Starting phenix.real_space_refine on Sat Aug 23 01:38:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6j_36006/08_2025/8j6j_36006.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6j_36006/08_2025/8j6j_36006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j6j_36006/08_2025/8j6j_36006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6j_36006/08_2025/8j6j_36006.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j6j_36006/08_2025/8j6j_36006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6j_36006/08_2025/8j6j_36006.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 68 5.16 5 Cl 1 4.86 5 C 5747 2.51 5 N 1537 2.21 5 O 1626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8979 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1731 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2560 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "G" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 404 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1736 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "R" Number of atoms: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2531 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 296} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'OKL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.49, per 1000 atoms: 0.28 Number of scatterers: 8979 At special positions: 0 Unit cell: (93.936, 112.064, 139.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 68 16.00 O 1626 8.00 N 1537 7.00 C 5747 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: 0.89 Conformation dependent library (CDL) restraints added in 324.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 37.7% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.748A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 52 removed outlier: 3.859A pdb=" N LYS A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 205 removed outlier: 3.578A pdb=" N ARG A 205 " --> pdb=" O GLY A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.809A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.556A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.621A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.674A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.573A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 36 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 220 through 224 Processing helix chain 'R' and resid 5 through 10 Processing helix chain 'R' and resid 25 through 53 removed outlier: 3.599A pdb=" N VAL R 29 " --> pdb=" O PHE R 25 " (cutoff:3.500A) Proline residue: R 31 - end of helix removed outlier: 3.529A pdb=" N CYS R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 89 Proline residue: R 81 - end of helix Processing helix chain 'R' and resid 96 through 131 Processing helix chain 'R' and resid 131 through 136 removed outlier: 3.898A pdb=" N LEU R 136 " --> pdb=" O PRO R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 139 No H-bonds generated for 'chain 'R' and resid 137 through 139' Processing helix chain 'R' and resid 140 through 160 Processing helix chain 'R' and resid 161 through 163 No H-bonds generated for 'chain 'R' and resid 161 through 163' Processing helix chain 'R' and resid 187 through 219 removed outlier: 3.558A pdb=" N ALA R 191 " --> pdb=" O GLN R 187 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 200 - end of helix removed outlier: 3.694A pdb=" N ARG R 218 " --> pdb=" O SER R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 257 removed outlier: 4.007A pdb=" N LYS R 227 " --> pdb=" O HIS R 223 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 269 through 295 removed outlier: 3.849A pdb=" N ASP R 273 " --> pdb=" O TYR R 269 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing helix chain 'R' and resid 296 through 298 No H-bonds generated for 'chain 'R' and resid 296 through 298' Processing helix chain 'R' and resid 299 through 308 removed outlier: 3.937A pdb=" N ASN R 303 " --> pdb=" O PRO R 299 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.824A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.892A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.669A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.502A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.676A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.791A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.012A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.539A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.028A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.958A pdb=" N VAL H 155 " --> pdb=" O ILE H 216 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE H 216 " --> pdb=" O VAL H 155 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE H 212 " --> pdb=" O CYS H 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.682A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY H 225 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE H 189 " --> pdb=" O TRP H 176 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 170 through 171 427 hydrogen bonds defined for protein. 1194 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: 1.45 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1429 1.31 - 1.44: 2591 1.44 - 1.56: 5062 1.56 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 9182 Sorted by residual: bond pdb=" C13 OKL R 501 " pdb=" N06 OKL R 501 " ideal model delta sigma weight residual 1.366 1.503 -0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C10 OKL R 501 " pdb=" C12 OKL R 501 " ideal model delta sigma weight residual 1.426 1.547 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" C15 OKL R 501 " pdb="CL17 OKL R 501 " ideal model delta sigma weight residual 1.692 1.782 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C07 OKL R 501 " pdb=" N06 OKL R 501 " ideal model delta sigma weight residual 1.374 1.462 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C07 OKL R 501 " pdb=" N09 OKL R 501 " ideal model delta sigma weight residual 1.384 1.442 -0.058 2.00e-02 2.50e+03 8.31e+00 ... (remaining 9177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 12257 2.24 - 4.49: 163 4.49 - 6.73: 14 6.73 - 8.97: 4 8.97 - 11.22: 3 Bond angle restraints: 12441 Sorted by residual: angle pdb=" C HIS R 4 " pdb=" CA HIS R 4 " pdb=" CB HIS R 4 " ideal model delta sigma weight residual 115.89 110.74 5.15 1.32e+00 5.74e-01 1.52e+01 angle pdb=" N ASP R 14 " pdb=" CA ASP R 14 " pdb=" C ASP R 14 " ideal model delta sigma weight residual 113.18 108.41 4.77 1.33e+00 5.65e-01 1.29e+01 angle pdb=" C12 OKL R 501 " pdb=" C10 OKL R 501 " pdb=" N09 OKL R 501 " ideal model delta sigma weight residual 109.84 119.86 -10.02 3.00e+00 1.11e-01 1.12e+01 angle pdb=" C07 OKL R 501 " pdb=" N09 OKL R 501 " pdb=" C10 OKL R 501 " ideal model delta sigma weight residual 129.77 119.76 10.01 3.00e+00 1.11e-01 1.11e+01 angle pdb=" CA LEU R 43 " pdb=" CB LEU R 43 " pdb=" CG LEU R 43 " ideal model delta sigma weight residual 116.30 127.52 -11.22 3.50e+00 8.16e-02 1.03e+01 ... (remaining 12436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 4788 17.35 - 34.71: 459 34.71 - 52.06: 134 52.06 - 69.42: 10 69.42 - 86.77: 5 Dihedral angle restraints: 5396 sinusoidal: 2060 harmonic: 3336 Sorted by residual: dihedral pdb=" CA MET R 167 " pdb=" C MET R 167 " pdb=" N PRO R 168 " pdb=" CA PRO R 168 " ideal model delta harmonic sigma weight residual -180.00 -162.27 -17.73 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ASP B 154 " pdb=" CB ASP B 154 " pdb=" CG ASP B 154 " pdb=" OD1 ASP B 154 " ideal model delta sinusoidal sigma weight residual -30.00 -88.24 58.24 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CG ARG A 205 " pdb=" CD ARG A 205 " pdb=" NE ARG A 205 " pdb=" CZ ARG A 205 " ideal model delta sinusoidal sigma weight residual -180.00 -135.07 -44.93 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 5393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 976 0.032 - 0.064: 278 0.064 - 0.096: 97 0.096 - 0.128: 51 0.128 - 0.160: 3 Chirality restraints: 1405 Sorted by residual: chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CG LEU A 232 " pdb=" CB LEU A 232 " pdb=" CD1 LEU A 232 " pdb=" CD2 LEU A 232 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA ILE G 28 " pdb=" N ILE G 28 " pdb=" C ILE G 28 " pdb=" CB ILE G 28 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 1402 not shown) Planarity restraints: 1567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP R 290 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.64e+00 pdb=" N PRO R 291 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO R 291 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO R 291 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO B 39 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 80 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO R 81 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO R 81 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 81 " 0.022 5.00e-02 4.00e+02 ... (remaining 1564 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 151 2.66 - 3.22: 8663 3.22 - 3.78: 13703 3.78 - 4.34: 18802 4.34 - 4.90: 31338 Nonbonded interactions: 72657 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.098 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.163 3.040 nonbonded pdb=" O PHE R 276 " pdb=" OG1 THR R 279 " model vdw 2.165 3.040 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.177 3.120 nonbonded pdb=" O THR H 63 " pdb=" NH2 ARG H 67 " model vdw 2.178 3.120 ... (remaining 72652 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: 1.030 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.270 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6077 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 0.137 9182 Z= 0.176 Angle : 0.617 11.216 12441 Z= 0.317 Chirality : 0.039 0.160 1405 Planarity : 0.004 0.069 1567 Dihedral : 14.729 86.772 3238 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.21 % Allowed : 26.17 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.26), residues: 1135 helix: 2.43 (0.28), residues: 378 sheet: 1.18 (0.32), residues: 268 loop : 0.09 (0.30), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 208 TYR 0.017 0.001 TYR H 190 PHE 0.007 0.001 PHE H 239 TRP 0.008 0.001 TRP R 59 HIS 0.004 0.000 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9182) covalent geometry : angle 0.61676 (12441) hydrogen bonds : bond 0.18735 ( 427) hydrogen bonds : angle 6.56917 ( 1194) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.6122 (ttm110) cc_final: 0.5877 (mpt90) REVERT: A 198 MET cc_start: 0.8225 (ttp) cc_final: 0.7958 (ttp) REVERT: A 247 MET cc_start: 0.7309 (mtp) cc_final: 0.7087 (mtp) REVERT: A 248 LYS cc_start: 0.7329 (ttmm) cc_final: 0.7058 (pttp) REVERT: A 275 GLU cc_start: 0.7257 (mm-30) cc_final: 0.7035 (mt-10) REVERT: A 276 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6793 (mp0) REVERT: A 305 CYS cc_start: 0.6879 (m) cc_final: 0.6678 (p) REVERT: A 346 ASN cc_start: 0.6160 (m-40) cc_final: 0.5893 (m-40) REVERT: B 45 MET cc_start: 0.8288 (mtt) cc_final: 0.7999 (mmm) REVERT: B 46 ARG cc_start: 0.7048 (mmm-85) cc_final: 0.6577 (mmp80) REVERT: B 96 ARG cc_start: 0.6151 (tpt170) cc_final: 0.5544 (tpp80) REVERT: B 146 LEU cc_start: 0.7343 (tp) cc_final: 0.6995 (mm) REVERT: B 195 ASP cc_start: 0.7199 (p0) cc_final: 0.6951 (p0) REVERT: B 325 MET cc_start: 0.7883 (tpt) cc_final: 0.7673 (tpp) REVERT: G 21 MET cc_start: 0.1974 (mtp) cc_final: 0.1563 (pmm) REVERT: G 38 MET cc_start: 0.1958 (mpm) cc_final: 0.0488 (mpm) REVERT: H 55 SER cc_start: 0.6386 (m) cc_final: 0.6118 (m) REVERT: H 234 GLU cc_start: 0.5905 (mt-10) cc_final: 0.5049 (mm-30) REVERT: R 43 LEU cc_start: 0.5118 (pp) cc_final: 0.4691 (tt) REVERT: R 50 TRP cc_start: 0.3153 (m-10) cc_final: 0.2559 (m-10) REVERT: R 234 MET cc_start: 0.6108 (mmt) cc_final: 0.5452 (ptp) REVERT: R 253 ARG cc_start: 0.4945 (ttt180) cc_final: 0.4740 (tpt-90) outliers start: 2 outliers final: 0 residues processed: 162 average time/residue: 0.5305 time to fit residues: 91.9917 Evaluate side-chains 116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 142 HIS B 266 HIS H 171 ASN R 112 GLN R 161 HIS R 219 GLN ** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.225646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.171489 restraints weight = 9320.810| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 1.94 r_work: 0.3753 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9182 Z= 0.196 Angle : 0.699 8.872 12441 Z= 0.363 Chirality : 0.046 0.155 1405 Planarity : 0.005 0.064 1567 Dihedral : 4.787 21.278 1241 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.53 % Allowed : 20.13 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.26), residues: 1135 helix: 1.78 (0.26), residues: 391 sheet: 0.89 (0.30), residues: 298 loop : -0.33 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 89 TYR 0.029 0.003 TYR B 85 PHE 0.022 0.002 PHE R 232 TRP 0.016 0.002 TRP B 169 HIS 0.012 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 9182) covalent geometry : angle 0.69873 (12441) hydrogen bonds : bond 0.04960 ( 427) hydrogen bonds : angle 4.91873 ( 1194) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 121 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.6778 (mmtt) cc_final: 0.6525 (ptpt) REVERT: A 17 LYS cc_start: 0.7438 (mttt) cc_final: 0.7178 (mmtt) REVERT: A 209 LYS cc_start: 0.8227 (ttmm) cc_final: 0.8021 (ttmm) REVERT: A 247 MET cc_start: 0.8192 (mtp) cc_final: 0.7894 (mtp) REVERT: A 309 ASP cc_start: 0.7585 (m-30) cc_final: 0.7243 (t70) REVERT: A 313 ARG cc_start: 0.6207 (OUTLIER) cc_final: 0.5999 (ptp-170) REVERT: A 331 ASN cc_start: 0.7619 (t0) cc_final: 0.6743 (m-40) REVERT: B 96 ARG cc_start: 0.7576 (tpt170) cc_final: 0.7374 (mtt180) REVERT: B 154 ASP cc_start: 0.7431 (m-30) cc_final: 0.7230 (m-30) REVERT: B 217 MET cc_start: 0.8191 (pmt) cc_final: 0.7837 (pmm) REVERT: G 21 MET cc_start: 0.1972 (mtp) cc_final: 0.1468 (pmm) REVERT: G 38 MET cc_start: 0.2629 (mpm) cc_final: 0.0376 (mpm) REVERT: G 50 LEU cc_start: 0.2687 (OUTLIER) cc_final: 0.2328 (tt) REVERT: H 30 SER cc_start: 0.7128 (p) cc_final: 0.6861 (p) REVERT: H 55 SER cc_start: 0.6637 (OUTLIER) cc_final: 0.6308 (m) REVERT: H 71 SER cc_start: 0.5821 (p) cc_final: 0.5347 (t) REVERT: H 82 GLN cc_start: 0.6420 (tt0) cc_final: 0.6113 (mm-40) REVERT: H 96 CYS cc_start: 0.7541 (OUTLIER) cc_final: 0.6932 (p) REVERT: H 234 GLU cc_start: 0.6645 (mt-10) cc_final: 0.6376 (mt-10) REVERT: R 164 LYS cc_start: 0.5634 (mptp) cc_final: 0.4948 (mppt) REVERT: R 183 CYS cc_start: 0.8112 (t) cc_final: 0.7831 (m) REVERT: R 234 MET cc_start: 0.6246 (mmt) cc_final: 0.5732 (mtp) REVERT: R 253 ARG cc_start: 0.5000 (ttt180) cc_final: 0.4669 (tpt-90) REVERT: R 270 ARG cc_start: 0.6346 (OUTLIER) cc_final: 0.6141 (ttt-90) REVERT: R 288 MET cc_start: 0.5787 (OUTLIER) cc_final: 0.5279 (tmm) outliers start: 53 outliers final: 14 residues processed: 162 average time/residue: 0.5288 time to fit residues: 92.2138 Evaluate side-chains 121 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 270 ARG Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 288 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 72 optimal weight: 50.0000 chunk 39 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN R 161 HIS ** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 286 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.226099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.3928 r_free = 0.3928 target = 0.166911 restraints weight = 9291.062| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.14 r_work: 0.3744 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9182 Z= 0.133 Angle : 0.583 7.040 12441 Z= 0.301 Chirality : 0.042 0.146 1405 Planarity : 0.004 0.050 1567 Dihedral : 4.449 20.640 1241 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.90 % Allowed : 20.86 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.26), residues: 1135 helix: 1.82 (0.26), residues: 397 sheet: 0.84 (0.31), residues: 286 loop : -0.49 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 49 TYR 0.013 0.002 TYR B 85 PHE 0.017 0.002 PHE R 232 TRP 0.013 0.001 TRP R 59 HIS 0.009 0.001 HIS R 161 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9182) covalent geometry : angle 0.58253 (12441) hydrogen bonds : bond 0.04218 ( 427) hydrogen bonds : angle 4.62404 ( 1194) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 110 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 SER cc_start: 0.6953 (m) cc_final: 0.6600 (t) REVERT: A 309 ASP cc_start: 0.7722 (m-30) cc_final: 0.7412 (t70) REVERT: A 331 ASN cc_start: 0.7695 (t0) cc_final: 0.6954 (m-40) REVERT: B 45 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8244 (mtm) REVERT: B 96 ARG cc_start: 0.7641 (tpt170) cc_final: 0.7320 (mtt180) REVERT: B 217 MET cc_start: 0.8270 (pmt) cc_final: 0.7884 (pmm) REVERT: B 325 MET cc_start: 0.8441 (tpp) cc_final: 0.8197 (mmm) REVERT: G 21 MET cc_start: 0.1967 (mtp) cc_final: 0.1369 (pmm) REVERT: G 38 MET cc_start: 0.2687 (mpm) cc_final: 0.0345 (mpm) REVERT: G 50 LEU cc_start: 0.2662 (OUTLIER) cc_final: 0.2375 (tt) REVERT: H 30 SER cc_start: 0.7203 (p) cc_final: 0.6947 (p) REVERT: H 55 SER cc_start: 0.6570 (m) cc_final: 0.6260 (m) REVERT: H 71 SER cc_start: 0.6129 (p) cc_final: 0.5681 (t) REVERT: H 82 GLN cc_start: 0.6493 (tt0) cc_final: 0.6197 (mm-40) REVERT: H 93 MET cc_start: 0.7273 (ttt) cc_final: 0.6216 (tpp) REVERT: H 96 CYS cc_start: 0.7507 (OUTLIER) cc_final: 0.6976 (p) REVERT: H 142 GLN cc_start: 0.3224 (OUTLIER) cc_final: 0.2886 (mm110) REVERT: H 179 GLN cc_start: 0.6481 (OUTLIER) cc_final: 0.6233 (tt0) REVERT: H 234 GLU cc_start: 0.6754 (mt-10) cc_final: 0.6507 (mt-10) REVERT: R 164 LYS cc_start: 0.5478 (mptp) cc_final: 0.4914 (mppt) REVERT: R 170 GLN cc_start: 0.4174 (OUTLIER) cc_final: 0.3113 (tm130) REVERT: R 234 MET cc_start: 0.6360 (mmt) cc_final: 0.5870 (mtp) REVERT: R 253 ARG cc_start: 0.5000 (ttt180) cc_final: 0.4776 (tpt-90) REVERT: R 270 ARG cc_start: 0.6240 (OUTLIER) cc_final: 0.6004 (ttt-90) outliers start: 47 outliers final: 16 residues processed: 149 average time/residue: 0.5555 time to fit residues: 88.8583 Evaluate side-chains 124 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 142 GLN Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 179 GLN Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 170 GLN Chi-restraints excluded: chain R residue 217 GLN Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 270 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 75 GLN R 161 HIS ** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.220935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.3936 r_free = 0.3936 target = 0.165010 restraints weight = 9334.400| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.61 r_work: 0.3682 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9182 Z= 0.171 Angle : 0.625 9.058 12441 Z= 0.325 Chirality : 0.044 0.149 1405 Planarity : 0.004 0.050 1567 Dihedral : 4.829 23.553 1241 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.01 % Allowed : 20.23 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.25), residues: 1135 helix: 1.67 (0.26), residues: 393 sheet: 0.82 (0.30), residues: 282 loop : -0.66 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 218 TYR 0.015 0.002 TYR B 85 PHE 0.021 0.002 PHE R 21 TRP 0.012 0.002 TRP B 99 HIS 0.008 0.001 HIS R 161 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9182) covalent geometry : angle 0.62464 (12441) hydrogen bonds : bond 0.04603 ( 427) hydrogen bonds : angle 4.75627 ( 1194) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 111 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7257 (ttt90) REVERT: A 281 SER cc_start: 0.6951 (m) cc_final: 0.6590 (t) REVERT: A 309 ASP cc_start: 0.7625 (m-30) cc_final: 0.7335 (t70) REVERT: A 313 ARG cc_start: 0.6307 (OUTLIER) cc_final: 0.5945 (mtm180) REVERT: A 331 ASN cc_start: 0.7671 (t0) cc_final: 0.7227 (m110) REVERT: B 96 ARG cc_start: 0.7695 (tpt170) cc_final: 0.7373 (mtt180) REVERT: B 217 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7900 (pmm) REVERT: B 294 CYS cc_start: 0.7421 (OUTLIER) cc_final: 0.7168 (m) REVERT: G 21 MET cc_start: 0.1870 (mtp) cc_final: 0.1280 (pmm) REVERT: G 38 MET cc_start: 0.2510 (mpm) cc_final: 0.2192 (mpm) REVERT: G 50 LEU cc_start: 0.2564 (OUTLIER) cc_final: 0.2334 (tt) REVERT: H 30 SER cc_start: 0.7424 (p) cc_final: 0.7165 (p) REVERT: H 55 SER cc_start: 0.6628 (m) cc_final: 0.6366 (m) REVERT: H 82 GLN cc_start: 0.6476 (tt0) cc_final: 0.6137 (mm-40) REVERT: H 93 MET cc_start: 0.7479 (ttt) cc_final: 0.6674 (tpp) REVERT: H 96 CYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7065 (p) REVERT: H 98 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7424 (ptt-90) REVERT: H 179 GLN cc_start: 0.6595 (OUTLIER) cc_final: 0.6276 (tt0) REVERT: H 234 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6684 (mt-10) REVERT: R 1 MET cc_start: 0.2562 (mtm) cc_final: 0.1677 (tpt) REVERT: R 47 LEU cc_start: 0.2915 (pp) cc_final: 0.2294 (tp) REVERT: R 91 TRP cc_start: 0.5491 (OUTLIER) cc_final: 0.3942 (m100) REVERT: R 164 LYS cc_start: 0.5326 (mptp) cc_final: 0.4724 (mppt) REVERT: R 170 GLN cc_start: 0.4318 (OUTLIER) cc_final: 0.3243 (tm130) REVERT: R 234 MET cc_start: 0.6541 (mmt) cc_final: 0.6021 (mtm) REVERT: R 253 ARG cc_start: 0.5015 (ttt180) cc_final: 0.4640 (tpt-90) REVERT: R 288 MET cc_start: 0.5606 (OUTLIER) cc_final: 0.5133 (tmm) outliers start: 48 outliers final: 19 residues processed: 146 average time/residue: 0.5564 time to fit residues: 87.3868 Evaluate side-chains 134 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 179 GLN Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 91 TRP Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 170 GLN Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 288 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 68 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 0.0010 chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 161 HIS ** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.223446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.172869 restraints weight = 9295.042| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 1.36 r_work: 0.3738 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9182 Z= 0.118 Angle : 0.552 8.451 12441 Z= 0.286 Chirality : 0.041 0.137 1405 Planarity : 0.004 0.052 1567 Dihedral : 4.432 21.224 1241 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.86 % Allowed : 22.42 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.25), residues: 1135 helix: 1.93 (0.26), residues: 393 sheet: 0.79 (0.31), residues: 278 loop : -0.60 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 49 TYR 0.009 0.001 TYR R 269 PHE 0.017 0.001 PHE R 232 TRP 0.013 0.001 TRP R 59 HIS 0.007 0.001 HIS R 161 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9182) covalent geometry : angle 0.55159 (12441) hydrogen bonds : bond 0.03869 ( 427) hydrogen bonds : angle 4.53930 ( 1194) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.397 Fit side-chains REVERT: A 22 ASN cc_start: 0.7830 (m-40) cc_final: 0.7620 (m-40) REVERT: A 281 SER cc_start: 0.6801 (m) cc_final: 0.6600 (t) REVERT: A 309 ASP cc_start: 0.7653 (m-30) cc_final: 0.7359 (t70) REVERT: A 313 ARG cc_start: 0.6309 (OUTLIER) cc_final: 0.5816 (mtm180) REVERT: A 331 ASN cc_start: 0.7585 (t0) cc_final: 0.7236 (m110) REVERT: B 96 ARG cc_start: 0.7691 (tpt170) cc_final: 0.7361 (mtt180) REVERT: B 217 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7920 (pmm) REVERT: G 21 MET cc_start: 0.1890 (mtp) cc_final: 0.1336 (pmm) REVERT: G 38 MET cc_start: 0.2532 (mpm) cc_final: 0.2304 (mpm) REVERT: H 30 SER cc_start: 0.7431 (p) cc_final: 0.7159 (p) REVERT: H 55 SER cc_start: 0.6666 (m) cc_final: 0.6402 (m) REVERT: H 63 THR cc_start: 0.6626 (t) cc_final: 0.6419 (p) REVERT: H 82 GLN cc_start: 0.6459 (tt0) cc_final: 0.6125 (mm-40) REVERT: H 93 MET cc_start: 0.7521 (ttt) cc_final: 0.6705 (tpp) REVERT: H 96 CYS cc_start: 0.7427 (OUTLIER) cc_final: 0.7140 (p) REVERT: H 98 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7388 (ptt-90) REVERT: H 179 GLN cc_start: 0.6719 (OUTLIER) cc_final: 0.6372 (tt0) REVERT: H 230 MET cc_start: 0.7554 (ttp) cc_final: 0.6508 (ttp) REVERT: H 234 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6637 (mt-10) REVERT: R 1 MET cc_start: 0.2576 (mtm) cc_final: 0.1654 (tpt) REVERT: R 47 LEU cc_start: 0.2885 (pp) cc_final: 0.2414 (tp) REVERT: R 60 LYS cc_start: 0.5800 (OUTLIER) cc_final: 0.5212 (mttp) REVERT: R 164 LYS cc_start: 0.5371 (mptp) cc_final: 0.4779 (mppt) REVERT: R 234 MET cc_start: 0.6573 (mmt) cc_final: 0.6071 (mtm) REVERT: R 253 ARG cc_start: 0.5035 (ttt180) cc_final: 0.4642 (tpt-90) REVERT: R 288 MET cc_start: 0.5378 (OUTLIER) cc_final: 0.4903 (tmm) outliers start: 37 outliers final: 16 residues processed: 140 average time/residue: 0.5070 time to fit residues: 76.6875 Evaluate side-chains 128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 179 GLN Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 288 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 176 GLN ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 112 GLN R 133 HIS R 137 ASN R 161 HIS ** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.216460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 133)---------------| | r_work = 0.3758 r_free = 0.3758 target = 0.153061 restraints weight = 9279.681| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.05 r_work: 0.3567 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9182 Z= 0.230 Angle : 0.678 8.540 12441 Z= 0.357 Chirality : 0.046 0.151 1405 Planarity : 0.005 0.050 1567 Dihedral : 5.277 27.633 1241 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 5.11 % Allowed : 21.58 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.25), residues: 1135 helix: 1.33 (0.26), residues: 394 sheet: 0.36 (0.30), residues: 300 loop : -0.64 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 137 TYR 0.017 0.002 TYR R 269 PHE 0.028 0.003 PHE R 21 TRP 0.014 0.002 TRP B 82 HIS 0.007 0.002 HIS R 223 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 9182) covalent geometry : angle 0.67843 (12441) hydrogen bonds : bond 0.05188 ( 427) hydrogen bonds : angle 5.04753 ( 1194) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 104 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7398 (ttt90) REVERT: A 24 ARG cc_start: 0.6912 (tpp-160) cc_final: 0.6691 (mtm-85) REVERT: A 281 SER cc_start: 0.6960 (m) cc_final: 0.6752 (t) REVERT: A 309 ASP cc_start: 0.7735 (m-30) cc_final: 0.7438 (t70) REVERT: B 96 ARG cc_start: 0.7699 (tpt170) cc_final: 0.7315 (mtt180) REVERT: B 219 ARG cc_start: 0.7708 (mmm160) cc_final: 0.7354 (ttm-80) REVERT: B 294 CYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7541 (m) REVERT: G 21 MET cc_start: 0.1584 (mtp) cc_final: 0.1044 (pmm) REVERT: G 38 MET cc_start: 0.2343 (mpm) cc_final: 0.1978 (mpm) REVERT: H 30 SER cc_start: 0.7673 (p) cc_final: 0.7353 (p) REVERT: H 55 SER cc_start: 0.6731 (m) cc_final: 0.6169 (t) REVERT: H 82 GLN cc_start: 0.6471 (tt0) cc_final: 0.6140 (mm-40) REVERT: H 93 MET cc_start: 0.7434 (ttt) cc_final: 0.6812 (tpp) REVERT: H 96 CYS cc_start: 0.7474 (OUTLIER) cc_final: 0.7097 (p) REVERT: H 98 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7303 (ptt-90) REVERT: H 234 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6954 (mt-10) REVERT: R 1 MET cc_start: 0.2313 (mtm) cc_final: 0.1506 (tpt) REVERT: R 47 LEU cc_start: 0.2701 (pp) cc_final: 0.2320 (tp) REVERT: R 60 LYS cc_start: 0.6072 (OUTLIER) cc_final: 0.5550 (mttp) REVERT: R 90 ARG cc_start: 0.6081 (OUTLIER) cc_final: 0.5859 (tpt-90) REVERT: R 91 TRP cc_start: 0.5497 (OUTLIER) cc_final: 0.3808 (m100) REVERT: R 170 GLN cc_start: 0.4681 (OUTLIER) cc_final: 0.3240 (tm130) REVERT: R 234 MET cc_start: 0.6719 (mmt) cc_final: 0.6110 (mtm) REVERT: R 253 ARG cc_start: 0.5162 (ttt180) cc_final: 0.4772 (tpt-90) REVERT: R 288 MET cc_start: 0.5751 (OUTLIER) cc_final: 0.5319 (tmm) outliers start: 49 outliers final: 22 residues processed: 143 average time/residue: 0.5599 time to fit residues: 85.9916 Evaluate side-chains 130 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain R residue 91 TRP Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 170 GLN Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 288 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 64 optimal weight: 0.4980 chunk 74 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 ASN R 161 HIS ** R 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.219120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.167659 restraints weight = 9378.916| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.35 r_work: 0.3687 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9182 Z= 0.152 Angle : 0.604 8.502 12441 Z= 0.314 Chirality : 0.042 0.141 1405 Planarity : 0.004 0.052 1567 Dihedral : 4.904 24.761 1241 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.07 % Allowed : 22.11 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.25), residues: 1135 helix: 1.50 (0.26), residues: 396 sheet: 0.29 (0.30), residues: 284 loop : -0.62 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 205 TYR 0.010 0.001 TYR A 290 PHE 0.024 0.002 PHE R 117 TRP 0.013 0.002 TRP B 99 HIS 0.012 0.001 HIS R 223 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9182) covalent geometry : angle 0.60368 (12441) hydrogen bonds : bond 0.04374 ( 427) hydrogen bonds : angle 4.80256 ( 1194) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7339 (ttt90) REVERT: A 205 ARG cc_start: 0.5684 (ttp-110) cc_final: 0.5385 (mtm110) REVERT: A 313 ARG cc_start: 0.6281 (OUTLIER) cc_final: 0.5893 (mtm180) REVERT: A 346 ASN cc_start: 0.7739 (m-40) cc_final: 0.7464 (m-40) REVERT: B 96 ARG cc_start: 0.7693 (tpt170) cc_final: 0.7430 (mtt180) REVERT: B 219 ARG cc_start: 0.7519 (mmm160) cc_final: 0.7275 (ttm-80) REVERT: B 294 CYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7362 (m) REVERT: G 21 MET cc_start: 0.1798 (mtp) cc_final: 0.1248 (pmm) REVERT: G 38 MET cc_start: 0.2358 (mpm) cc_final: 0.2142 (mpm) REVERT: H 30 SER cc_start: 0.7762 (p) cc_final: 0.7461 (p) REVERT: H 55 SER cc_start: 0.6743 (m) cc_final: 0.6156 (t) REVERT: H 82 GLN cc_start: 0.6400 (tt0) cc_final: 0.6051 (mm-40) REVERT: H 93 MET cc_start: 0.7601 (ttt) cc_final: 0.6996 (tpp) REVERT: H 96 CYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7306 (p) REVERT: H 98 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7354 (ptt-90) REVERT: H 234 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6867 (mt-10) REVERT: R 1 MET cc_start: 0.2404 (mtm) cc_final: 0.1572 (tpt) REVERT: R 47 LEU cc_start: 0.2801 (pp) cc_final: 0.2346 (tp) REVERT: R 60 LYS cc_start: 0.5979 (OUTLIER) cc_final: 0.5507 (mttp) REVERT: R 100 CYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6651 (t) REVERT: R 164 LYS cc_start: 0.5465 (mptp) cc_final: 0.4643 (mppt) REVERT: R 170 GLN cc_start: 0.4567 (OUTLIER) cc_final: 0.3098 (tm130) REVERT: R 227 LYS cc_start: 0.6584 (mttp) cc_final: 0.5804 (mtmt) REVERT: R 234 MET cc_start: 0.6630 (mmt) cc_final: 0.6122 (mtm) REVERT: R 253 ARG cc_start: 0.5142 (ttt180) cc_final: 0.4743 (tpt-90) outliers start: 39 outliers final: 19 residues processed: 131 average time/residue: 0.5939 time to fit residues: 83.1392 Evaluate side-chains 124 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 170 GLN Chi-restraints excluded: chain R residue 288 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 5 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 93 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 8 optimal weight: 0.0980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 112 GLN R 161 HIS ** R 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.219434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3949 r_free = 0.3949 target = 0.166339 restraints weight = 9365.393| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 1.44 r_work: 0.3700 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9182 Z= 0.145 Angle : 0.607 12.092 12441 Z= 0.312 Chirality : 0.042 0.136 1405 Planarity : 0.004 0.052 1567 Dihedral : 4.811 23.529 1241 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.96 % Allowed : 22.42 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.26), residues: 1135 helix: 1.57 (0.26), residues: 397 sheet: 0.27 (0.30), residues: 290 loop : -0.56 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 205 TYR 0.010 0.001 TYR A 290 PHE 0.021 0.002 PHE R 117 TRP 0.013 0.001 TRP B 99 HIS 0.009 0.001 HIS R 223 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9182) covalent geometry : angle 0.60719 (12441) hydrogen bonds : bond 0.04271 ( 427) hydrogen bonds : angle 4.75697 ( 1194) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 97 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7294 (ttt90) REVERT: A 309 ASP cc_start: 0.7771 (t70) cc_final: 0.7456 (t70) REVERT: A 313 ARG cc_start: 0.6279 (OUTLIER) cc_final: 0.5821 (mtm180) REVERT: A 346 ASN cc_start: 0.7766 (m-40) cc_final: 0.7501 (m-40) REVERT: B 96 ARG cc_start: 0.7690 (tpt170) cc_final: 0.7445 (mtt180) REVERT: B 219 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7284 (ttm-80) REVERT: B 294 CYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7301 (m) REVERT: G 21 MET cc_start: 0.1763 (mtp) cc_final: 0.1187 (pmm) REVERT: G 38 MET cc_start: 0.2275 (mpm) cc_final: 0.2059 (mpm) REVERT: H 30 SER cc_start: 0.7767 (p) cc_final: 0.7460 (p) REVERT: H 55 SER cc_start: 0.6735 (m) cc_final: 0.6152 (t) REVERT: H 82 GLN cc_start: 0.6340 (tt0) cc_final: 0.6041 (mm-40) REVERT: H 93 MET cc_start: 0.7639 (ttt) cc_final: 0.7039 (tpp) REVERT: H 96 CYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7381 (p) REVERT: H 98 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7371 (ptt-90) REVERT: H 179 GLN cc_start: 0.6833 (OUTLIER) cc_final: 0.6461 (tt0) REVERT: H 234 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6810 (mt-10) REVERT: R 1 MET cc_start: 0.2370 (mtm) cc_final: 0.1561 (tpt) REVERT: R 25 PHE cc_start: 0.6341 (t80) cc_final: 0.5999 (t80) REVERT: R 47 LEU cc_start: 0.2808 (pp) cc_final: 0.2378 (tp) REVERT: R 60 LYS cc_start: 0.5868 (OUTLIER) cc_final: 0.5415 (mttp) REVERT: R 100 CYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6644 (t) REVERT: R 164 LYS cc_start: 0.5499 (mptp) cc_final: 0.4756 (mppt) REVERT: R 227 LYS cc_start: 0.6641 (mttp) cc_final: 0.5895 (mtmt) REVERT: R 234 MET cc_start: 0.6575 (mmt) cc_final: 0.6084 (mtm) REVERT: R 253 ARG cc_start: 0.5146 (ttt180) cc_final: 0.4761 (tpt-90) outliers start: 38 outliers final: 24 residues processed: 128 average time/residue: 0.5586 time to fit residues: 76.6075 Evaluate side-chains 129 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 96 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 179 GLN Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 141 ASN Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 288 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 88 ASN ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 ASN R 161 HIS R 170 GLN ** R 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 286 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.221081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 131)---------------| | r_work = 0.3946 r_free = 0.3946 target = 0.165869 restraints weight = 9299.447| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.65 r_work: 0.3709 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9182 Z= 0.124 Angle : 0.576 11.046 12441 Z= 0.295 Chirality : 0.041 0.131 1405 Planarity : 0.004 0.054 1567 Dihedral : 4.572 22.339 1241 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.55 % Allowed : 23.15 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.26), residues: 1135 helix: 1.75 (0.26), residues: 397 sheet: 0.36 (0.31), residues: 285 loop : -0.59 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 137 TYR 0.009 0.001 TYR A 290 PHE 0.020 0.001 PHE R 117 TRP 0.012 0.001 TRP B 339 HIS 0.008 0.001 HIS R 223 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9182) covalent geometry : angle 0.57571 (12441) hydrogen bonds : bond 0.03885 ( 427) hydrogen bonds : angle 4.58288 ( 1194) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7766 (t70) cc_final: 0.7461 (t70) REVERT: A 313 ARG cc_start: 0.6247 (OUTLIER) cc_final: 0.5735 (mtm180) REVERT: A 346 ASN cc_start: 0.7782 (m-40) cc_final: 0.7522 (m-40) REVERT: B 96 ARG cc_start: 0.7650 (tpt170) cc_final: 0.7367 (mtt180) REVERT: B 219 ARG cc_start: 0.7527 (mmm160) cc_final: 0.7279 (ttm-80) REVERT: B 294 CYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7216 (m) REVERT: G 38 MET cc_start: 0.2384 (mpm) cc_final: 0.2161 (mpm) REVERT: H 30 SER cc_start: 0.7640 (p) cc_final: 0.7352 (p) REVERT: H 55 SER cc_start: 0.6664 (m) cc_final: 0.6071 (t) REVERT: H 82 GLN cc_start: 0.6359 (tt0) cc_final: 0.5969 (mm-40) REVERT: H 93 MET cc_start: 0.7547 (ttt) cc_final: 0.6895 (tpp) REVERT: H 96 CYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7367 (p) REVERT: H 98 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7289 (ptt-90) REVERT: H 179 GLN cc_start: 0.6803 (OUTLIER) cc_final: 0.6386 (tt0) REVERT: H 230 MET cc_start: 0.7615 (ttp) cc_final: 0.6759 (ttp) REVERT: H 234 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6779 (mt-10) REVERT: R 1 MET cc_start: 0.2474 (mtm) cc_final: 0.1593 (tpt) REVERT: R 25 PHE cc_start: 0.6181 (t80) cc_final: 0.5480 (t80) REVERT: R 47 LEU cc_start: 0.2712 (pp) cc_final: 0.2317 (tp) REVERT: R 60 LYS cc_start: 0.5653 (OUTLIER) cc_final: 0.5196 (mttp) REVERT: R 100 CYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6594 (t) REVERT: R 164 LYS cc_start: 0.5471 (mptp) cc_final: 0.4677 (mppt) REVERT: R 194 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.7090 (mp) REVERT: R 227 LYS cc_start: 0.6521 (mttp) cc_final: 0.5783 (mtmt) REVERT: R 234 MET cc_start: 0.6569 (mmt) cc_final: 0.6057 (mtm) REVERT: R 253 ARG cc_start: 0.5195 (ttt180) cc_final: 0.4809 (tpt-90) outliers start: 34 outliers final: 17 residues processed: 131 average time/residue: 0.5559 time to fit residues: 78.1974 Evaluate side-chains 120 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 179 GLN Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 141 ASN Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 288 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.4980 chunk 95 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 90 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 161 HIS R 170 GLN ** R 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.220412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 137)---------------| | r_work = 0.3938 r_free = 0.3938 target = 0.165011 restraints weight = 9276.752| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 1.65 r_work: 0.3716 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9182 Z= 0.130 Angle : 0.594 12.923 12441 Z= 0.302 Chirality : 0.042 0.132 1405 Planarity : 0.004 0.052 1567 Dihedral : 4.589 22.617 1241 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.23 % Allowed : 23.77 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.26), residues: 1135 helix: 1.74 (0.26), residues: 397 sheet: 0.40 (0.31), residues: 284 loop : -0.66 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 205 TYR 0.009 0.001 TYR A 290 PHE 0.024 0.002 PHE R 117 TRP 0.012 0.001 TRP B 99 HIS 0.008 0.001 HIS R 161 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9182) covalent geometry : angle 0.59364 (12441) hydrogen bonds : bond 0.04007 ( 427) hydrogen bonds : angle 4.60173 ( 1194) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7284 (ttt90) REVERT: A 309 ASP cc_start: 0.7703 (t70) cc_final: 0.7406 (t70) REVERT: A 313 ARG cc_start: 0.6256 (OUTLIER) cc_final: 0.5737 (mtm180) REVERT: A 346 ASN cc_start: 0.7807 (m-40) cc_final: 0.7543 (m-40) REVERT: B 96 ARG cc_start: 0.7707 (tpt170) cc_final: 0.7406 (mtt180) REVERT: B 219 ARG cc_start: 0.7547 (mmm160) cc_final: 0.7317 (ttm-80) REVERT: B 294 CYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7210 (m) REVERT: G 38 MET cc_start: 0.2280 (mpm) cc_final: 0.2055 (mpm) REVERT: H 30 SER cc_start: 0.7581 (p) cc_final: 0.7269 (p) REVERT: H 55 SER cc_start: 0.6656 (m) cc_final: 0.6053 (t) REVERT: H 82 GLN cc_start: 0.6353 (tt0) cc_final: 0.5966 (mm-40) REVERT: H 93 MET cc_start: 0.7553 (ttt) cc_final: 0.6905 (tpp) REVERT: H 96 CYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7354 (p) REVERT: H 98 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7291 (ptt-90) REVERT: H 179 GLN cc_start: 0.6820 (OUTLIER) cc_final: 0.6404 (tt0) REVERT: H 234 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6776 (mt-10) REVERT: R 1 MET cc_start: 0.2505 (mtm) cc_final: 0.1788 (tpt) REVERT: R 25 PHE cc_start: 0.6206 (t80) cc_final: 0.5549 (t80) REVERT: R 43 LEU cc_start: 0.5661 (pt) cc_final: 0.4950 (tt) REVERT: R 47 LEU cc_start: 0.2656 (pp) cc_final: 0.2246 (tp) REVERT: R 60 LYS cc_start: 0.5699 (OUTLIER) cc_final: 0.5250 (mttp) REVERT: R 100 CYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6629 (t) REVERT: R 164 LYS cc_start: 0.5476 (mptp) cc_final: 0.4683 (mppt) REVERT: R 227 LYS cc_start: 0.6522 (mttp) cc_final: 0.5781 (mtmt) REVERT: R 234 MET cc_start: 0.6583 (mmt) cc_final: 0.6097 (mtm) REVERT: R 253 ARG cc_start: 0.5161 (ttt180) cc_final: 0.4827 (tpt-90) outliers start: 31 outliers final: 18 residues processed: 125 average time/residue: 0.5427 time to fit residues: 72.6335 Evaluate side-chains 126 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 179 GLN Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 141 ASN Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 288 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.0370 chunk 102 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 161 HIS R 170 GLN ** R 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.221745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 126)---------------| | r_work = 0.3957 r_free = 0.3957 target = 0.166769 restraints weight = 9222.701| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 1.67 r_work: 0.3732 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9182 Z= 0.117 Angle : 0.580 12.735 12441 Z= 0.295 Chirality : 0.041 0.131 1405 Planarity : 0.004 0.053 1567 Dihedral : 4.461 21.863 1241 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.02 % Allowed : 24.09 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.26), residues: 1135 helix: 1.80 (0.26), residues: 401 sheet: 0.41 (0.31), residues: 285 loop : -0.70 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 205 TYR 0.007 0.001 TYR R 295 PHE 0.020 0.001 PHE R 117 TRP 0.012 0.001 TRP B 339 HIS 0.009 0.001 HIS R 161 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9182) covalent geometry : angle 0.58033 (12441) hydrogen bonds : bond 0.03784 ( 427) hydrogen bonds : angle 4.51563 ( 1194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4325.08 seconds wall clock time: 74 minutes 24.31 seconds (4464.31 seconds total)