Starting phenix.real_space_refine on Fri Nov 15 07:47:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihi_35445/11_2024/8ihi_35445.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihi_35445/11_2024/8ihi_35445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihi_35445/11_2024/8ihi_35445.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihi_35445/11_2024/8ihi_35445.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihi_35445/11_2024/8ihi_35445.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihi_35445/11_2024/8ihi_35445.cif" } resolution = 3.11 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= -0.000 sd= 0.077 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5545 2.51 5 N 1472 2.21 5 O 1591 1.98 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-5513/modules/chem_data/mon_lib" Total number of atoms: 8665 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1695 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 1, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 30 Chain: "S" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1706 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2477 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 91 Chain: "C" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 376 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "R" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2381 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 281} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 1, 'P9X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.68, per 1000 atoms: 0.66 Number of scatterers: 8665 At special positions: 0 Unit cell: (89.1, 117.81, 135.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1591 8.00 N 1472 7.00 C 5545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.86 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.03 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 Links applied NAG-ASN " NAG R 601 " - " ASN R 17 " Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.0 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 15 sheets defined 36.4% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.517A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.718A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.293A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.726A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.523A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.973A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.534A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.545A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.581A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'R' and resid 24 through 55 removed outlier: 3.842A pdb=" N LYS R 28 " --> pdb=" O ASP R 24 " (cutoff:3.500A) Proline residue: R 31 - end of helix removed outlier: 3.520A pdb=" N LEU R 36 " --> pdb=" O PRO R 32 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE R 38 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU R 43 " --> pdb=" O ILE R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 78 removed outlier: 3.548A pdb=" N ILE R 78 " --> pdb=" O PHE R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 89 removed outlier: 3.529A pdb=" N ASN R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 128 removed outlier: 3.863A pdb=" N LEU R 107 " --> pdb=" O MET R 103 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG R 111 " --> pdb=" O LEU R 107 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VAL R 121 " --> pdb=" O PHE R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 139 removed outlier: 3.798A pdb=" N ILE R 139 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 158 Processing helix chain 'R' and resid 159 through 163 Processing helix chain 'R' and resid 187 through 218 removed outlier: 4.064A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) Proline residue: R 200 - end of helix Processing helix chain 'R' and resid 223 through 261 removed outlier: 3.536A pdb=" N PHE R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET R 234 " --> pdb=" O ILE R 230 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 269 through 281 removed outlier: 3.615A pdb=" N LEU R 274 " --> pdb=" O ARG R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 295 removed outlier: 3.827A pdb=" N ASN R 286 " --> pdb=" O PHE R 282 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER R 287 " --> pdb=" O THR R 283 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.683A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'S' and resid 6 through 7 removed outlier: 3.715A pdb=" N SER S 7 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 58 through 60 removed outlier: 3.538A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 45 through 46 removed outlier: 3.582A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 155 through 160 Processing sheet with id=AA6, first strand: chain 'S' and resid 194 through 195 removed outlier: 5.383A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR S 227 " --> pdb=" O THR S 243 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.720A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.738A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.616A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.781A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.815A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.465A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.559A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 10 through 12 removed outlier: 3.962A pdb=" N ILE R 182 " --> pdb=" O CYS R 19 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 169 through 171 removed outlier: 3.584A pdb=" N ILE R 169 " --> pdb=" O LEU R 176 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2784 1.34 - 1.46: 2206 1.46 - 1.58: 3792 1.58 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 8861 Sorted by residual: bond pdb=" C5 P9X R 602 " pdb=" O2 P9X R 602 " ideal model delta sigma weight residual 1.250 1.306 -0.056 2.00e-02 2.50e+03 7.81e+00 bond pdb=" C4 P9X R 602 " pdb=" C5 P9X R 602 " ideal model delta sigma weight residual 1.530 1.476 0.054 2.00e-02 2.50e+03 7.34e+00 bond pdb=" CA LYS R 165 " pdb=" C LYS R 165 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.24e-02 6.50e+03 5.43e+00 bond pdb=" N LYS R 165 " pdb=" CA LYS R 165 " ideal model delta sigma weight residual 1.455 1.432 0.024 1.22e-02 6.72e+03 3.83e+00 bond pdb=" CB PRO S 151 " pdb=" CG PRO S 151 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.40e+00 ... (remaining 8856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 11912 2.16 - 4.33: 106 4.33 - 6.49: 15 6.49 - 8.65: 3 8.65 - 10.81: 2 Bond angle restraints: 12038 Sorted by residual: angle pdb=" CB MET R 167 " pdb=" CG MET R 167 " pdb=" SD MET R 167 " ideal model delta sigma weight residual 112.70 123.51 -10.81 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CA PRO S 151 " pdb=" N PRO S 151 " pdb=" CD PRO S 151 " ideal model delta sigma weight residual 112.00 107.01 4.99 1.40e+00 5.10e-01 1.27e+01 angle pdb=" C ASP R 97 " pdb=" N ILE R 98 " pdb=" CA ILE R 98 " ideal model delta sigma weight residual 120.33 122.69 -2.36 8.00e-01 1.56e+00 8.73e+00 angle pdb=" CA LEU A 283 " pdb=" CB LEU A 283 " pdb=" CG LEU A 283 " ideal model delta sigma weight residual 116.30 125.82 -9.52 3.50e+00 8.16e-02 7.41e+00 angle pdb=" CA LEU R 47 " pdb=" CB LEU R 47 " pdb=" CG LEU R 47 " ideal model delta sigma weight residual 116.30 124.60 -8.30 3.50e+00 8.16e-02 5.62e+00 ... (remaining 12033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4497 17.92 - 35.84: 543 35.84 - 53.77: 138 53.77 - 71.69: 29 71.69 - 89.61: 5 Dihedral angle restraints: 5212 sinusoidal: 1936 harmonic: 3276 Sorted by residual: dihedral pdb=" CB CYS R 100 " pdb=" SG CYS R 100 " pdb=" SG CYS R 177 " pdb=" CB CYS R 177 " ideal model delta sinusoidal sigma weight residual -86.00 -138.25 52.25 1 1.00e+01 1.00e-02 3.72e+01 dihedral pdb=" CA PHE R 117 " pdb=" C PHE R 117 " pdb=" N LEU R 118 " pdb=" CA LEU R 118 " ideal model delta harmonic sigma weight residual 180.00 155.66 24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CB CYS R 19 " pdb=" SG CYS R 19 " pdb=" SG CYS R 266 " pdb=" CB CYS R 266 " ideal model delta sinusoidal sigma weight residual -86.00 -55.41 -30.59 1 1.00e+01 1.00e-02 1.34e+01 ... (remaining 5209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 804 0.027 - 0.054: 360 0.054 - 0.080: 120 0.080 - 0.107: 67 0.107 - 0.134: 27 Chirality restraints: 1378 Sorted by residual: chirality pdb=" CA VAL S 147 " pdb=" N VAL S 147 " pdb=" C VAL S 147 " pdb=" CB VAL S 147 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ASP S 90 " pdb=" N ASP S 90 " pdb=" C ASP S 90 " pdb=" CB ASP S 90 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 1375 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR S 150 " -0.082 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO S 151 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO S 151 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO S 151 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 31 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO R 32 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO R 32 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 32 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 52 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO C 53 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 53 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 53 " -0.027 5.00e-02 4.00e+02 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1386 2.76 - 3.29: 7952 3.29 - 3.83: 13782 3.83 - 4.36: 16840 4.36 - 4.90: 29890 Nonbonded interactions: 69850 Sorted by model distance: nonbonded pdb=" O LEU R 280 " pdb=" OG1 THR R 283 " model vdw 2.221 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.239 3.040 nonbonded pdb=" O GLY R 262 " pdb=" OH TYR R 269 " model vdw 2.255 3.040 nonbonded pdb=" O LEU R 257 " pdb=" OG SER R 261 " model vdw 2.264 3.040 ... (remaining 69845 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.840 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.800 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 : 0.003 0.077 8861 Z= 0.176 Angle : 0.532 10.813 12038 Z= 0.273 Chirality : 0.040 0.134 1378 Planarity : 0.005 0.122 1522 Dihedral : 16.775 89.608 3082 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.22 % Allowed : 25.98 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.25), residues: 1115 helix: 0.14 (0.28), residues: 352 sheet: -0.02 (0.31), residues: 269 loop : -0.92 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 152 HIS 0.002 0.000 HIS R 189 PHE 0.026 0.001 PHE R 38 TYR 0.021 0.001 TYR S 235 ARG 0.005 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 144 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: S 69 THR cc_start: 0.8404 (t) cc_final: 0.8071 (m) REVERT: S 87 ARG cc_start: 0.7915 (mtt180) cc_final: 0.7526 (mtm-85) REVERT: C 42 GLU cc_start: 0.7684 (mp0) cc_final: 0.7262 (mp0) outliers start: 2 outliers final: 2 residues processed: 145 average time/residue: 0.2369 time to fit residues: 47.0200 Evaluate side-chains 136 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain R residue 272 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8861 Z= 0.330 Angle : 0.615 7.902 12038 Z= 0.324 Chirality : 0.044 0.185 1378 Planarity : 0.005 0.082 1522 Dihedral : 5.356 59.881 1259 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.79 % Allowed : 24.30 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.09 (0.25), residues: 1115 helix: 1.07 (0.27), residues: 360 sheet: 0.04 (0.32), residues: 262 loop : -0.91 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 47 HIS 0.004 0.001 HIS A 188 PHE 0.015 0.002 PHE R 232 TYR 0.024 0.002 TYR S 235 ARG 0.005 0.001 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.802 Fit side-chains REVERT: A 197 LYS cc_start: 0.8829 (mmtm) cc_final: 0.8440 (mtmt) REVERT: A 244 HIS cc_start: 0.7401 (m90) cc_final: 0.7084 (m90) REVERT: S 67 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7712 (mtm180) REVERT: S 202 ARG cc_start: 0.8552 (mtm110) cc_final: 0.8321 (mtm110) REVERT: B 234 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.8757 (m-80) outliers start: 25 outliers final: 15 residues processed: 155 average time/residue: 0.2363 time to fit residues: 49.3307 Evaluate side-chains 138 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain R residue 284 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 89 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 34 optimal weight: 0.0980 chunk 80 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8861 Z= 0.137 Angle : 0.511 9.985 12038 Z= 0.265 Chirality : 0.041 0.160 1378 Planarity : 0.004 0.065 1522 Dihedral : 4.518 45.090 1256 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.90 % Allowed : 25.31 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.25), residues: 1115 helix: 1.81 (0.27), residues: 360 sheet: 0.13 (0.32), residues: 269 loop : -0.91 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.003 0.001 HIS A 188 PHE 0.017 0.001 PHE R 38 TYR 0.020 0.001 TYR S 235 ARG 0.003 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.818 Fit side-chains REVERT: A 197 LYS cc_start: 0.8850 (mmtm) cc_final: 0.8487 (mtmt) REVERT: S 202 ARG cc_start: 0.8493 (mtm110) cc_final: 0.8247 (mtm110) REVERT: B 234 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8700 (m-80) REVERT: R 14 ASP cc_start: 0.7243 (m-30) cc_final: 0.6576 (t0) REVERT: R 165 LYS cc_start: 0.7190 (mmtt) cc_final: 0.6607 (mtmt) REVERT: R 167 MET cc_start: 0.6045 (tpp) cc_final: 0.5789 (tpp) REVERT: R 217 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7292 (tt0) REVERT: R 285 MET cc_start: 0.7481 (tpt) cc_final: 0.7270 (tpt) outliers start: 26 outliers final: 12 residues processed: 162 average time/residue: 0.2434 time to fit residues: 52.7842 Evaluate side-chains 142 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 217 GLN Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 263 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8861 Z= 0.203 Angle : 0.522 6.853 12038 Z= 0.273 Chirality : 0.042 0.146 1378 Planarity : 0.004 0.056 1522 Dihedral : 4.319 26.252 1256 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.01 % Allowed : 25.98 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.40 (0.26), residues: 1115 helix: 1.95 (0.28), residues: 360 sheet: 0.15 (0.32), residues: 271 loop : -0.96 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.023 0.001 PHE R 38 TYR 0.024 0.001 TYR S 235 ARG 0.003 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.953 Fit side-chains REVERT: S 202 ARG cc_start: 0.8461 (mtm110) cc_final: 0.8210 (mtm110) REVERT: B 234 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8759 (m-80) REVERT: R 14 ASP cc_start: 0.7308 (m-30) cc_final: 0.6529 (t0) REVERT: R 150 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8019 (tt) REVERT: R 165 LYS cc_start: 0.7207 (mmtt) cc_final: 0.6613 (mtmt) REVERT: R 190 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6618 (mm-30) REVERT: R 217 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7293 (tt0) REVERT: R 285 MET cc_start: 0.7617 (tpt) cc_final: 0.7283 (tpt) outliers start: 27 outliers final: 14 residues processed: 153 average time/residue: 0.2078 time to fit residues: 43.4874 Evaluate side-chains 142 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 190 GLU Chi-restraints excluded: chain R residue 217 GLN Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 284 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.5980 chunk 60 optimal weight: 0.0770 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8861 Z= 0.143 Angle : 0.506 7.152 12038 Z= 0.261 Chirality : 0.041 0.146 1378 Planarity : 0.004 0.049 1522 Dihedral : 3.990 20.614 1256 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.90 % Allowed : 26.53 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.26), residues: 1115 helix: 2.18 (0.28), residues: 361 sheet: 0.15 (0.31), residues: 281 loop : -0.86 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.002 0.000 HIS A 188 PHE 0.024 0.001 PHE R 38 TYR 0.019 0.001 TYR S 235 ARG 0.003 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.987 Fit side-chains REVERT: A 197 LYS cc_start: 0.8795 (mmtm) cc_final: 0.8464 (mtmt) REVERT: B 234 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8702 (m-80) REVERT: R 14 ASP cc_start: 0.7269 (m-30) cc_final: 0.6496 (t0) REVERT: R 165 LYS cc_start: 0.7270 (mmtt) cc_final: 0.6675 (mtmt) REVERT: R 167 MET cc_start: 0.5652 (tpp) cc_final: 0.5175 (tpp) REVERT: R 217 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7333 (tt0) REVERT: R 285 MET cc_start: 0.7726 (tpt) cc_final: 0.7497 (tpt) outliers start: 26 outliers final: 16 residues processed: 150 average time/residue: 0.2196 time to fit residues: 45.3167 Evaluate side-chains 145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 217 GLN Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 263 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8861 Z= 0.222 Angle : 0.532 7.012 12038 Z= 0.276 Chirality : 0.042 0.168 1378 Planarity : 0.004 0.052 1522 Dihedral : 4.153 19.792 1256 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.57 % Allowed : 25.98 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.26), residues: 1115 helix: 2.10 (0.28), residues: 361 sheet: 0.20 (0.31), residues: 270 loop : -0.98 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.002 0.001 HIS A 188 PHE 0.025 0.001 PHE R 38 TYR 0.021 0.001 TYR S 235 ARG 0.003 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 1.103 Fit side-chains REVERT: A 197 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8515 (mtmt) REVERT: B 234 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8697 (m-80) REVERT: C 42 GLU cc_start: 0.7279 (mp0) cc_final: 0.6537 (mp0) REVERT: R 14 ASP cc_start: 0.7265 (m-30) cc_final: 0.6455 (t0) REVERT: R 165 LYS cc_start: 0.7329 (mmtt) cc_final: 0.6710 (mtmt) REVERT: R 190 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6669 (mm-30) REVERT: R 217 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7425 (tt0) REVERT: R 285 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7475 (tpt) outliers start: 32 outliers final: 19 residues processed: 157 average time/residue: 0.2231 time to fit residues: 47.9113 Evaluate side-chains 151 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 190 GLU Chi-restraints excluded: chain R residue 217 GLN Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain R residue 285 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 0.0270 chunk 77 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 322 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8861 Z= 0.163 Angle : 0.519 7.029 12038 Z= 0.267 Chirality : 0.041 0.163 1378 Planarity : 0.004 0.046 1522 Dihedral : 4.016 19.079 1256 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.46 % Allowed : 26.76 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.26), residues: 1115 helix: 2.21 (0.28), residues: 361 sheet: 0.27 (0.32), residues: 269 loop : -0.93 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 47 HIS 0.002 0.000 HIS C 44 PHE 0.026 0.001 PHE R 38 TYR 0.020 0.001 TYR S 235 ARG 0.003 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.974 Fit side-chains REVERT: A 197 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8507 (mtmt) REVERT: S 18 ARG cc_start: 0.7680 (tpp80) cc_final: 0.7212 (tpt170) REVERT: B 137 ARG cc_start: 0.8083 (tpt90) cc_final: 0.7652 (tpp-160) REVERT: B 234 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8723 (m-80) REVERT: C 42 GLU cc_start: 0.7291 (mp0) cc_final: 0.6561 (mp0) REVERT: R 14 ASP cc_start: 0.7245 (m-30) cc_final: 0.6418 (t0) REVERT: R 165 LYS cc_start: 0.7343 (mmtt) cc_final: 0.6738 (mtmt) REVERT: R 190 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6679 (mm-30) REVERT: R 217 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7411 (tt0) REVERT: R 285 MET cc_start: 0.7852 (tpt) cc_final: 0.7610 (tpt) outliers start: 31 outliers final: 18 residues processed: 152 average time/residue: 0.2196 time to fit residues: 45.6363 Evaluate side-chains 150 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 190 GLU Chi-restraints excluded: chain R residue 217 GLN Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 263 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.0370 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 322 HIS S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8861 Z= 0.144 Angle : 0.512 7.181 12038 Z= 0.262 Chirality : 0.041 0.161 1378 Planarity : 0.004 0.051 1522 Dihedral : 3.948 18.038 1256 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.79 % Allowed : 27.54 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.67 (0.26), residues: 1115 helix: 2.31 (0.28), residues: 360 sheet: 0.32 (0.32), residues: 266 loop : -0.91 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.002 0.000 HIS C 44 PHE 0.026 0.001 PHE R 38 TYR 0.023 0.001 TYR S 235 ARG 0.003 0.000 ARG S 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.972 Fit side-chains REVERT: S 18 ARG cc_start: 0.7673 (tpp80) cc_final: 0.7206 (tpt170) REVERT: B 137 ARG cc_start: 0.8068 (tpt90) cc_final: 0.7695 (tpp-160) REVERT: B 234 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8698 (m-80) REVERT: C 42 GLU cc_start: 0.7288 (mp0) cc_final: 0.6558 (mp0) REVERT: R 14 ASP cc_start: 0.7272 (m-30) cc_final: 0.6383 (t0) REVERT: R 165 LYS cc_start: 0.7315 (mmtt) cc_final: 0.6746 (mtmt) REVERT: R 190 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6558 (mp0) REVERT: R 285 MET cc_start: 0.7824 (tpt) cc_final: 0.7621 (tpt) outliers start: 25 outliers final: 18 residues processed: 146 average time/residue: 0.2234 time to fit residues: 44.5798 Evaluate side-chains 147 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 190 GLU Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 263 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS S 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8861 Z= 0.371 Angle : 0.616 7.618 12038 Z= 0.320 Chirality : 0.046 0.187 1378 Planarity : 0.004 0.048 1522 Dihedral : 4.670 21.365 1256 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.90 % Allowed : 27.54 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.26), residues: 1115 helix: 1.88 (0.28), residues: 361 sheet: 0.18 (0.32), residues: 268 loop : -1.02 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 47 HIS 0.004 0.001 HIS B 91 PHE 0.027 0.002 PHE R 38 TYR 0.032 0.002 TYR S 235 ARG 0.006 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 1.049 Fit side-chains REVERT: S 18 ARG cc_start: 0.7723 (tpp80) cc_final: 0.7268 (tpt170) REVERT: B 137 ARG cc_start: 0.8111 (tpt90) cc_final: 0.7742 (tpp-160) REVERT: B 234 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8795 (m-80) REVERT: C 42 GLU cc_start: 0.7211 (mp0) cc_final: 0.6395 (mp0) REVERT: R 14 ASP cc_start: 0.7289 (m-30) cc_final: 0.6322 (t0) REVERT: R 165 LYS cc_start: 0.7406 (mmtt) cc_final: 0.6872 (mtmt) REVERT: R 190 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6614 (mm-30) REVERT: R 217 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7423 (tt0) outliers start: 26 outliers final: 19 residues processed: 148 average time/residue: 0.2308 time to fit residues: 46.4308 Evaluate side-chains 145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 190 GLU Chi-restraints excluded: chain R residue 217 GLN Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 268 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8861 Z= 0.201 Angle : 0.567 11.558 12038 Z= 0.288 Chirality : 0.042 0.171 1378 Planarity : 0.004 0.048 1522 Dihedral : 4.320 20.346 1256 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.56 % Allowed : 27.76 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.26), residues: 1115 helix: 2.04 (0.28), residues: 360 sheet: 0.20 (0.32), residues: 267 loop : -1.01 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 188 HIS 0.002 0.001 HIS B 225 PHE 0.027 0.001 PHE R 38 TYR 0.026 0.001 TYR S 235 ARG 0.012 0.000 ARG C 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.943 Fit side-chains REVERT: S 18 ARG cc_start: 0.7687 (tpp80) cc_final: 0.7218 (tpt170) REVERT: B 234 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8710 (m-80) REVERT: C 42 GLU cc_start: 0.7180 (mp0) cc_final: 0.6375 (mp0) REVERT: R 14 ASP cc_start: 0.7304 (m-30) cc_final: 0.6269 (t0) REVERT: R 16 LYS cc_start: 0.6482 (mtmt) cc_final: 0.6127 (mtmm) REVERT: R 165 LYS cc_start: 0.7305 (mmtt) cc_final: 0.6819 (mtmt) REVERT: R 190 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6648 (mm-30) REVERT: R 217 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7428 (tt0) outliers start: 23 outliers final: 18 residues processed: 144 average time/residue: 0.2187 time to fit residues: 43.1269 Evaluate side-chains 149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 190 GLU Chi-restraints excluded: chain R residue 217 GLN Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 268 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 76 optimal weight: 40.0000 chunk 4 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.151153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.117085 restraints weight = 11325.953| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.49 r_work: 0.3308 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8861 Z= 0.280 Angle : 0.588 8.011 12038 Z= 0.302 Chirality : 0.044 0.170 1378 Planarity : 0.004 0.049 1522 Dihedral : 4.498 20.952 1256 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.01 % Allowed : 27.09 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.26), residues: 1115 helix: 1.97 (0.28), residues: 361 sheet: 0.17 (0.31), residues: 268 loop : -1.05 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 47 HIS 0.003 0.001 HIS B 91 PHE 0.027 0.002 PHE R 38 TYR 0.027 0.002 TYR S 235 ARG 0.004 0.000 ARG R 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2086.40 seconds wall clock time: 38 minutes 53.49 seconds (2333.49 seconds total)