Starting phenix.real_space_refine on Fri Jun 13 10:40:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oug_13076/06_2025/7oug_13076.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oug_13076/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7oug_13076/06_2025/7oug_13076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oug_13076/06_2025/7oug_13076.map" model { file = "/net/cci-nas-00/data/ceres_data/7oug_13076/06_2025/7oug_13076.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oug_13076/06_2025/7oug_13076.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15090 Number of models: 1 Model: "" Number of chains: 9 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: "A" 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: "B" 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: "C" 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: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" 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 7744 SG CYS A 35 22.183 45.021 25.936 1.00 64.00 S ATOM 7765 SG CYS A 38 24.283 42.718 27.481 1.00 58.68 S ATOM 9801 SG CYS B 35 54.346 109.350 37.975 1.00 18.65 S ATOM 9822 SG CYS B 38 57.179 107.339 38.919 1.00 9.34 S Restraints were copied for chains: D, E, L, K, F Time building chain proxies: 10.32, per 1000 atoms: 0.68 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: 3.53 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 4.87 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: 5.00 Time building geometry restraints manager: 4.22 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.420 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 42.360 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.020 ------------------------------------------------------------------------------- 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 : 5.66 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP C 131 HIS 0.004 0.001 HIS D 33 PHE 0.019 0.001 PHE C 274 TYR 0.013 0.001 TYR F 138 ARG 0.004 0.000 ARG E 240 Details of bonding type rmsd hydrogen bonds : bond 0.16919 ( 689) hydrogen bonds : angle 6.25417 ( 1965) metal coordination : bond 0.02060 ( 16) metal coordination : angle 24.18352 ( 6) covalent geometry : bond 0.00379 (15672) covalent geometry : angle 0.67825 (21678) *********************** 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 : 1.465 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: 0.7526 (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: 0.6563 (tm-30) REVERT: C 154 ILE cc_start: 0.7912 (mm) cc_final: 0.7697 (pt) REVERT: C 174 GLU cc_start: 0.6887 (pp20) cc_final: 0.6619 (pp20) REVERT: C 201 ARG cc_start: 0.7051 (mtm-85) cc_final: 0.6808 (mtm-85) REVERT: C 241 GLU cc_start: 0.4459 (tm-30) cc_final: 0.4008 (tm-30) REVERT: C 245 ILE cc_start: 0.6937 (mt) cc_final: 0.6410 (mt) REVERT: C 308 LEU cc_start: 0.8335 (mt) cc_final: 0.8061 (mt) outliers start: 2 outliers final: 0 residues processed: 477 average time/residue: 0.3545 time to fit residues: 229.3125 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 : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.4980 chunk 127 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 0.3980 chunk 98 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 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 = 0.3977 r_free = 0.3977 target = 0.154836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.124291 restraints weight = 22521.140| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.24 r_work: 0.3411 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15688 Z= 0.161 Angle : 0.592 9.233 21684 Z= 0.312 Chirality : 0.042 0.186 2406 Planarity : 0.006 0.140 2466 Dihedral : 20.600 167.696 2698 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.72 % Allowed : 10.65 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.20), residues: 1640 helix: 1.33 (0.19), residues: 756 sheet: 0.37 (0.32), residues: 222 loop : -0.75 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 229 HIS 0.006 0.001 HIS D 8 PHE 0.008 0.001 PHE F 99 TYR 0.018 0.002 TYR F 79 ARG 0.013 0.001 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.04691 ( 689) hydrogen bonds : angle 4.59974 ( 1965) metal coordination : bond 0.00587 ( 16) metal coordination : angle 2.88840 ( 6) covalent geometry : bond 0.00354 (15672) covalent geometry : angle 0.58966 (21678) *********************** 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 453 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 428 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 GLU cc_start: 0.7555 (tp30) cc_final: 0.7296 (tp30) REVERT: E 47 MET cc_start: 0.8499 (mmm) cc_final: 0.8172 (mmm) REVERT: E 70 LYS cc_start: 0.8307 (ttpt) cc_final: 0.8102 (tttt) REVERT: E 127 TYR cc_start: 0.8146 (m-10) cc_final: 0.7821 (m-10) REVERT: E 133 GLN cc_start: 0.7475 (mm-40) cc_final: 0.7239 (mm-40) REVERT: F 67 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6495 (tm-30) REVERT: F 78 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6995 (tm-30) REVERT: F 169 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7516 (tm-30) REVERT: F 210 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7672 (ttp80) REVERT: F 287 MET cc_start: 0.8097 (mmm) cc_final: 0.7882 (mmm) REVERT: F 300 LYS cc_start: 0.8250 (ttpt) cc_final: 0.8020 (ttpt) REVERT: F 308 LEU cc_start: 0.8278 (mt) cc_final: 0.7882 (tp) REVERT: F 310 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7615 (mm-30) REVERT: A 131 GLU cc_start: 0.7630 (tp30) cc_final: 0.7300 (tp30) REVERT: B 29 LEU cc_start: 0.8229 (mt) cc_final: 0.7970 (mp) REVERT: B 47 MET cc_start: 0.8435 (mmm) cc_final: 0.8124 (mmm) REVERT: B 133 GLN cc_start: 0.7507 (mm-40) cc_final: 0.7254 (mm-40) REVERT: B 161 ASN cc_start: 0.8241 (m110) cc_final: 0.7936 (m-40) REVERT: C 41 LEU cc_start: 0.8332 (tt) cc_final: 0.8127 (tt) REVERT: C 67 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6746 (tm-30) REVERT: C 70 ARG cc_start: 0.7951 (ptm-80) cc_final: 0.7606 (ttp80) REVERT: C 139 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7392 (tm-30) REVERT: C 154 ILE cc_start: 0.8097 (mm) cc_final: 0.7767 (pt) REVERT: C 165 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7535 (mm) REVERT: C 169 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7491 (tm-30) REVERT: C 190 TYR cc_start: 0.8030 (t80) cc_final: 0.7736 (t80) REVERT: C 201 ARG cc_start: 0.8088 (mtm-85) cc_final: 0.7600 (mtm-85) REVERT: C 223 GLU cc_start: 0.7232 (mp0) cc_final: 0.7021 (mp0) REVERT: C 227 ILE cc_start: 0.8595 (mt) cc_final: 0.8314 (tt) REVERT: C 241 GLU cc_start: 0.5655 (tm-30) cc_final: 0.5199 (tm-30) REVERT: C 246 PHE cc_start: 0.7641 (t80) cc_final: 0.7258 (t80) REVERT: C 283 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7751 (tm-30) REVERT: C 287 MET cc_start: 0.7914 (mmm) cc_final: 0.7607 (mmm) REVERT: C 310 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7134 (mm-30) outliers start: 25 outliers final: 14 residues processed: 439 average time/residue: 0.3611 time to fit residues: 212.9226 Evaluate side-chains 428 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 413 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 182 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 B residue 99 SER Chi-restraints excluded: chain C residue 165 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 43 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 139 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 0.0470 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 0.0010 chunk 152 optimal weight: 1.9990 overall best weight: 0.4086 ------------------------------------------------------------------------------- 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 182 ASN D 206 GLN 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 182 ASN A 238 ASN B 59 ASN ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.155805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.125168 restraints weight = 22585.799| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.27 r_work: 0.3414 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15688 Z= 0.132 Angle : 0.545 7.382 21684 Z= 0.284 Chirality : 0.040 0.203 2406 Planarity : 0.005 0.094 2466 Dihedral : 20.453 164.015 2698 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.27 % Allowed : 12.71 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.20), residues: 1640 helix: 1.43 (0.19), residues: 756 sheet: 0.48 (0.32), residues: 222 loop : -0.71 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 293 HIS 0.005 0.001 HIS D 143 PHE 0.013 0.001 PHE C 141 TYR 0.019 0.002 TYR A 231 ARG 0.009 0.001 ARG F 143 Details of bonding type rmsd hydrogen bonds : bond 0.04021 ( 689) hydrogen bonds : angle 4.37609 ( 1965) metal coordination : bond 0.00551 ( 16) metal coordination : angle 2.91923 ( 6) covalent geometry : bond 0.00291 (15672) covalent geometry : angle 0.54256 (21678) *********************** 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 464 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 431 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 120 ASN cc_start: 0.8187 (t0) cc_final: 0.7958 (t0) REVERT: D 131 GLU cc_start: 0.7643 (tp30) cc_final: 0.7252 (tp30) REVERT: E 32 LEU cc_start: 0.8647 (mm) cc_final: 0.8368 (mt) REVERT: E 47 MET cc_start: 0.8501 (mmm) cc_final: 0.8168 (mmm) REVERT: E 54 ARG cc_start: 0.8172 (mtp85) cc_final: 0.7913 (mmt180) REVERT: E 70 LYS cc_start: 0.8348 (ttpt) cc_final: 0.8141 (tttt) REVERT: E 202 LYS cc_start: 0.8447 (mtmm) cc_final: 0.8174 (mtmm) REVERT: F 78 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6966 (tm-30) REVERT: F 169 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7468 (tm-30) REVERT: F 177 ARG cc_start: 0.8286 (mpp80) cc_final: 0.7756 (mtm180) REVERT: F 183 LYS cc_start: 0.8627 (ttpp) cc_final: 0.8357 (ptpp) REVERT: F 210 ARG cc_start: 0.8059 (ttp80) cc_final: 0.7648 (ttp80) REVERT: F 287 MET cc_start: 0.8114 (mmm) cc_final: 0.7898 (mmm) REVERT: F 300 LYS cc_start: 0.8283 (ttpt) cc_final: 0.8047 (ttpt) REVERT: F 304 PHE cc_start: 0.8623 (m-80) cc_final: 0.8392 (m-80) REVERT: F 308 LEU cc_start: 0.8253 (mt) cc_final: 0.8029 (tt) REVERT: F 310 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7616 (mm-30) REVERT: A 131 GLU cc_start: 0.7690 (tp30) cc_final: 0.7362 (tp30) REVERT: A 142 ARG cc_start: 0.7692 (mtt-85) cc_final: 0.7486 (mtt-85) REVERT: A 206 GLN cc_start: 0.8213 (tt0) cc_final: 0.7999 (tt0) REVERT: B 32 LEU cc_start: 0.8670 (mm) cc_final: 0.8463 (mt) REVERT: B 34 SER cc_start: 0.8427 (m) cc_final: 0.8086 (p) REVERT: B 47 MET cc_start: 0.8446 (mmm) cc_final: 0.8149 (mmm) REVERT: B 133 GLN cc_start: 0.7530 (mm-40) cc_final: 0.7300 (mm-40) REVERT: B 175 ASN cc_start: 0.7574 (OUTLIER) cc_final: 0.7341 (t0) REVERT: C 41 LEU cc_start: 0.8315 (tt) cc_final: 0.8082 (tt) REVERT: C 67 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6779 (tm-30) REVERT: C 83 ASN cc_start: 0.8163 (m-40) cc_final: 0.7833 (m-40) REVERT: C 94 GLU cc_start: 0.6963 (pm20) cc_final: 0.6420 (tp30) REVERT: C 139 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7453 (tm-30) REVERT: C 169 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7480 (tm-30) REVERT: C 174 GLU cc_start: 0.7965 (pp20) cc_final: 0.7745 (pp20) REVERT: C 177 ARG cc_start: 0.8309 (mpp80) cc_final: 0.7763 (mtm180) REVERT: C 190 TYR cc_start: 0.8060 (t80) cc_final: 0.7762 (t80) REVERT: C 192 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8446 (mmmm) REVERT: C 201 ARG cc_start: 0.8073 (mtm-85) cc_final: 0.7561 (mtm-85) REVERT: C 210 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.7640 (mtm-85) REVERT: C 223 GLU cc_start: 0.7230 (mp0) cc_final: 0.7005 (mp0) REVERT: C 241 GLU cc_start: 0.5885 (tm-30) cc_final: 0.5370 (tm-30) REVERT: C 246 PHE cc_start: 0.7686 (t80) cc_final: 0.7386 (t80) REVERT: C 283 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7643 (tm-30) REVERT: C 287 MET cc_start: 0.7951 (mmm) cc_final: 0.7609 (mmm) REVERT: C 310 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7047 (mm-30) outliers start: 33 outliers final: 17 residues processed: 440 average time/residue: 0.3536 time to fit residues: 209.4968 Evaluate side-chains 433 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 415 time to evaluate : 1.553 ------------------------------------------------------------------------------- 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 134 HIS Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 228 LEU 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 73 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 238 ASN E 59 ASN E 112 HIS E 118 HIS ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 59 ASN B 112 HIS ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.154439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123986 restraints weight = 22598.373| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.25 r_work: 0.3393 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15688 Z= 0.158 Angle : 0.559 8.356 21684 Z= 0.290 Chirality : 0.041 0.183 2406 Planarity : 0.004 0.057 2466 Dihedral : 20.310 159.652 2698 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.68 % Allowed : 14.56 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.20), residues: 1640 helix: 1.32 (0.18), residues: 760 sheet: 0.43 (0.31), residues: 242 loop : -0.67 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 65 HIS 0.008 0.001 HIS B 134 PHE 0.014 0.001 PHE C 141 TYR 0.022 0.002 TYR F 269 ARG 0.011 0.001 ARG F 143 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 689) hydrogen bonds : angle 4.32806 ( 1965) metal coordination : bond 0.00901 ( 16) metal coordination : angle 1.93550 ( 6) covalent geometry : bond 0.00348 (15672) covalent geometry : angle 0.55814 (21678) *********************** 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 474 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 435 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 120 ASN cc_start: 0.8237 (t0) cc_final: 0.8031 (t0) REVERT: D 131 GLU cc_start: 0.7795 (tp30) cc_final: 0.7228 (tp30) REVERT: E 47 MET cc_start: 0.8488 (mmm) cc_final: 0.8157 (mmm) REVERT: E 49 ARG cc_start: 0.8081 (mtp85) cc_final: 0.7657 (mtp85) REVERT: E 54 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7961 (mmt180) REVERT: E 70 LYS cc_start: 0.8360 (ttpt) cc_final: 0.8151 (tttt) REVERT: F 44 GLN cc_start: 0.7971 (mt0) cc_final: 0.7770 (mp10) REVERT: F 75 GLU cc_start: 0.7955 (tt0) cc_final: 0.7653 (tt0) REVERT: F 78 GLU cc_start: 0.7349 (tm-30) cc_final: 0.7057 (tm-30) REVERT: F 164 VAL cc_start: 0.8592 (t) cc_final: 0.8244 (m) REVERT: F 165 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7445 (mm) REVERT: F 169 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7504 (tm-30) REVERT: F 210 ARG cc_start: 0.8132 (ttp80) cc_final: 0.7708 (ttp80) REVERT: F 251 LEU cc_start: 0.7803 (tp) cc_final: 0.7504 (tt) REVERT: F 300 LYS cc_start: 0.8274 (ttpt) cc_final: 0.7998 (ttpt) REVERT: F 304 PHE cc_start: 0.8686 (m-80) cc_final: 0.8421 (m-80) REVERT: F 308 LEU cc_start: 0.8120 (mt) cc_final: 0.7593 (mt) REVERT: F 310 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7612 (mm-30) REVERT: A 131 GLU cc_start: 0.7797 (tp30) cc_final: 0.7368 (tp30) REVERT: A 206 GLN cc_start: 0.8251 (tt0) cc_final: 0.8042 (tt0) REVERT: B 34 SER cc_start: 0.8416 (m) cc_final: 0.8073 (p) REVERT: B 47 MET cc_start: 0.8472 (mmm) cc_final: 0.8138 (mmm) REVERT: C 41 LEU cc_start: 0.8344 (tt) cc_final: 0.8095 (tt) REVERT: C 67 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6876 (tm-30) REVERT: C 77 VAL cc_start: 0.7692 (p) cc_final: 0.7442 (p) REVERT: C 83 ASN cc_start: 0.8183 (m-40) cc_final: 0.7846 (m-40) REVERT: C 94 GLU cc_start: 0.7436 (pm20) cc_final: 0.7185 (mm-30) REVERT: C 95 VAL cc_start: 0.8205 (t) cc_final: 0.7730 (p) REVERT: C 139 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7397 (tm-30) REVERT: C 154 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7684 (tp) REVERT: C 164 VAL cc_start: 0.8548 (t) cc_final: 0.8326 (m) REVERT: C 169 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7585 (tm-30) REVERT: C 174 GLU cc_start: 0.8014 (pp20) cc_final: 0.7718 (pp20) REVERT: C 192 LYS cc_start: 0.8711 (mmmt) cc_final: 0.8502 (mmmt) REVERT: C 201 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7639 (mtm-85) REVERT: C 210 ARG cc_start: 0.7919 (mtm-85) cc_final: 0.7609 (mtm-85) REVERT: C 221 ILE cc_start: 0.8674 (tp) cc_final: 0.8425 (tp) REVERT: C 223 GLU cc_start: 0.7527 (mp0) cc_final: 0.7213 (mp0) REVERT: C 227 ILE cc_start: 0.8598 (mt) cc_final: 0.8276 (tt) REVERT: C 241 GLU cc_start: 0.5890 (tm-30) cc_final: 0.5343 (tm-30) REVERT: C 246 PHE cc_start: 0.7706 (t80) cc_final: 0.7481 (t80) REVERT: C 283 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7639 (tm-30) REVERT: C 287 MET cc_start: 0.7975 (mmm) cc_final: 0.7628 (mmm) REVERT: C 310 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7088 (mm-30) outliers start: 39 outliers final: 22 residues processed: 446 average time/residue: 0.3477 time to fit residues: 209.1343 Evaluate side-chains 452 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 428 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 175 ASN 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 B residue 49 ARG Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 275 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 71 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 157 optimal weight: 0.0670 chunk 52 optimal weight: 0.2980 chunk 64 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 165 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.4118 ------------------------------------------------------------------------------- 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 238 ASN E 59 ASN E 112 HIS E 134 HIS F 203 GLN F 243 HIS ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 59 ASN B 112 HIS B 134 HIS C 133 HIS ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.154366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.123985 restraints weight = 22783.673| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.26 r_work: 0.3408 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15688 Z= 0.129 Angle : 0.542 9.315 21684 Z= 0.281 Chirality : 0.040 0.166 2406 Planarity : 0.004 0.066 2466 Dihedral : 20.209 158.451 2698 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.13 % Allowed : 17.45 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.21), residues: 1640 helix: 1.37 (0.18), residues: 760 sheet: 0.45 (0.31), residues: 242 loop : -0.60 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 229 HIS 0.008 0.001 HIS F 264 PHE 0.014 0.001 PHE F 141 TYR 0.022 0.002 TYR F 269 ARG 0.009 0.000 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 689) hydrogen bonds : angle 4.26074 ( 1965) metal coordination : bond 0.00431 ( 16) metal coordination : angle 2.10316 ( 6) covalent geometry : bond 0.00288 (15672) covalent geometry : angle 0.54108 (21678) *********************** 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 454 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 423 time to evaluate : 1.500 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: 0.7779 (tp30) cc_final: 0.7238 (tp30) REVERT: E 47 MET cc_start: 0.8489 (mmm) cc_final: 0.8132 (mmm) REVERT: E 70 LYS cc_start: 0.8363 (ttpt) cc_final: 0.8150 (tttt) REVERT: E 131 GLU cc_start: 0.8158 (pt0) cc_final: 0.7786 (pt0) REVERT: E 161 ASN cc_start: 0.7920 (m-40) cc_final: 0.7703 (m-40) REVERT: F 40 LYS cc_start: 0.8191 (mtpp) cc_final: 0.7991 (mtpp) REVERT: F 44 GLN cc_start: 0.7981 (mt0) cc_final: 0.7731 (mt0) REVERT: F 76 MET cc_start: 0.7659 (ptp) cc_final: 0.7360 (ptp) REVERT: F 164 VAL cc_start: 0.8597 (t) cc_final: 0.8220 (m) REVERT: F 165 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7385 (mm) REVERT: F 169 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7413 (tm-30) REVERT: F 183 LYS cc_start: 0.8643 (ttpp) cc_final: 0.8385 (ptpp) REVERT: F 210 ARG cc_start: 0.8160 (ttp80) cc_final: 0.7734 (ttp80) REVERT: F 244 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7607 (mtmt) REVERT: F 300 LYS cc_start: 0.8253 (ttpt) cc_final: 0.7964 (ttpt) REVERT: A 131 GLU cc_start: 0.7805 (tp30) cc_final: 0.7402 (tp30) REVERT: A 206 GLN cc_start: 0.8239 (tt0) cc_final: 0.8039 (tt0) REVERT: B 34 SER cc_start: 0.8404 (m) cc_final: 0.8051 (p) REVERT: B 47 MET cc_start: 0.8468 (mmm) cc_final: 0.8161 (mmm) REVERT: C 41 LEU cc_start: 0.8262 (tt) cc_final: 0.7922 (tt) REVERT: C 44 GLN cc_start: 0.8084 (mt0) cc_final: 0.7828 (mt0) REVERT: C 67 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6919 (tm-30) REVERT: C 77 VAL cc_start: 0.7691 (p) cc_final: 0.7413 (p) REVERT: C 83 ASN cc_start: 0.8151 (m-40) cc_final: 0.7870 (m-40) REVERT: C 94 GLU cc_start: 0.7502 (pm20) cc_final: 0.7291 (mm-30) REVERT: C 95 VAL cc_start: 0.8276 (t) cc_final: 0.7886 (p) REVERT: C 139 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7410 (tm-30) REVERT: C 154 ILE cc_start: 0.8038 (tp) cc_final: 0.7807 (tp) REVERT: C 164 VAL cc_start: 0.8499 (t) cc_final: 0.8287 (m) REVERT: C 165 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7649 (mm) REVERT: C 167 LEU cc_start: 0.8266 (tt) cc_final: 0.8044 (tp) REVERT: C 169 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7525 (tm-30) REVERT: C 174 GLU cc_start: 0.8026 (pp20) cc_final: 0.7722 (pp20) REVERT: C 192 LYS cc_start: 0.8694 (mmmt) cc_final: 0.8492 (mmmt) REVERT: C 201 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.7598 (mtm-85) REVERT: C 210 ARG cc_start: 0.7918 (mtm-85) cc_final: 0.7542 (mtm-85) REVERT: C 221 ILE cc_start: 0.8672 (tp) cc_final: 0.8443 (tp) REVERT: C 223 GLU cc_start: 0.7556 (mp0) cc_final: 0.7243 (mp0) REVERT: C 227 ILE cc_start: 0.8574 (mt) cc_final: 0.8260 (tt) REVERT: C 283 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7585 (tm-30) REVERT: C 287 MET cc_start: 0.7969 (mmm) cc_final: 0.7625 (mmm) REVERT: C 291 LYS cc_start: 0.8408 (ttpp) cc_final: 0.8151 (ttpp) REVERT: C 310 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7125 (mm-30) outliers start: 31 outliers final: 21 residues processed: 434 average time/residue: 0.3588 time to fit residues: 209.4950 Evaluate side-chains 438 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 415 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 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 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 165 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 300 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 37 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 52 optimal weight: 0.0870 chunk 137 optimal weight: 1.9990 chunk 120 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 59 ASN B 130 GLN B 134 HIS ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.152714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.122114 restraints weight = 22414.001| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.25 r_work: 0.3390 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15688 Z= 0.160 Angle : 0.564 9.494 21684 Z= 0.293 Chirality : 0.041 0.172 2406 Planarity : 0.004 0.062 2466 Dihedral : 20.185 157.818 2698 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.47 % Allowed : 18.54 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.20), residues: 1640 helix: 1.36 (0.18), residues: 760 sheet: 0.51 (0.31), residues: 242 loop : -0.63 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 229 HIS 0.005 0.001 HIS F 187 PHE 0.013 0.001 PHE F 141 TYR 0.022 0.002 TYR F 269 ARG 0.009 0.000 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 689) hydrogen bonds : angle 4.27624 ( 1965) metal coordination : bond 0.00947 ( 16) metal coordination : angle 1.71813 ( 6) covalent geometry : bond 0.00359 (15672) covalent geometry : angle 0.56364 (21678) *********************** 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 466 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 430 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 GLU cc_start: 0.7828 (tp30) cc_final: 0.7234 (tp30) REVERT: D 142 ARG cc_start: 0.7752 (mtt-85) cc_final: 0.7541 (mtt-85) REVERT: D 180 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7727 (tpp) REVERT: E 47 MET cc_start: 0.8472 (mmm) cc_final: 0.8155 (mmm) REVERT: E 70 LYS cc_start: 0.8380 (ttpt) cc_final: 0.8166 (tttt) REVERT: E 202 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8262 (mtmm) REVERT: F 40 LYS cc_start: 0.8225 (mtpp) cc_final: 0.8007 (mtpp) REVERT: F 78 GLU cc_start: 0.7312 (tm-30) cc_final: 0.7009 (tm-30) REVERT: F 139 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7475 (tm-30) REVERT: F 164 VAL cc_start: 0.8599 (t) cc_final: 0.8220 (m) REVERT: F 165 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7471 (mm) REVERT: F 169 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7403 (tm-30) REVERT: F 183 LYS cc_start: 0.8657 (ttpp) cc_final: 0.8389 (ptpp) REVERT: F 244 LYS cc_start: 0.7891 (mtmt) cc_final: 0.7596 (mtmt) REVERT: F 254 LEU cc_start: 0.7552 (tp) cc_final: 0.6886 (tt) REVERT: F 300 LYS cc_start: 0.8241 (ttpt) cc_final: 0.7974 (ttpt) REVERT: F 308 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7790 (tt) REVERT: A 131 GLU cc_start: 0.7826 (tp30) cc_final: 0.7386 (tp30) REVERT: A 206 GLN cc_start: 0.8258 (tt0) cc_final: 0.8047 (tt0) REVERT: B 47 MET cc_start: 0.8501 (mmm) cc_final: 0.8178 (mmm) REVERT: C 41 LEU cc_start: 0.8349 (tt) cc_final: 0.8093 (tt) REVERT: C 67 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6992 (tm-30) REVERT: C 77 VAL cc_start: 0.7750 (OUTLIER) cc_final: 0.7534 (p) REVERT: C 83 ASN cc_start: 0.8188 (m-40) cc_final: 0.7904 (m-40) REVERT: C 95 VAL cc_start: 0.8382 (t) cc_final: 0.7998 (p) REVERT: C 139 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7439 (tm-30) REVERT: C 152 PRO cc_start: 0.8131 (Cg_endo) cc_final: 0.7576 (Cg_exo) REVERT: C 154 ILE cc_start: 0.8115 (tp) cc_final: 0.7906 (tp) REVERT: C 164 VAL cc_start: 0.8555 (t) cc_final: 0.8329 (m) REVERT: C 165 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7712 (mm) REVERT: C 167 LEU cc_start: 0.8295 (tt) cc_final: 0.8081 (tp) REVERT: C 169 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7477 (tm-30) REVERT: C 174 GLU cc_start: 0.8099 (pp20) cc_final: 0.7801 (pp20) REVERT: C 192 LYS cc_start: 0.8665 (mmmt) cc_final: 0.8431 (mmmt) REVERT: C 201 ARG cc_start: 0.8015 (mtm-85) cc_final: 0.7550 (mtm-85) REVERT: C 210 ARG cc_start: 0.7892 (mtm-85) cc_final: 0.7495 (mtm-85) REVERT: C 221 ILE cc_start: 0.8661 (tp) cc_final: 0.8445 (tp) REVERT: C 223 GLU cc_start: 0.7633 (mp0) cc_final: 0.7283 (mp0) REVERT: C 227 ILE cc_start: 0.8535 (mt) cc_final: 0.8206 (tt) REVERT: C 283 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7526 (tm-30) REVERT: C 287 MET cc_start: 0.7983 (mmm) cc_final: 0.7624 (mmm) REVERT: C 291 LYS cc_start: 0.8431 (ttpp) cc_final: 0.8144 (ttpp) REVERT: C 310 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7191 (mm-30) outliers start: 36 outliers final: 22 residues processed: 442 average time/residue: 0.3565 time to fit residues: 212.3202 Evaluate side-chains 446 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 418 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 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 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 260 LEU 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 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 182 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 275 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 76 optimal weight: 0.0270 chunk 115 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 206 GLN D 238 ASN E 59 ASN E 112 HIS E 134 HIS E 241 GLN F 203 GLN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 59 ASN B 112 HIS B 134 HIS C 203 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.152542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.122062 restraints weight = 22553.736| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.24 r_work: 0.3379 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15688 Z= 0.153 Angle : 0.578 10.230 21684 Z= 0.299 Chirality : 0.041 0.170 2406 Planarity : 0.004 0.060 2466 Dihedral : 20.167 157.770 2698 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.47 % Allowed : 18.96 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.20), residues: 1640 helix: 1.38 (0.18), residues: 762 sheet: 0.55 (0.31), residues: 242 loop : -0.62 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 65 HIS 0.005 0.001 HIS B 134 PHE 0.011 0.001 PHE F 141 TYR 0.023 0.002 TYR F 158 ARG 0.010 0.000 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 689) hydrogen bonds : angle 4.28524 ( 1965) metal coordination : bond 0.00810 ( 16) metal coordination : angle 1.76525 ( 6) covalent geometry : bond 0.00345 (15672) covalent geometry : angle 0.57752 (21678) *********************** 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 460 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 424 time to evaluate : 1.680 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: 0.7859 (tp30) cc_final: 0.7230 (tp30) REVERT: E 47 MET cc_start: 0.8523 (mmm) cc_final: 0.8216 (mmm) REVERT: E 70 LYS cc_start: 0.8359 (ttpt) cc_final: 0.8145 (tttt) REVERT: E 161 ASN cc_start: 0.7925 (m-40) cc_final: 0.7707 (m-40) REVERT: E 202 LYS cc_start: 0.8524 (mtmm) cc_final: 0.8246 (mtmm) REVERT: F 40 LYS cc_start: 0.8249 (mtpp) cc_final: 0.8022 (mtpp) REVERT: F 95 VAL cc_start: 0.8313 (t) cc_final: 0.7950 (p) REVERT: F 164 VAL cc_start: 0.8588 (t) cc_final: 0.8212 (m) REVERT: F 165 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7445 (mm) REVERT: F 169 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7413 (tm-30) REVERT: F 183 LYS cc_start: 0.8661 (ttpp) cc_final: 0.8382 (ptpp) REVERT: F 201 ARG cc_start: 0.8149 (mtm-85) cc_final: 0.7628 (mtm-85) REVERT: F 254 LEU cc_start: 0.7500 (tp) cc_final: 0.6831 (tt) REVERT: F 300 LYS cc_start: 0.8236 (ttpt) cc_final: 0.7950 (ttpt) REVERT: F 303 MET cc_start: 0.7517 (ttt) cc_final: 0.7255 (ttt) REVERT: F 308 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7716 (tt) REVERT: A 131 GLU cc_start: 0.7819 (tp30) cc_final: 0.7366 (tp30) REVERT: A 206 GLN cc_start: 0.8233 (tt0) cc_final: 0.8032 (tt0) REVERT: B 47 MET cc_start: 0.8497 (mmm) cc_final: 0.8189 (mmm) REVERT: C 41 LEU cc_start: 0.8340 (tt) cc_final: 0.7959 (tt) REVERT: C 44 GLN cc_start: 0.8091 (mt0) cc_final: 0.7842 (mt0) REVERT: C 67 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7008 (tm-30) REVERT: C 75 GLU cc_start: 0.7984 (tt0) cc_final: 0.7667 (tt0) REVERT: C 77 VAL cc_start: 0.7841 (OUTLIER) cc_final: 0.7553 (p) REVERT: C 83 ASN cc_start: 0.8199 (m-40) cc_final: 0.7906 (m-40) REVERT: C 95 VAL cc_start: 0.8403 (t) cc_final: 0.8142 (p) REVERT: C 139 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7438 (tm-30) REVERT: C 152 PRO cc_start: 0.8157 (Cg_endo) cc_final: 0.7541 (Cg_exo) REVERT: C 154 ILE cc_start: 0.8140 (tp) cc_final: 0.7939 (tp) REVERT: C 164 VAL cc_start: 0.8584 (t) cc_final: 0.8356 (m) REVERT: C 165 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7718 (mm) REVERT: C 167 LEU cc_start: 0.8273 (tt) cc_final: 0.8063 (tp) REVERT: C 169 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7513 (tm-30) REVERT: C 174 GLU cc_start: 0.8115 (pp20) cc_final: 0.7787 (pp20) REVERT: C 192 LYS cc_start: 0.8650 (mmmt) cc_final: 0.8405 (mmmt) REVERT: C 201 ARG cc_start: 0.8041 (mtm-85) cc_final: 0.7575 (mtm-85) REVERT: C 210 ARG cc_start: 0.7956 (mtm-85) cc_final: 0.7653 (mtm-85) REVERT: C 221 ILE cc_start: 0.8647 (tp) cc_final: 0.8419 (tp) REVERT: C 223 GLU cc_start: 0.7644 (mp0) cc_final: 0.7287 (mp0) REVERT: C 227 ILE cc_start: 0.8518 (mt) cc_final: 0.8247 (tt) REVERT: C 247 LEU cc_start: 0.8646 (tp) cc_final: 0.8329 (tt) REVERT: C 256 LYS cc_start: 0.7987 (ptpp) cc_final: 0.7736 (mtmm) REVERT: C 283 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7550 (tm-30) REVERT: C 287 MET cc_start: 0.7972 (mmm) cc_final: 0.7586 (mmm) REVERT: C 291 LYS cc_start: 0.8353 (ttpp) cc_final: 0.8079 (ttpp) REVERT: C 308 LEU cc_start: 0.8135 (tt) cc_final: 0.7905 (tt) REVERT: C 310 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7161 (mm-30) outliers start: 36 outliers final: 24 residues processed: 438 average time/residue: 0.3552 time to fit residues: 209.8252 Evaluate side-chains 449 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 421 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain F residue 260 LEU 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 77 VAL Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 275 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 64 optimal weight: 0.8980 chunk 160 optimal weight: 0.0670 chunk 142 optimal weight: 0.8980 chunk 63 optimal weight: 0.4980 chunk 165 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 238 ASN E 59 ASN E 112 HIS E 134 HIS E 250 GLN F 203 GLN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 41 ASN B 59 ASN B 112 HIS B 134 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.152083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.121784 restraints weight = 22340.088| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.22 r_work: 0.3380 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15688 Z= 0.153 Angle : 0.584 10.956 21684 Z= 0.303 Chirality : 0.041 0.169 2406 Planarity : 0.004 0.059 2466 Dihedral : 20.151 157.959 2698 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.61 % Allowed : 19.30 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.20), residues: 1640 helix: 1.39 (0.18), residues: 762 sheet: 0.58 (0.31), residues: 242 loop : -0.59 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 65 HIS 0.006 0.001 HIS D 33 PHE 0.011 0.001 PHE C 246 TYR 0.022 0.002 TYR C 269 ARG 0.010 0.000 ARG D 142 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 689) hydrogen bonds : angle 4.29328 ( 1965) metal coordination : bond 0.00791 ( 16) metal coordination : angle 1.76162 ( 6) covalent geometry : bond 0.00345 (15672) covalent geometry : angle 0.58372 (21678) *********************** 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 464 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 426 time to evaluate : 2.694 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: 0.7870 (tp30) cc_final: 0.7338 (tp30) REVERT: D 180 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7618 (tpp) REVERT: E 47 MET cc_start: 0.8521 (mmm) cc_final: 0.8235 (mmm) REVERT: E 70 LYS cc_start: 0.8371 (ttpt) cc_final: 0.8155 (tttt) REVERT: E 202 LYS cc_start: 0.8524 (mtmm) cc_final: 0.8234 (mtmm) REVERT: F 40 LYS cc_start: 0.8249 (mtpp) cc_final: 0.8013 (mtpp) REVERT: F 78 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6999 (tm-30) REVERT: F 95 VAL cc_start: 0.8302 (t) cc_final: 0.8042 (p) REVERT: F 139 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: F 164 VAL cc_start: 0.8620 (t) cc_final: 0.8262 (m) REVERT: F 165 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7511 (mm) REVERT: F 169 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7407 (tm-30) REVERT: F 201 ARG cc_start: 0.8203 (mtm-85) cc_final: 0.7698 (mtm-85) REVERT: F 254 LEU cc_start: 0.7524 (tp) cc_final: 0.6861 (tt) REVERT: F 291 LYS cc_start: 0.8462 (ttpp) cc_final: 0.8005 (ttpp) REVERT: F 300 LYS cc_start: 0.8251 (ttpt) cc_final: 0.7955 (ttpt) REVERT: F 308 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7684 (tt) REVERT: A 131 GLU cc_start: 0.7833 (tp30) cc_final: 0.7383 (tp30) REVERT: A 206 GLN cc_start: 0.8217 (tt0) cc_final: 0.8017 (tt0) REVERT: B 47 MET cc_start: 0.8498 (mmm) cc_final: 0.8188 (mmm) REVERT: C 41 LEU cc_start: 0.8339 (tt) cc_final: 0.8095 (tt) REVERT: C 67 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7007 (tm-30) REVERT: C 75 GLU cc_start: 0.7977 (tt0) cc_final: 0.7667 (tt0) REVERT: C 77 VAL cc_start: 0.7876 (OUTLIER) cc_final: 0.7564 (p) REVERT: C 83 ASN cc_start: 0.8203 (m-40) cc_final: 0.7904 (m-40) REVERT: C 92 TYR cc_start: 0.7509 (m-80) cc_final: 0.7043 (m-80) REVERT: C 95 VAL cc_start: 0.8481 (t) cc_final: 0.8209 (p) REVERT: C 139 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7460 (tm-30) REVERT: C 152 PRO cc_start: 0.8215 (Cg_endo) cc_final: 0.7590 (Cg_exo) REVERT: C 154 ILE cc_start: 0.8194 (tp) cc_final: 0.7977 (tp) REVERT: C 164 VAL cc_start: 0.8592 (t) cc_final: 0.8362 (m) REVERT: C 165 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7757 (mm) REVERT: C 169 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7504 (tm-30) REVERT: C 174 GLU cc_start: 0.8112 (pp20) cc_final: 0.7787 (pp20) REVERT: C 192 LYS cc_start: 0.8641 (mmmt) cc_final: 0.8392 (mmmt) REVERT: C 201 ARG cc_start: 0.8055 (mtm-85) cc_final: 0.7599 (mtm-85) REVERT: C 210 ARG cc_start: 0.7957 (mtm-85) cc_final: 0.7641 (mtm-85) REVERT: C 223 GLU cc_start: 0.7648 (mp0) cc_final: 0.7291 (mp0) REVERT: C 227 ILE cc_start: 0.8564 (mt) cc_final: 0.8311 (tt) REVERT: C 256 LYS cc_start: 0.8001 (ptpp) cc_final: 0.7761 (mtmm) REVERT: C 283 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7508 (tm-30) REVERT: C 287 MET cc_start: 0.7970 (mmm) cc_final: 0.7591 (mmm) REVERT: C 291 LYS cc_start: 0.8364 (ttpp) cc_final: 0.8093 (ttpp) REVERT: C 308 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7919 (tt) REVERT: C 310 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7221 (mm-30) outliers start: 38 outliers final: 24 residues processed: 439 average time/residue: 0.4776 time to fit residues: 284.0710 Evaluate side-chains 443 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 412 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 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 20 LEU 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 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 182 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 275 LEU 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 32 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 21 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.3934 r_free = 0.3934 target = 0.151290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.121011 restraints weight = 22386.914| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.22 r_work: 0.3374 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15688 Z= 0.166 Angle : 0.608 12.022 21684 Z= 0.314 Chirality : 0.041 0.177 2406 Planarity : 0.005 0.066 2466 Dihedral : 20.156 158.061 2698 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.34 % Allowed : 19.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.20), residues: 1640 helix: 1.38 (0.18), residues: 760 sheet: 0.59 (0.31), residues: 242 loop : -0.62 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 65 HIS 0.009 0.001 HIS A 134 PHE 0.011 0.001 PHE F 304 TYR 0.024 0.002 TYR F 269 ARG 0.010 0.001 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 689) hydrogen bonds : angle 4.31316 ( 1965) metal coordination : bond 0.00993 ( 16) metal coordination : angle 1.71839 ( 6) covalent geometry : bond 0.00374 (15672) covalent geometry : angle 0.60772 (21678) *********************** 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 463 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 429 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 GLU cc_start: 0.7874 (tp30) cc_final: 0.7340 (tp30) REVERT: E 47 MET cc_start: 0.8532 (mmm) cc_final: 0.8247 (mmm) REVERT: E 70 LYS cc_start: 0.8365 (ttpt) cc_final: 0.8151 (tttt) REVERT: F 40 LYS cc_start: 0.8251 (mtpp) cc_final: 0.8028 (mtpp) REVERT: F 44 GLN cc_start: 0.8007 (mt0) cc_final: 0.7675 (mp10) REVERT: F 77 VAL cc_start: 0.7459 (p) cc_final: 0.7102 (p) REVERT: F 78 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6903 (tm-30) REVERT: F 94 GLU cc_start: 0.7867 (pm20) cc_final: 0.7589 (mm-30) REVERT: F 95 VAL cc_start: 0.8398 (t) cc_final: 0.7971 (p) REVERT: F 139 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7419 (tm-30) REVERT: F 164 VAL cc_start: 0.8699 (t) cc_final: 0.8404 (m) REVERT: F 165 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7629 (mm) REVERT: F 169 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7407 (tm-30) REVERT: F 183 LYS cc_start: 0.8635 (ttpp) cc_final: 0.8408 (ptpp) REVERT: F 201 ARG cc_start: 0.8216 (mtm-85) cc_final: 0.7706 (mtm-85) REVERT: F 254 LEU cc_start: 0.7623 (tp) cc_final: 0.6923 (tt) REVERT: F 300 LYS cc_start: 0.8241 (ttpt) cc_final: 0.7957 (ttpt) REVERT: F 308 LEU cc_start: 0.7904 (mt) cc_final: 0.7695 (tt) REVERT: A 131 GLU cc_start: 0.7835 (tp30) cc_final: 0.7450 (tp30) REVERT: B 47 MET cc_start: 0.8505 (mmm) cc_final: 0.8225 (mmm) REVERT: C 41 LEU cc_start: 0.8350 (tt) cc_final: 0.7967 (tt) REVERT: C 44 GLN cc_start: 0.8052 (mt0) cc_final: 0.7827 (mt0) REVERT: C 67 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7015 (tm-30) REVERT: C 75 GLU cc_start: 0.7956 (tt0) cc_final: 0.7662 (tt0) REVERT: C 77 VAL cc_start: 0.7815 (OUTLIER) cc_final: 0.7474 (p) REVERT: C 83 ASN cc_start: 0.8216 (m-40) cc_final: 0.8014 (m-40) REVERT: C 95 VAL cc_start: 0.8581 (t) cc_final: 0.8348 (p) REVERT: C 139 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7472 (tm-30) REVERT: C 152 PRO cc_start: 0.8294 (Cg_endo) cc_final: 0.7682 (Cg_exo) REVERT: C 154 ILE cc_start: 0.8270 (tp) cc_final: 0.8066 (tp) REVERT: C 164 VAL cc_start: 0.8627 (t) cc_final: 0.8380 (m) REVERT: C 165 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7762 (mm) REVERT: C 169 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7513 (tm-30) REVERT: C 174 GLU cc_start: 0.8152 (pp20) cc_final: 0.7823 (pp20) REVERT: C 192 LYS cc_start: 0.8624 (mmmt) cc_final: 0.8358 (mmmt) REVERT: C 201 ARG cc_start: 0.8042 (mtm-85) cc_final: 0.7572 (mtm-85) REVERT: C 210 ARG cc_start: 0.7948 (mtm-85) cc_final: 0.7653 (mtm-85) REVERT: C 223 GLU cc_start: 0.7720 (mp0) cc_final: 0.7331 (mp0) REVERT: C 227 ILE cc_start: 0.8636 (mt) cc_final: 0.8293 (tt) REVERT: C 241 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7077 (mm-30) REVERT: C 247 LEU cc_start: 0.8581 (tp) cc_final: 0.8243 (tt) REVERT: C 256 LYS cc_start: 0.8012 (ptpp) cc_final: 0.7809 (mtmm) REVERT: C 283 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7596 (tm-30) REVERT: C 287 MET cc_start: 0.7946 (mmm) cc_final: 0.7600 (mmm) REVERT: C 291 LYS cc_start: 0.8356 (ttpp) cc_final: 0.8097 (ttpp) REVERT: C 308 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7968 (tt) REVERT: C 310 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7226 (mm-30) outliers start: 34 outliers final: 24 residues processed: 440 average time/residue: 0.4245 time to fit residues: 254.8076 Evaluate side-chains 447 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 418 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain F residue 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 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 182 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 77 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 97 optimal weight: 0.0980 chunk 41 optimal weight: 0.8980 chunk 73 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 238 ASN E 59 ASN E 112 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.151470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.121298 restraints weight = 22430.426| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.23 r_work: 0.3372 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 15688 Z= 0.164 Angle : 0.614 12.059 21684 Z= 0.317 Chirality : 0.041 0.194 2406 Planarity : 0.005 0.059 2466 Dihedral : 20.163 158.288 2698 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.06 % Allowed : 20.88 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.20), residues: 1640 helix: 1.35 (0.18), residues: 760 sheet: 0.63 (0.32), residues: 242 loop : -0.62 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 131 HIS 0.005 0.001 HIS A 33 PHE 0.024 0.001 PHE C 246 TYR 0.040 0.002 TYR F 292 ARG 0.011 0.001 ARG F 177 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 689) hydrogen bonds : angle 4.37704 ( 1965) metal coordination : bond 0.00857 ( 16) metal coordination : angle 1.81326 ( 6) covalent geometry : bond 0.00373 (15672) covalent geometry : angle 0.61349 (21678) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 431 time to evaluate : 1.549 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: 0.7884 (tp30) cc_final: 0.7355 (tp30) REVERT: E 47 MET cc_start: 0.8534 (mmm) cc_final: 0.8239 (mmm) REVERT: E 70 LYS cc_start: 0.8366 (ttpt) cc_final: 0.8151 (tttt) REVERT: F 40 LYS cc_start: 0.8256 (mtpp) cc_final: 0.8042 (mtpp) REVERT: F 44 GLN cc_start: 0.7958 (mt0) cc_final: 0.7606 (mp10) REVERT: F 77 VAL cc_start: 0.7517 (p) cc_final: 0.7294 (p) REVERT: F 78 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6892 (tm-30) REVERT: F 94 GLU cc_start: 0.7889 (pm20) cc_final: 0.7505 (mm-30) REVERT: F 95 VAL cc_start: 0.8469 (t) cc_final: 0.8043 (p) REVERT: F 139 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7414 (tm-30) REVERT: F 164 VAL cc_start: 0.8696 (t) cc_final: 0.8414 (m) REVERT: F 165 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7633 (mm) REVERT: F 169 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7398 (tm-30) REVERT: F 183 LYS cc_start: 0.8655 (ttpp) cc_final: 0.8409 (ptpp) REVERT: F 192 LYS cc_start: 0.8673 (mmmt) cc_final: 0.8371 (mmmt) REVERT: F 201 ARG cc_start: 0.8200 (mtm-85) cc_final: 0.7689 (mtm-85) REVERT: F 254 LEU cc_start: 0.7679 (tp) cc_final: 0.6980 (tt) REVERT: F 300 LYS cc_start: 0.8279 (ttpt) cc_final: 0.7979 (ttpt) REVERT: F 308 LEU cc_start: 0.7856 (mt) cc_final: 0.7633 (tt) REVERT: A 131 GLU cc_start: 0.7843 (tp30) cc_final: 0.7444 (tp30) REVERT: B 47 MET cc_start: 0.8553 (mmm) cc_final: 0.8241 (mmm) REVERT: C 41 LEU cc_start: 0.8312 (tt) cc_final: 0.7941 (tt) REVERT: C 44 GLN cc_start: 0.8061 (mt0) cc_final: 0.7845 (mt0) REVERT: C 67 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7044 (tm-30) REVERT: C 76 MET cc_start: 0.7683 (ptp) cc_final: 0.7394 (ptp) REVERT: C 77 VAL cc_start: 0.7811 (OUTLIER) cc_final: 0.7476 (p) REVERT: C 83 ASN cc_start: 0.8222 (m-40) cc_final: 0.8001 (m-40) REVERT: C 95 VAL cc_start: 0.8620 (t) cc_final: 0.8391 (p) REVERT: C 139 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7437 (tm-30) REVERT: C 152 PRO cc_start: 0.8323 (Cg_endo) cc_final: 0.7677 (Cg_exo) REVERT: C 154 ILE cc_start: 0.8331 (tp) cc_final: 0.8122 (tp) REVERT: C 164 VAL cc_start: 0.8614 (t) cc_final: 0.8365 (m) REVERT: C 165 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7756 (mm) REVERT: C 169 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7552 (tm-30) REVERT: C 174 GLU cc_start: 0.8106 (pp20) cc_final: 0.7752 (pp20) REVERT: C 177 ARG cc_start: 0.8490 (mtm180) cc_final: 0.8288 (mtm180) REVERT: C 192 LYS cc_start: 0.8585 (mmmt) cc_final: 0.8308 (mmmt) REVERT: C 201 ARG cc_start: 0.8074 (mtm-85) cc_final: 0.7611 (mtm-85) REVERT: C 223 GLU cc_start: 0.7695 (mp0) cc_final: 0.7289 (mp0) REVERT: C 227 ILE cc_start: 0.8656 (mt) cc_final: 0.8294 (tt) REVERT: C 241 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6968 (mm-30) REVERT: C 254 LEU cc_start: 0.7499 (tp) cc_final: 0.6937 (tt) REVERT: C 272 VAL cc_start: 0.8384 (t) cc_final: 0.8014 (p) REVERT: C 283 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7808 (tm-30) REVERT: C 291 LYS cc_start: 0.8339 (ttpp) cc_final: 0.7818 (ttpp) REVERT: C 292 TYR cc_start: 0.8573 (m-80) cc_final: 0.7755 (m-80) REVERT: C 308 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7977 (tt) REVERT: C 310 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7303 (mm-30) outliers start: 30 outliers final: 21 residues processed: 442 average time/residue: 0.3577 time to fit residues: 212.4635 Evaluate side-chains 448 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 422 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 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 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 182 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 8 optimal weight: 0.2980 chunk 73 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 238 ASN E 59 ASN E 112 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 C 203 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.151299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.121279 restraints weight = 22626.194| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.22 r_work: 0.3366 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15688 Z= 0.179 Angle : 0.630 12.767 21684 Z= 0.326 Chirality : 0.042 0.186 2406 Planarity : 0.005 0.059 2466 Dihedral : 20.178 158.355 2698 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.13 % Allowed : 20.95 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.20), residues: 1640 helix: 1.20 (0.18), residues: 780 sheet: 0.67 (0.32), residues: 242 loop : -0.56 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 293 HIS 0.005 0.001 HIS A 33 PHE 0.020 0.001 PHE C 246 TYR 0.035 0.002 TYR F 292 ARG 0.010 0.001 ARG D 142 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 689) hydrogen bonds : angle 4.42961 ( 1965) metal coordination : bond 0.01054 ( 16) metal coordination : angle 1.70791 ( 6) covalent geometry : bond 0.00406 (15672) covalent geometry : angle 0.62961 (21678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10657.98 seconds wall clock time: 185 minutes 2.50 seconds (11102.50 seconds total)