (m-40) cc_final: 0.7882 (m-40) REVERT: C 94 GLU cc_start: 0.6980 (pm20) cc_final: 0.6460 (tp30) REVERT: C 95 VAL cc_start: 0.7851 (t) cc_final: 0.7537 (t) REVERT: C 139 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7399 (tm-30) REVERT: C 169 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7442 (tm-30) REVERT: C 174 GLU cc_start: 0.7966 (pp20) cc_final: 0.7654 (pp20) REVERT: C 192 LYS cc_start: 0.8641 (mmmt) cc_final: 0.8440 (mmmm) REVERT: C 201 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7639 (mtm-85) REVERT: C 210 ARG cc_start: 0.7920 (mtm-85) cc_final: 0.7551 (mtm-85) REVERT: C 223 GLU cc_start: 0.7271 (mp0) cc_final: 0.7018 (mp0) REVERT: C 241 GLU cc_start: 0.5870 (tm-30) cc_final: 0.5349 (tm-30) REVERT: C 283 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7612 (tm-30) REVERT: C 287 MET cc_start: 0.7930 (mmm) cc_final: 0.7593 (mmm) REVERT: C 310 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7018 (mm-30) outliers start: 25 outliers final: 13 residues processed: 432 average time/residue: 0.1754 time to fit residues: 101.6963 Evaluate side-chains 434 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 420 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 216 GLU 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 175 ASN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 242 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 119 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 105 optimal weight: 0.0170 chunk 44 optimal weight: 0.6980 chunk 139 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN D 206 GLN D 238 ASN E 59 ASN E 112 HIS E 134 HIS F 203 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** C 203 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.154488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.124022 restraints weight = 22723.191| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.26 r_work: 0.3386 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15688 Z= 0.156 Angle : 0.554 6.915 21684 Z= 0.288 Chirality : 0.041 0.215 2406 Planarity : 0.005 0.069 2466 Dihedral : 20.294 160.098 2698 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.82 % Allowed : 15.25 % Favored : 81.94 % 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: 0.63 (0.20), residues: 1640 helix: 1.38 (0.19), residues: 760 sheet: 0.52 (0.32), residues: 222 loop : -0.73 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 143 TYR 0.021 0.002 TYR C 79 PHE 0.014 0.001 PHE C 141 TRP 0.010 0.001 TRP C 65 HIS 0.006 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00347 (15672) covalent geometry : angle 0.55287 (21678) hydrogen bonds : bond 0.03828 ( 689) hydrogen bonds : angle 4.31827 ( 1965) metal coordination : bond 0.01006 ( 16) metal coordination : angle 1.89509 ( 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 473 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 432 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 GLU cc_start: 0.7778 (tp30) cc_final: 0.7248 (tp30) REVERT: D 274 LYS cc_start: 0.8878 (ttmt) cc_final: 0.8541 (ttmt) REVERT: E 47 MET cc_start: 0.8498 (mmm) cc_final: 0.8169 (mmm) REVERT: E 49 ARG cc_start: 0.8078 (mtp85) cc_final: 0.7656 (mtp85) REVERT: E 54 ARG cc_start: 0.8170 (mtp85) cc_final: 0.7956 (mmt180) REVERT: E 70 LYS cc_start: 0.8348 (ttpt) cc_final: 0.8148 (tttt) REVERT: F 44 GLN cc_start: 0.7984 (mt0) cc_final: 0.7772 (mt0) REVERT: F 164 VAL cc_start: 0.8589 (t) cc_final: 0.8246 (m) REVERT: F 165 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7449 (mm) REVERT: F 169 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7476 (tm-30) REVERT: F 177 ARG cc_start: 0.8289 (mpp80) cc_final: 0.7733 (mpp80) REVERT: F 202 LYS cc_start: 0.8419 (mmmm) cc_final: 0.8206 (mmmm) REVERT: F 300 LYS cc_start: 0.8267 (ttpt) cc_final: 0.7955 (ttpt) REVERT: F 304 PHE cc_start: 0.8678 (m-80) cc_final: 0.8270 (m-80) REVERT: F 308 LEU cc_start: 0.8157 (mt) cc_final: 0.7637 (mt) REVERT: F 310 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7602 (mm-30) REVERT: A 131 GLU cc_start: 0.7764 (tp30) cc_final: 0.7395 (tp30) REVERT: A 206 GLN cc_start: 0.8239 (tt0) cc_final: 0.8030 (tt0) REVERT: B 47 MET cc_start: 0.8496 (mmm) cc_final: 0.8151 (mmm) REVERT: C 41 LEU cc_start: 0.8434 (tt) cc_final: 0.8230 (tt) REVERT: C 67 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6876 (tm-30) REVERT: C 77 VAL cc_start: 0.7682 (p) cc_final: 0.7471 (p) REVERT: C 83 ASN cc_start: 0.8211 (m-40) cc_final: 0.7924 (m-40) REVERT: C 94 GLU cc_start: 0.7385 (pm20) cc_final: 0.7062 (tp30) REVERT: C 95 VAL cc_start: 0.8125 (t) cc_final: 0.7618 (p) REVERT: C 139 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7480 (tm-30) REVERT: C 154 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7747 (tp) REVERT: C 164 VAL cc_start: 0.8490 (t) cc_final: 0.8190 (m) REVERT: C 165 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7696 (mm) REVERT: C 169 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7515 (tm-30) REVERT: C 174 GLU cc_start: 0.8011 (pp20) cc_final: 0.7701 (pp20) REVERT: C 192 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8426 (mmmt) REVERT: C 201 ARG cc_start: 0.8147 (mtm-85) cc_final: 0.7643 (mtm-85) REVERT: C 210 ARG cc_start: 0.7927 (mtm-85) cc_final: 0.7451 (mtm-85) REVERT: C 221 ILE cc_start: 0.8669 (tp) cc_final: 0.8417 (tp) REVERT: C 223 GLU cc_start: 0.7361 (mp0) cc_final: 0.7095 (mp0) REVERT: C 227 ILE cc_start: 0.8562 (mt) cc_final: 0.8329 (tt) REVERT: C 241 GLU cc_start: 0.5859 (tm-30) cc_final: 0.5317 (tm-30) REVERT: C 283 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7679 (tm-30) REVERT: C 287 MET cc_start: 0.7937 (mmm) cc_final: 0.7596 (mmm) REVERT: C 310 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7015 (mm-30) outliers start: 41 outliers final: 24 residues processed: 445 average time/residue: 0.1701 time to fit residues: 102.3875 Evaluate side-chains 444 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 417 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 216 ILE Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain F residue 77 VAL 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 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 99 SER Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 189 ILE 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: 0.9980 chunk 49 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN D 238 ASN E 59 ASN E 112 HIS E 118 HIS E 134 HIS ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 HIS A 238 ASN B 59 ASN B 112 HIS B 134 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.154037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.123979 restraints weight = 22698.323| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.25 r_work: 0.3382 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15688 Z= 0.154 Angle : 0.553 6.867 21684 Z= 0.289 Chirality : 0.041 0.188 2406 Planarity : 0.004 0.065 2466 Dihedral : 20.227 158.020 2698 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.47 % Allowed : 17.65 % Favored : 79.88 % 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: 0.62 (0.21), residues: 1640 helix: 1.32 (0.18), residues: 760 sheet: 0.49 (0.31), residues: 242 loop : -0.66 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 142 TYR 0.024 0.002 TYR F 269 PHE 0.013 0.001 PHE F 141 TRP 0.008 0.001 TRP D 229 HIS 0.006 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00339 (15672) covalent geometry : angle 0.55182 (21678) hydrogen bonds : bond 0.03766 ( 689) hydrogen bonds : angle 4.31995 ( 1965) metal coordination : bond 0.00782 ( 16) metal coordination : angle 1.89954 ( 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 462 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 426 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 GLU cc_start: 0.7823 (tp30) cc_final: 0.7237 (tp30) REVERT: D 274 LYS cc_start: 0.8867 (ttmt) cc_final: 0.8519 (ttmt) REVERT: E 47 MET cc_start: 0.8507 (mmm) cc_final: 0.8180 (mmm) REVERT: E 70 LYS cc_start: 0.8365 (ttpt) cc_final: 0.8157 (tttt) REVERT: F 164 VAL cc_start: 0.8579 (t) cc_final: 0.8207 (m) REVERT: F 165 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7499 (mm) REVERT: F 169 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7459 (tm-30) REVERT: F 183 LYS cc_start: 0.8670 (ttpp) cc_final: 0.8413 (ptpp) REVERT: F 202 LYS cc_start: 0.8456 (mmmm) cc_final: 0.8165 (mmmm) REVERT: F 254 LEU cc_start: 0.7601 (tp) cc_final: 0.7067 (tt) REVERT: F 300 LYS cc_start: 0.8269 (ttpt) cc_final: 0.8022 (ttpt) REVERT: F 303 MET cc_start: 0.7524 (ttt) cc_final: 0.7277 (ttt) REVERT: A 131 GLU cc_start: 0.7821 (tp30) cc_final: 0.7374 (tp30) REVERT: A 206 GLN cc_start: 0.8253 (tt0) cc_final: 0.8035 (tt0) REVERT: B 47 MET cc_start: 0.8545 (mmm) cc_final: 0.8242 (mmm) REVERT: C 41 LEU cc_start: 0.8467 (tt) cc_final: 0.8143 (tt) REVERT: C 44 GLN cc_start: 0.8057 (mt0) cc_final: 0.7776 (mt0) REVERT: C 67 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6990 (tm-30) REVERT: C 75 GLU cc_start: 0.7886 (tt0) cc_final: 0.7637 (tt0) REVERT: C 77 VAL cc_start: 0.7645 (p) cc_final: 0.7439 (p) REVERT: C 83 ASN cc_start: 0.8179 (m-40) cc_final: 0.7895 (m-40) REVERT: C 95 VAL cc_start: 0.8282 (t) cc_final: 0.7807 (p) REVERT: C 139 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7502 (tm-30) REVERT: C 154 ILE cc_start: 0.8148 (tp) cc_final: 0.7917 (tp) REVERT: C 164 VAL cc_start: 0.8522 (t) cc_final: 0.8318 (m) REVERT: C 165 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7657 (mm) REVERT: C 167 LEU cc_start: 0.8327 (tt) cc_final: 0.8100 (tp) REVERT: C 169 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7525 (tm-30) REVERT: C 174 GLU cc_start: 0.8057 (pp20) cc_final: 0.7732 (pp20) REVERT: C 192 LYS cc_start: 0.8618 (mmmt) cc_final: 0.8393 (mmmt) REVERT: C 201 ARG cc_start: 0.8142 (mtm-85) cc_final: 0.7653 (mtm-85) REVERT: C 210 ARG cc_start: 0.7873 (mtm-85) cc_final: 0.7409 (mtm-85) REVERT: C 221 ILE cc_start: 0.8681 (tp) cc_final: 0.8434 (tp) REVERT: C 223 GLU cc_start: 0.7584 (mp0) cc_final: 0.7261 (mp0) REVERT: C 227 ILE cc_start: 0.8613 (mt) cc_final: 0.8306 (tt) REVERT: C 283 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7622 (tm-30) REVERT: C 287 MET cc_start: 0.7948 (mmm) cc_final: 0.7591 (mmm) REVERT: C 291 LYS cc_start: 0.8401 (ttpp) cc_final: 0.8147 (ttpp) REVERT: C 310 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7097 (mm-30) outliers start: 36 outliers final: 26 residues processed: 439 average time/residue: 0.1774 time to fit residues: 104.6956 Evaluate side-chains 451 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 423 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain F residue 77 VAL 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 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 C residue 78 GLU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 189 ILE 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: 3.9990 chunk 121 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 164 optimal weight: 0.0060 chunk 39 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN E 59 ASN E 112 HIS E 130 GLN E 134 HIS F 203 GLN ** 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 203 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.151136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.120762 restraints weight = 22389.228| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.25 r_work: 0.3365 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3025 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= 0.200 Angle : 0.579 7.775 21684 Z= 0.304 Chirality : 0.042 0.194 2406 Planarity : 0.005 0.064 2466 Dihedral : 20.256 157.581 2698 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.88 % Allowed : 18.34 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.21), residues: 1640 helix: 1.28 (0.18), residues: 762 sheet: 0.57 (0.32), residues: 242 loop : -0.72 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 142 TYR 0.024 0.002 TYR F 269 PHE 0.013 0.001 PHE C 246 TRP 0.009 0.001 TRP D 229 HIS 0.005 0.001 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00445 (15672) covalent geometry : angle 0.57820 (21678) hydrogen bonds : bond 0.04012 ( 689) hydrogen bonds : angle 4.37990 ( 1965) metal coordination : bond 0.01431 ( 16) metal coordination : angle 1.76129 ( 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 471 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 429 time to evaluate : 0.543 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: 0.7837 (tp30) cc_final: 0.7283 (tp30) REVERT: D 274 LYS cc_start: 0.8837 (ttmt) cc_final: 0.8492 (ttmt) REVERT: E 47 MET cc_start: 0.8531 (mmm) cc_final: 0.8204 (mmm) REVERT: E 99 SER cc_start: 0.7629 (OUTLIER) cc_final: 0.7375 (p) REVERT: F 44 GLN cc_start: 0.8001 (mt0) cc_final: 0.7690 (mp10) REVERT: F 164 VAL cc_start: 0.8612 (t) cc_final: 0.8317 (m) REVERT: F 165 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7527 (mm) REVERT: F 169 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7461 (tm-30) REVERT: F 183 LYS cc_start: 0.8655 (ttpp) cc_final: 0.8386 (ptpp) REVERT: F 202 LYS cc_start: 0.8430 (mmmm) cc_final: 0.8150 (mmmm) REVERT: F 233 ASN cc_start: 0.8327 (t0) cc_final: 0.7787 (m-40) REVERT: F 254 LEU cc_start: 0.7625 (tp) cc_final: 0.6941 (tt) REVERT: F 292 TYR cc_start: 0.8352 (m-80) cc_final: 0.8084 (m-80) REVERT: F 300 LYS cc_start: 0.8241 (ttpt) cc_final: 0.7983 (ttpt) REVERT: F 303 MET cc_start: 0.7587 (ttt) cc_final: 0.7329 (ttt) REVERT: F 308 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7802 (tt) REVERT: A 131 GLU cc_start: 0.7801 (tp30) cc_final: 0.7360 (tp30) REVERT: A 206 GLN cc_start: 0.8268 (tt0) cc_final: 0.8055 (tt0) REVERT: B 47 MET cc_start: 0.8534 (mmm) cc_final: 0.8204 (mmm) REVERT: C 41 LEU cc_start: 0.8475 (tt) cc_final: 0.8243 (tt) REVERT: C 67 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6994 (tm-30) REVERT: C 75 GLU cc_start: 0.7960 (tt0) cc_final: 0.7714 (tt0) REVERT: C 77 VAL cc_start: 0.7765 (OUTLIER) cc_final: 0.7464 (p) REVERT: C 83 ASN cc_start: 0.8253 (m-40) cc_final: 0.7964 (m-40) REVERT: C 95 VAL cc_start: 0.8419 (t) cc_final: 0.8129 (p) REVERT: C 139 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7461 (tm-30) REVERT: C 152 PRO cc_start: 0.8218 (Cg_endo) cc_final: 0.7573 (Cg_exo) REVERT: C 154 ILE cc_start: 0.8209 (tp) cc_final: 0.7999 (tp) REVERT: C 164 VAL cc_start: 0.8579 (t) cc_final: 0.8322 (m) REVERT: C 165 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7743 (mm) REVERT: C 167 LEU cc_start: 0.8351 (tt) cc_final: 0.8134 (tp) REVERT: C 169 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7513 (tm-30) REVERT: C 174 GLU cc_start: 0.8147 (pp20) cc_final: 0.7834 (pp20) REVERT: C 192 LYS cc_start: 0.8555 (mmmt) cc_final: 0.8295 (mmmt) REVERT: C 201 ARG cc_start: 0.8082 (mtm-85) cc_final: 0.7592 (mtm-85) REVERT: C 221 ILE cc_start: 0.8670 (tp) cc_final: 0.8447 (tp) REVERT: C 223 GLU cc_start: 0.7687 (mp0) cc_final: 0.7309 (mp0) REVERT: C 227 ILE cc_start: 0.8568 (mt) cc_final: 0.8220 (tt) REVERT: C 246 PHE cc_start: 0.7759 (t80) cc_final: 0.7499 (t80) REVERT: C 283 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7572 (tm-30) REVERT: C 287 MET cc_start: 0.8017 (mmm) cc_final: 0.7659 (mmm) REVERT: C 291 LYS cc_start: 0.8379 (ttpp) cc_final: 0.8120 (ttpp) REVERT: C 310 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7164 (mm-30) outliers start: 42 outliers final: 26 residues processed: 442 average time/residue: 0.1737 time to fit residues: 103.5442 Evaluate side-chains 440 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 409 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 177 ASN 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 308 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 C residue 51 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 189 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 76 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 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 59 ASN B 112 HIS B 134 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.151490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.121386 restraints weight = 22587.638| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.24 r_work: 0.3365 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3171 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= 0.167 Angle : 0.571 8.408 21684 Z= 0.300 Chirality : 0.041 0.171 2406 Planarity : 0.004 0.063 2466 Dihedral : 20.235 157.612 2698 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.88 % Allowed : 19.23 % Favored : 77.88 % 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: 1.26 (0.18), residues: 768 sheet: 0.61 (0.32), residues: 242 loop : -0.69 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 142 TYR 0.021 0.002 TYR F 269 PHE 0.012 0.001 PHE F 141 TRP 0.008 0.001 TRP D 229 HIS 0.006 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00373 (15672) covalent geometry : angle 0.57047 (21678) hydrogen bonds : bond 0.03809 ( 689) hydrogen bonds : angle 4.37041 ( 1965) metal coordination : bond 0.00949 ( 16) metal coordination : angle 1.80537 ( 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 467 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 425 time to evaluate : 0.595 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: 0.7882 (tp30) cc_final: 0.7295 (tp30) REVERT: D 142 ARG cc_start: 0.7771 (mtt-85) cc_final: 0.7552 (mtt-85) REVERT: D 180 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7654 (tpp) REVERT: D 274 LYS cc_start: 0.8809 (ttmt) cc_final: 0.8497 (ttmt) REVERT: E 47 MET cc_start: 0.8533 (mmm) cc_final: 0.8225 (mmm) REVERT: F 78 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6921 (tm-30) REVERT: F 139 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7484 (tm-30) REVERT: F 165 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7596 (mm) REVERT: F 169 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7452 (tm-30) REVERT: F 177 ARG cc_start: 0.8325 (mpp80) cc_final: 0.7672 (mtm180) REVERT: F 183 LYS cc_start: 0.8650 (ttpp) cc_final: 0.8356 (ptpp) REVERT: F 201 ARG cc_start: 0.8205 (mtm-85) cc_final: 0.7682 (mtm-85) REVERT: F 202 LYS cc_start: 0.8480 (mmmm) cc_final: 0.8221 (mmmm) REVERT: F 254 LEU cc_start: 0.7605 (tp) cc_final: 0.6942 (tt) REVERT: F 300 LYS cc_start: 0.8242 (ttpt) cc_final: 0.7954 (ttpt) REVERT: F 308 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7730 (tt) REVERT: A 131 GLU cc_start: 0.7835 (tp30) cc_final: 0.7395 (tp30) REVERT: A 206 GLN cc_start: 0.8255 (tt0) cc_final: 0.8046 (tt0) REVERT: B 47 MET cc_start: 0.8551 (mmm) cc_final: 0.8246 (mmm) REVERT: B 49 ARG cc_start: 0.8000 (mtp85) cc_final: 0.7739 (mtp85) REVERT: C 41 LEU cc_start: 0.8474 (tt) cc_final: 0.8103 (tt) REVERT: C 44 GLN cc_start: 0.8043 (mt0) cc_final: 0.7635 (mp10) REVERT: C 67 GLU cc_start: 0.7330 (mm-30) cc_final: 0.6990 (tm-30) REVERT: C 75 GLU cc_start: 0.7956 (tt0) cc_final: 0.7723 (tt0) REVERT: C 77 VAL cc_start: 0.7863 (OUTLIER) cc_final: 0.7574 (p) REVERT: C 83 ASN cc_start: 0.8240 (m-40) cc_final: 0.7950 (m-40) REVERT: C 95 VAL cc_start: 0.8474 (t) cc_final: 0.8223 (p) REVERT: C 139 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7479 (tm-30) REVERT: C 152 PRO cc_start: 0.8246 (Cg_endo) cc_final: 0.8042 (Cg_exo) REVERT: C 154 ILE cc_start: 0.8279 (tp) cc_final: 0.8069 (tp) REVERT: C 164 VAL cc_start: 0.8588 (t) cc_final: 0.8339 (m) REVERT: C 165 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7758 (mm) REVERT: C 167 LEU cc_start: 0.8317 (tt) cc_final: 0.8094 (tp) REVERT: C 169 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7581 (tm-30) REVERT: C 174 GLU cc_start: 0.8105 (pp20) cc_final: 0.7772 (pp20) REVERT: C 201 ARG cc_start: 0.8054 (mtm-85) cc_final: 0.7576 (mtm-85) REVERT: C 221 ILE cc_start: 0.8645 (tp) cc_final: 0.8422 (tp) REVERT: C 223 GLU cc_start: 0.7693 (mp0) cc_final: 0.7291 (mp0) REVERT: C 227 ILE cc_start: 0.8595 (mt) cc_final: 0.8235 (tt) REVERT: C 246 PHE cc_start: 0.7746 (t80) cc_final: 0.7480 (t80) REVERT: C 283 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7617 (tm-30) REVERT: C 287 MET cc_start: 0.7964 (mmm) cc_final: 0.7577 (mmm) REVERT: C 291 LYS cc_start: 0.8367 (ttpp) cc_final: 0.8111 (ttpp) REVERT: C 308 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7940 (tt) REVERT: C 310 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7199 (mm-30) outliers start: 42 outliers final: 25 residues processed: 439 average time/residue: 0.1738 time to fit residues: 102.4745 Evaluate side-chains 451 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 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 180 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 99 optimal weight: 0.1980 chunk 159 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN E 59 ASN E 112 HIS E 134 HIS E 250 GLN F 203 GLN F 243 HIS ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN A 238 ASN B 59 ASN B 112 HIS B 134 HIS C 203 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.152067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121923 restraints weight = 22681.621| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.25 r_work: 0.3375 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15688 Z= 0.148 Angle : 0.580 8.875 21684 Z= 0.303 Chirality : 0.041 0.208 2406 Planarity : 0.004 0.062 2466 Dihedral : 20.186 157.684 2698 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.47 % Allowed : 19.85 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.21), residues: 1640 helix: 1.25 (0.18), residues: 766 sheet: 0.61 (0.32), residues: 242 loop : -0.60 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 142 TYR 0.022 0.002 TYR F 269 PHE 0.015 0.001 PHE F 208 TRP 0.006 0.001 TRP D 229 HIS 0.005 0.001 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00332 (15672) covalent geometry : angle 0.57940 (21678) hydrogen bonds : bond 0.03604 ( 689) hydrogen bonds : angle 4.39060 ( 1965) metal coordination : bond 0.00666 ( 16) metal coordination : angle 1.86601 ( 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 469 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 433 time to evaluate : 0.526 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: 0.7868 (tp30) cc_final: 0.7342 (tp30) REVERT: D 142 ARG cc_start: 0.7786 (mtt-85) cc_final: 0.7577 (mtt-85) REVERT: D 180 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7644 (tpp) REVERT: D 274 LYS cc_start: 0.8818 (ttmt) cc_final: 0.8509 (ttmt) REVERT: E 47 MET cc_start: 0.8523 (mmm) cc_final: 0.8184 (mmm) REVERT: E 131 GLU cc_start: 0.7952 (pt0) cc_final: 0.7678 (pt0) REVERT: F 44 GLN cc_start: 0.8002 (mt0) cc_final: 0.7687 (mp10) REVERT: F 77 VAL cc_start: 0.7679 (p) cc_final: 0.7337 (p) REVERT: F 139 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7448 (tm-30) REVERT: F 164 VAL cc_start: 0.8634 (t) cc_final: 0.8389 (m) REVERT: F 165 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7547 (mt) REVERT: F 169 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7422 (tm-30) REVERT: F 201 ARG cc_start: 0.8231 (mtm-85) cc_final: 0.7707 (mtm-85) REVERT: F 254 LEU cc_start: 0.7591 (tp) cc_final: 0.7000 (tt) REVERT: F 300 LYS cc_start: 0.8245 (ttpt) cc_final: 0.7968 (ttpt) REVERT: F 308 LEU cc_start: 0.7929 (mt) cc_final: 0.7441 (pp) REVERT: A 131 GLU cc_start: 0.7806 (tp30) cc_final: 0.7410 (tp30) REVERT: A 206 GLN cc_start: 0.8245 (tt0) cc_final: 0.8031 (tt0) REVERT: B 47 MET cc_start: 0.8528 (mmm) cc_final: 0.8233 (mmm) REVERT: B 49 ARG cc_start: 0.8027 (mtp85) cc_final: 0.7772 (mtp85) REVERT: C 41 LEU cc_start: 0.8458 (tt) cc_final: 0.8232 (tt) REVERT: C 67 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7032 (tm-30) REVERT: C 75 GLU cc_start: 0.7964 (tt0) cc_final: 0.7729 (tt0) REVERT: C 77 VAL cc_start: 0.7888 (OUTLIER) cc_final: 0.7568 (p) REVERT: C 83 ASN cc_start: 0.8240 (m-40) cc_final: 0.8031 (m-40) REVERT: C 95 VAL cc_start: 0.8535 (t) cc_final: 0.8288 (p) REVERT: C 139 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7479 (tm-30) REVERT: C 152 PRO cc_start: 0.8247 (Cg_endo) cc_final: 0.7634 (Cg_exo) REVERT: C 154 ILE cc_start: 0.8285 (tp) cc_final: 0.8078 (tp) REVERT: C 164 VAL cc_start: 0.8583 (t) cc_final: 0.8350 (m) REVERT: C 165 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7723 (mm) REVERT: C 169 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7565 (tm-30) REVERT: C 174 GLU cc_start: 0.8109 (pp20) cc_final: 0.7754 (pp20) REVERT: C 192 LYS cc_start: 0.8614 (mmmt) cc_final: 0.8353 (mmmt) REVERT: C 201 ARG cc_start: 0.8032 (mtm-85) cc_final: 0.7510 (mtm-85) REVERT: C 223 GLU cc_start: 0.7692 (mp0) cc_final: 0.7295 (mp0) REVERT: C 227 ILE cc_start: 0.8574 (mt) cc_final: 0.8271 (tt) REVERT: C 246 PHE cc_start: 0.7775 (t80) cc_final: 0.7518 (t80) REVERT: C 283 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7621 (tm-30) REVERT: C 287 MET cc_start: 0.7993 (mmm) cc_final: 0.7607 (mmm) REVERT: C 291 LYS cc_start: 0.8374 (ttpp) cc_final: 0.8111 (ttpp) REVERT: C 308 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7915 (tt) REVERT: C 310 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7223 (mm-30) outliers start: 36 outliers final: 22 residues processed: 444 average time/residue: 0.1697 time to fit residues: 101.2820 Evaluate side-chains 450 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 422 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain 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 C residue 77 VAL Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 153 optimal weight: 0.8980 chunk 161 optimal weight: 6.9990 chunk 147 optimal weight: 0.2980 chunk 118 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 33 HIS D 238 ASN E 59 ASN E 112 HIS E 134 HIS F 203 GLN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 HIS A 238 ASN B 59 ASN B 112 HIS B 134 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.151285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.121173 restraints weight = 22496.995| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.24 r_work: 0.3358 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15688 Z= 0.165 Angle : 0.593 9.640 21684 Z= 0.310 Chirality : 0.042 0.210 2406 Planarity : 0.004 0.061 2466 Dihedral : 20.174 158.041 2698 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.47 % Allowed : 20.19 % Favored : 77.34 % 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: 1.08 (0.18), residues: 778 sheet: 0.64 (0.32), residues: 242 loop : -0.68 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 142 TYR 0.022 0.002 TYR F 269 PHE 0.014 0.001 PHE F 208 TRP 0.007 0.001 TRP D 229 HIS 0.010 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00371 (15672) covalent geometry : angle 0.59232 (21678) hydrogen bonds : bond 0.03723 ( 689) hydrogen bonds : angle 4.43777 ( 1965) metal coordination : bond 0.00926 ( 16) metal coordination : angle 1.71765 ( 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 470 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 434 time to evaluate : 0.528 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: 0.8367 (t0) cc_final: 0.8147 (t0) REVERT: D 131 GLU cc_start: 0.7898 (tp30) cc_final: 0.7352 (tp30) REVERT: D 274 LYS cc_start: 0.8809 (ttmt) cc_final: 0.8494 (ttmt) REVERT: E 47 MET cc_start: 0.8528 (mmm) cc_final: 0.8231 (mmm) REVERT: F 77 VAL cc_start: 0.7495 (p) cc_final: 0.7257 (p) REVERT: F 94 GLU cc_start: 0.7968 (pm20) cc_final: 0.7551 (mm-30) REVERT: F 139 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: F 164 VAL cc_start: 0.8664 (t) cc_final: 0.8416 (m) REVERT: F 165 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7572 (mt) REVERT: F 169 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7383 (tm-30) REVERT: F 183 LYS cc_start: 0.8622 (ttpp) cc_final: 0.8296 (ptpp) REVERT: F 201 ARG cc_start: 0.8234 (mtm-85) cc_final: 0.7722 (mtm-85) REVERT: F 254 LEU cc_start: 0.7599 (tp) cc_final: 0.7138 (tp) REVERT: F 300 LYS cc_start: 0.8249 (ttpt) cc_final: 0.7953 (ttpt) REVERT: F 303 MET cc_start: 0.7581 (ttt) cc_final: 0.7348 (ttt) REVERT: F 308 LEU cc_start: 0.7924 (mt) cc_final: 0.7385 (pp) REVERT: A 131 GLU cc_start: 0.7834 (tp30) cc_final: 0.7442 (tp30) REVERT: A 206 GLN cc_start: 0.8242 (tt0) cc_final: 0.8031 (tt0) REVERT: B 47 MET cc_start: 0.8555 (mmm) cc_final: 0.8237 (mmm) REVERT: B 49 ARG cc_start: 0.8007 (mtp85) cc_final: 0.7765 (mtp85) REVERT: C 41 LEU cc_start: 0.8456 (tt) cc_final: 0.8086 (tt) REVERT: C 44 GLN cc_start: 0.8052 (mt0) cc_final: 0.7627 (mp10) REVERT: C 67 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7054 (tm-30) REVERT: C 75 GLU cc_start: 0.8071 (tt0) cc_final: 0.7847 (tt0) REVERT: C 77 VAL cc_start: 0.7866 (OUTLIER) cc_final: 0.7543 (p) REVERT: C 83 ASN cc_start: 0.8251 (m-40) cc_final: 0.8042 (m-40) REVERT: C 95 VAL cc_start: 0.8598 (t) cc_final: 0.8360 (p) REVERT: C 139 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7523 (tm-30) REVERT: C 152 PRO cc_start: 0.8316 (Cg_endo) cc_final: 0.7688 (Cg_exo) REVERT: C 154 ILE cc_start: 0.8359 (tp) cc_final: 0.8159 (tp) REVERT: C 164 VAL cc_start: 0.8607 (t) cc_final: 0.8365 (m) REVERT: C 165 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7752 (mm) REVERT: C 169 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7524 (tm-30) REVERT: C 174 GLU cc_start: 0.8129 (pp20) cc_final: 0.7781 (pp20) REVERT: C 177 ARG cc_start: 0.8541 (mtm180) cc_final: 0.8306 (mtm180) REVERT: C 192 LYS cc_start: 0.8612 (mmmt) cc_final: 0.8346 (mmmt) REVERT: C 201 ARG cc_start: 0.8092 (mtm-85) cc_final: 0.7573 (mtm-85) REVERT: C 223 GLU cc_start: 0.7721 (mp0) cc_final: 0.7305 (mp0) REVERT: C 227 ILE cc_start: 0.8621 (mt) cc_final: 0.8348 (tt) REVERT: C 246 PHE cc_start: 0.7789 (t80) cc_final: 0.7461 (t80) REVERT: C 247 LEU cc_start: 0.8621 (tp) cc_final: 0.8316 (tt) REVERT: C 254 LEU cc_start: 0.7389 (tp) cc_final: 0.6830 (tt) REVERT: C 258 LYS cc_start: 0.7726 (tptp) cc_final: 0.7492 (tptp) REVERT: C 283 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7583 (tm-30) REVERT: C 287 MET cc_start: 0.7953 (mmm) cc_final: 0.7550 (mmm) REVERT: C 291 LYS cc_start: 0.8380 (ttpp) cc_final: 0.8118 (ttpp) REVERT: C 308 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7945 (tt) REVERT: C 310 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7264 (mm-30) outliers start: 36 outliers final: 25 residues processed: 444 average time/residue: 0.1749 time to fit residues: 103.7808 Evaluate side-chains 456 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 426 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 189 ILE 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 Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.1895 > 50: distance: 32 - 54: 12.707 distance: 36 - 62: 12.691 distance: 40 - 70: 6.255 distance: 45 - 54: 12.833 distance: 46 - 79: 21.112 distance: 54 - 55: 11.598 distance: 55 - 56: 13.629 distance: 55 - 58: 14.076 distance: 56 - 57: 29.134 distance: 56 - 62: 3.730 distance: 58 - 59: 6.759 distance: 59 - 60: 26.692 distance: 59 - 61: 16.390 distance: 62 - 63: 10.998 distance: 63 - 64: 14.701 distance: 63 - 66: 9.749 distance: 64 - 65: 9.559 distance: 64 - 70: 8.741 distance: 66 - 67: 15.060 distance: 67 - 68: 13.038 distance: 67 - 69: 7.837 distance: 70 - 71: 9.058 distance: 71 - 72: 12.932 distance: 71 - 74: 11.339 distance: 72 - 73: 33.918 distance: 72 - 79: 22.436 distance: 74 - 75: 10.117 distance: 75 - 76: 6.552 distance: 76 - 77: 3.406 distance: 77 - 78: 5.559 distance: 79 - 80: 26.976 distance: 80 - 81: 23.084 distance: 80 - 83: 22.353 distance: 81 - 82: 11.952 distance: 81 - 86: 37.699 distance: 83 - 84: 16.360 distance: 83 - 85: 25.733 distance: 86 - 87: 14.779 distance: 87 - 88: 23.876 distance: 87 - 90: 22.166 distance: 88 - 89: 18.082 distance: 88 - 94: 26.144 distance: 90 - 91: 20.256 distance: 91 - 92: 6.527 distance: 91 - 93: 9.349 distance: 94 - 95: 30.679 distance: 95 - 96: 22.533 distance: 95 - 98: 16.116 distance: 96 - 97: 23.887 distance: 96 - 102: 25.468 distance: 97 - 117: 41.791 distance: 98 - 99: 36.693 distance: 99 - 100: 5.441 distance: 99 - 101: 42.065 distance: 102 - 103: 8.837 distance: 102 - 108: 22.277 distance: 103 - 104: 10.037 distance: 103 - 106: 9.283 distance: 104 - 105: 7.392 distance: 104 - 109: 11.143 distance: 105 - 127: 17.054 distance: 106 - 107: 11.086 distance: 107 - 108: 8.911 distance: 109 - 110: 26.745 distance: 110 - 111: 19.791 distance: 110 - 113: 34.452 distance: 111 - 112: 31.407 distance: 111 - 117: 11.275 distance: 113 - 114: 33.853 distance: 114 - 115: 13.622 distance: 114 - 116: 31.954 distance: 117 - 118: 18.528 distance: 118 - 119: 19.415 distance: 118 - 121: 36.124 distance: 119 - 120: 23.420 distance: 119 - 127: 28.081 distance: 121 - 122: 28.056 distance: 122 - 123: 35.059 distance: 122 - 124: 23.177 distance: 123 - 125: 41.206 distance: 124 - 126: 32.570 distance: 125 - 126: 32.555 distance: 127 - 128: 7.602 distance: 128 - 129: 21.538 distance: 128 - 131: 21.690 distance: 129 - 130: 22.619 distance: 129 - 136: 4.294 distance: 131 - 132: 15.580 distance: 132 - 133: 12.197 distance: 133 - 134: 13.629 distance: 134 - 135: 14.953