Starting phenix.real_space_refine on Mon May 12 12:55:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6j_36006/05_2025/8j6j_36006.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6j_36006/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j6j_36006/05_2025/8j6j_36006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6j_36006/05_2025/8j6j_36006.map" model { file = "/net/cci-nas-00/data/ceres_data/8j6j_36006/05_2025/8j6j_36006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6j_36006/05_2025/8j6j_36006.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, '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, 'ARG:plan': 1, 'ASP: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, 'ARG:plan': 2, 'ASP: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: 5.43, per 1000 atoms: 0.60 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: 2.48 Conformation dependent library (CDL) restraints added in 996.6 milliseconds 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: 1.03 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: 2.49 Time building geometry restraints manager: 2.79 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: 1.130 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.460 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.500 ------------------------------------------------------------------------------- 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 : 8.22 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.008 0.001 TRP R 59 HIS 0.004 0.000 HIS B 266 PHE 0.007 0.001 PHE H 239 TYR 0.017 0.001 TYR H 190 ARG 0.007 0.000 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.18735 ( 427) hydrogen bonds : angle 6.56917 ( 1194) covalent geometry : bond 0.00354 ( 9182) covalent geometry : angle 0.61676 (12441) *********************** 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 : 0.933 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: 1.0476 time to fit residues: 182.5325 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 : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.231681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.4019 r_free = 0.4019 target = 0.175693 restraints weight = 9320.469| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.78 r_work: 0.3803 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9182 Z= 0.148 Angle : 0.626 8.446 12441 Z= 0.324 Chirality : 0.044 0.144 1405 Planarity : 0.005 0.066 1567 Dihedral : 4.294 17.622 1241 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.32 % Allowed : 21.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.26), residues: 1135 helix: 2.05 (0.27), residues: 391 sheet: 0.99 (0.30), residues: 283 loop : -0.30 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 59 HIS 0.009 0.002 HIS R 161 PHE 0.017 0.002 PHE R 232 TYR 0.023 0.002 TYR B 85 ARG 0.005 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.04322 ( 427) hydrogen bonds : angle 4.75276 ( 1194) covalent geometry : bond 0.00318 ( 9182) covalent geometry : angle 0.62594 (12441) *********************** 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 176 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 125 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 34 VAL cc_start: 0.7977 (OUTLIER) cc_final: 0.7487 (t) REVERT: A 247 MET cc_start: 0.8066 (mtp) cc_final: 0.7773 (mtp) REVERT: A 305 CYS cc_start: 0.7510 (m) cc_final: 0.7232 (t) REVERT: A 309 ASP cc_start: 0.7400 (m-30) cc_final: 0.7088 (t70) REVERT: B 96 ARG cc_start: 0.7420 (tpt170) cc_final: 0.7030 (mtt180) REVERT: B 217 MET cc_start: 0.8053 (pmt) cc_final: 0.7647 (pmm) REVERT: B 220 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7475 (mt0) REVERT: G 21 MET cc_start: 0.1918 (mtp) cc_final: 0.1423 (pmm) REVERT: G 38 MET cc_start: 0.2511 (mpm) cc_final: 0.0164 (mpm) REVERT: G 50 LEU cc_start: 0.2614 (OUTLIER) cc_final: 0.1565 (tt) REVERT: H 30 SER cc_start: 0.6887 (p) cc_final: 0.6617 (p) REVERT: H 55 SER cc_start: 0.6451 (m) cc_final: 0.6128 (m) REVERT: H 71 SER cc_start: 0.5527 (p) cc_final: 0.5188 (t) REVERT: H 82 GLN cc_start: 0.6441 (tt0) cc_final: 0.6145 (mm-40) REVERT: H 93 MET cc_start: 0.7032 (ttm) cc_final: 0.6817 (ttt) REVERT: H 234 GLU cc_start: 0.6225 (mt-10) cc_final: 0.5393 (mm-30) REVERT: R 50 TRP cc_start: 0.3092 (m-10) cc_final: 0.2551 (m-10) REVERT: R 164 LYS cc_start: 0.5478 (mptp) cc_final: 0.4810 (mppt) REVERT: R 183 CYS cc_start: 0.8107 (t) cc_final: 0.7848 (m) REVERT: R 234 MET cc_start: 0.6275 (mmt) cc_final: 0.5649 (mtp) REVERT: R 253 ARG cc_start: 0.4902 (ttt180) cc_final: 0.4666 (tpt-90) REVERT: R 288 MET cc_start: 0.5684 (OUTLIER) cc_final: 0.5068 (tmm) outliers start: 51 outliers final: 11 residues processed: 162 average time/residue: 0.9225 time to fit residues: 162.4567 Evaluate side-chains 116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 B residue 114 CYS Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 275 SER 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 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 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 25 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 37 optimal weight: 0.0770 chunk 95 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 chunk 107 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 88 ASN B 259 GLN B 268 ASN R 112 GLN 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 = 0.4536 r_free = 0.4536 target = 0.227751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.179932 restraints weight = 9455.455| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 1.27 r_work: 0.3837 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2935 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= 0.132 Angle : 0.579 7.218 12441 Z= 0.300 Chirality : 0.042 0.142 1405 Planarity : 0.004 0.049 1567 Dihedral : 4.259 20.818 1241 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.80 % Allowed : 20.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1135 helix: 1.89 (0.26), residues: 396 sheet: 0.88 (0.31), residues: 284 loop : -0.44 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 59 HIS 0.009 0.001 HIS R 161 PHE 0.016 0.002 PHE R 21 TYR 0.014 0.002 TYR B 85 ARG 0.004 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 427) hydrogen bonds : angle 4.58900 ( 1194) covalent geometry : bond 0.00285 ( 9182) covalent geometry : angle 0.57930 (12441) *********************** 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 151 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 105 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7511 (m-30) cc_final: 0.7202 (t70) REVERT: A 331 ASN cc_start: 0.7562 (t0) cc_final: 0.6764 (m-40) REVERT: B 217 MET cc_start: 0.8132 (pmt) cc_final: 0.7812 (pmm) REVERT: B 325 MET cc_start: 0.8373 (tpp) cc_final: 0.8166 (mmm) REVERT: G 21 MET cc_start: 0.2006 (mtp) cc_final: 0.1348 (pmm) REVERT: G 38 MET cc_start: 0.2615 (mpm) cc_final: 0.0289 (mpm) REVERT: G 50 LEU cc_start: 0.2554 (OUTLIER) cc_final: 0.2260 (tt) REVERT: H 30 SER cc_start: 0.7133 (p) cc_final: 0.6889 (p) REVERT: H 55 SER cc_start: 0.6570 (m) cc_final: 0.6267 (m) REVERT: H 71 SER cc_start: 0.6052 (p) cc_final: 0.5557 (t) REVERT: H 82 GLN cc_start: 0.6408 (tt0) cc_final: 0.6164 (mm-40) REVERT: H 96 CYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7003 (p) REVERT: H 179 GLN cc_start: 0.6522 (OUTLIER) cc_final: 0.6295 (tt0) REVERT: H 234 GLU cc_start: 0.6411 (mt-10) cc_final: 0.5595 (mm-30) REVERT: R 43 LEU cc_start: 0.5832 (pt) cc_final: 0.4878 (tt) REVERT: R 47 LEU cc_start: 0.2729 (pp) cc_final: 0.2237 (tp) REVERT: R 164 LYS cc_start: 0.5595 (mptp) cc_final: 0.4983 (mppt) REVERT: R 234 MET cc_start: 0.6295 (mmt) cc_final: 0.5843 (mtp) REVERT: R 288 MET cc_start: 0.5543 (OUTLIER) cc_final: 0.5097 (tmm) outliers start: 46 outliers final: 14 residues processed: 140 average time/residue: 0.9482 time to fit residues: 144.0495 Evaluate side-chains 116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 260 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 G residue 31 SER 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 144 THR Chi-restraints excluded: chain H residue 179 GLN Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 217 GLN Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 288 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 37 optimal weight: 0.0970 chunk 63 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 306 GLN R 112 GLN R 161 HIS R 170 GLN ** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.224563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.174417 restraints weight = 9273.543| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 1.36 r_work: 0.3765 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9182 Z= 0.139 Angle : 0.586 8.776 12441 Z= 0.303 Chirality : 0.042 0.143 1405 Planarity : 0.004 0.048 1567 Dihedral : 4.476 22.478 1241 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.59 % Allowed : 21.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 1135 helix: 1.89 (0.26), residues: 397 sheet: 0.77 (0.31), residues: 283 loop : -0.58 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 99 HIS 0.008 0.001 HIS R 161 PHE 0.018 0.002 PHE R 21 TYR 0.018 0.002 TYR B 105 ARG 0.003 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 427) hydrogen bonds : angle 4.57862 ( 1194) covalent geometry : bond 0.00311 ( 9182) covalent geometry : angle 0.58628 (12441) *********************** 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 155 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 281 SER cc_start: 0.6809 (m) cc_final: 0.6527 (t) REVERT: A 309 ASP cc_start: 0.7586 (m-30) cc_final: 0.7328 (t70) REVERT: A 331 ASN cc_start: 0.7686 (t0) cc_final: 0.7092 (m-40) REVERT: B 219 ARG cc_start: 0.7490 (mmm160) cc_final: 0.7259 (ttm-80) REVERT: B 294 CYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7110 (m) REVERT: G 21 MET cc_start: 0.1898 (mtp) cc_final: 0.1288 (pmm) REVERT: G 38 MET cc_start: 0.2532 (mpm) cc_final: 0.0233 (mpm) REVERT: G 50 LEU cc_start: 0.2669 (OUTLIER) cc_final: 0.2398 (tt) REVERT: H 30 SER cc_start: 0.7301 (p) cc_final: 0.7028 (p) REVERT: H 55 SER cc_start: 0.6596 (m) cc_final: 0.6312 (m) REVERT: H 71 SER cc_start: 0.6383 (p) cc_final: 0.5822 (t) REVERT: H 82 GLN cc_start: 0.6453 (tt0) cc_final: 0.6176 (mm-40) REVERT: H 93 MET cc_start: 0.7387 (ttt) cc_final: 0.6400 (tpp) REVERT: H 96 CYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7044 (p) REVERT: H 98 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7284 (ptt-90) REVERT: H 179 GLN cc_start: 0.6619 (OUTLIER) cc_final: 0.6361 (tt0) REVERT: H 234 GLU cc_start: 0.6606 (mt-10) cc_final: 0.6368 (mt-10) REVERT: R 1 MET cc_start: 0.2356 (mtm) cc_final: 0.1563 (tpt) REVERT: R 43 LEU cc_start: 0.5701 (OUTLIER) cc_final: 0.4791 (tt) REVERT: R 47 LEU cc_start: 0.2807 (pp) cc_final: 0.2248 (tp) REVERT: R 60 LYS cc_start: 0.5668 (OUTLIER) cc_final: 0.5130 (mttp) REVERT: R 164 LYS cc_start: 0.5579 (mptp) cc_final: 0.5032 (mppt) REVERT: R 234 MET cc_start: 0.6309 (mmt) cc_final: 0.5842 (mtm) outliers start: 44 outliers final: 21 residues processed: 147 average time/residue: 1.0594 time to fit residues: 167.5527 Evaluate side-chains 125 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 65 THR 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 165 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 31 SER 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 142 GLN Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 179 GLN Chi-restraints excluded: chain R residue 11 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 236 VAL Chi-restraints excluded: chain R residue 238 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 14 optimal weight: 0.4980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 294 ASN A 306 GLN B 75 GLN R 112 GLN R 161 HIS R 170 GLN ** 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 = 0.4459 r_free = 0.4459 target = 0.219392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 145)---------------| | r_work = 0.3913 r_free = 0.3913 target = 0.163233 restraints weight = 9264.208| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.71 r_work: 0.3661 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9182 Z= 0.184 Angle : 0.634 8.529 12441 Z= 0.333 Chirality : 0.044 0.150 1405 Planarity : 0.004 0.049 1567 Dihedral : 4.946 24.896 1241 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 5.63 % Allowed : 21.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.25), residues: 1135 helix: 1.75 (0.26), residues: 386 sheet: 0.63 (0.31), residues: 290 loop : -0.58 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.008 0.002 HIS R 161 PHE 0.024 0.002 PHE R 21 TYR 0.017 0.002 TYR B 105 ARG 0.005 0.001 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.04752 ( 427) hydrogen bonds : angle 4.85420 ( 1194) covalent geometry : bond 0.00417 ( 9182) covalent geometry : angle 0.63433 (12441) *********************** 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 164 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 110 time to evaluate : 0.967 Fit side-chains REVERT: A 15 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7224 (ttt90) REVERT: A 309 ASP cc_start: 0.7683 (m-30) cc_final: 0.7388 (t70) REVERT: B 294 CYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7284 (m) REVERT: G 21 MET cc_start: 0.1791 (mtp) cc_final: 0.1221 (pmm) REVERT: G 38 MET cc_start: 0.2467 (mpm) cc_final: 0.2100 (mpm) REVERT: H 30 SER cc_start: 0.7477 (p) cc_final: 0.7198 (p) REVERT: H 55 SER cc_start: 0.6613 (m) cc_final: 0.6331 (m) REVERT: H 82 GLN cc_start: 0.6484 (tt0) cc_final: 0.6166 (mm-40) REVERT: H 93 MET cc_start: 0.7450 (ttt) cc_final: 0.6660 (tpp) REVERT: H 96 CYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7102 (p) REVERT: H 98 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7357 (ptt-90) REVERT: H 179 GLN cc_start: 0.6616 (OUTLIER) cc_final: 0.6265 (tt0) REVERT: H 234 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6822 (mt-10) REVERT: R 1 MET cc_start: 0.2554 (mtm) cc_final: 0.1695 (tpt) REVERT: R 47 LEU cc_start: 0.2871 (pp) cc_final: 0.2302 (tp) REVERT: R 60 LYS cc_start: 0.5599 (OUTLIER) cc_final: 0.5147 (mttp) REVERT: R 91 TRP cc_start: 0.5423 (OUTLIER) cc_final: 0.3782 (m100) REVERT: R 164 LYS cc_start: 0.5257 (mptp) cc_final: 0.4684 (mppt) REVERT: R 234 MET cc_start: 0.6614 (mmt) cc_final: 0.6106 (mtm) REVERT: R 288 MET cc_start: 0.5726 (OUTLIER) cc_final: 0.5243 (tmm) outliers start: 54 outliers final: 26 residues processed: 151 average time/residue: 0.9831 time to fit residues: 160.4681 Evaluate side-chains 140 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 61 MET 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 279 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 VAL 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 H residue 184 SER Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 60 LYS 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 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 36 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 0.0870 chunk 13 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 306 GLN H 142 GLN R 161 HIS R 170 GLN ** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.221434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.171067 restraints weight = 9233.706| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 1.39 r_work: 0.3706 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4394 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= 0.134 Angle : 0.578 8.739 12441 Z= 0.300 Chirality : 0.042 0.137 1405 Planarity : 0.004 0.051 1567 Dihedral : 4.650 24.075 1241 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.69 % Allowed : 22.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.25), residues: 1135 helix: 1.76 (0.26), residues: 394 sheet: 0.63 (0.31), residues: 284 loop : -0.62 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.007 0.001 HIS R 161 PHE 0.018 0.002 PHE R 301 TYR 0.009 0.001 TYR B 85 ARG 0.010 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 427) hydrogen bonds : angle 4.67519 ( 1194) covalent geometry : bond 0.00296 ( 9182) covalent geometry : angle 0.57810 (12441) *********************** 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 152 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 107 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7749 (m-30) cc_final: 0.7439 (t70) REVERT: B 294 CYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7257 (m) REVERT: G 21 MET cc_start: 0.1884 (mtp) cc_final: 0.1295 (pmm) REVERT: G 38 MET cc_start: 0.2492 (mpm) cc_final: 0.2270 (mpm) REVERT: H 30 SER cc_start: 0.7511 (p) cc_final: 0.7253 (p) REVERT: H 55 SER cc_start: 0.6668 (m) cc_final: 0.6077 (t) REVERT: H 63 THR cc_start: 0.6673 (OUTLIER) cc_final: 0.6459 (p) REVERT: H 82 GLN cc_start: 0.6411 (tt0) cc_final: 0.6170 (mm-40) REVERT: H 93 MET cc_start: 0.7545 (ttt) cc_final: 0.6794 (tpp) REVERT: H 96 CYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7201 (p) REVERT: H 98 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7322 (ptt-90) REVERT: H 179 GLN cc_start: 0.6771 (OUTLIER) cc_final: 0.6488 (tt0) REVERT: H 230 MET cc_start: 0.7334 (ttp) cc_final: 0.6828 (ttp) REVERT: H 234 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6704 (mt-10) REVERT: R 1 MET cc_start: 0.2559 (mtm) cc_final: 0.1666 (tpt) REVERT: R 47 LEU cc_start: 0.2881 (pp) cc_final: 0.2361 (tp) REVERT: R 60 LYS cc_start: 0.5906 (OUTLIER) cc_final: 0.5403 (mttp) REVERT: R 164 LYS cc_start: 0.5266 (mptp) cc_final: 0.4705 (mppt) REVERT: R 234 MET cc_start: 0.6535 (mmt) cc_final: 0.6030 (mtm) outliers start: 45 outliers final: 26 residues processed: 142 average time/residue: 0.9361 time to fit residues: 144.2262 Evaluate side-chains 130 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 61 MET 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 279 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 VAL 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 H residue 184 SER Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 20 VAL 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 120 VAL Chi-restraints excluded: chain R residue 141 ASN Chi-restraints excluded: chain R residue 236 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 58 optimal weight: 0.0980 chunk 61 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 306 GLN H 194 ASN R 161 HIS R 170 GLN ** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.221658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 123)---------------| | r_work = 0.3944 r_free = 0.3944 target = 0.165819 restraints weight = 9373.102| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 1.66 r_work: 0.3725 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9182 Z= 0.127 Angle : 0.567 8.444 12441 Z= 0.295 Chirality : 0.041 0.134 1405 Planarity : 0.004 0.051 1567 Dihedral : 4.544 23.423 1241 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.48 % Allowed : 22.94 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1135 helix: 1.80 (0.26), residues: 395 sheet: 0.51 (0.31), residues: 286 loop : -0.57 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.008 0.001 HIS R 161 PHE 0.018 0.002 PHE R 21 TYR 0.009 0.001 TYR A 290 ARG 0.007 0.001 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 427) hydrogen bonds : angle 4.61449 ( 1194) covalent geometry : bond 0.00279 ( 9182) covalent geometry : angle 0.56741 (12441) *********************** 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 146 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 103 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7679 (m-30) cc_final: 0.7432 (t70) REVERT: B 294 CYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7222 (m) REVERT: G 21 MET cc_start: 0.1872 (mtp) cc_final: 0.1285 (pmm) REVERT: H 30 SER cc_start: 0.7425 (p) cc_final: 0.7139 (p) REVERT: H 55 SER cc_start: 0.6665 (m) cc_final: 0.6060 (t) REVERT: H 82 GLN cc_start: 0.6450 (tt0) cc_final: 0.6157 (mm-40) REVERT: H 93 MET cc_start: 0.7519 (ttt) cc_final: 0.6729 (tpp) REVERT: H 96 CYS cc_start: 0.7409 (OUTLIER) cc_final: 0.7132 (p) REVERT: H 98 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7171 (ptt-90) REVERT: H 179 GLN cc_start: 0.6741 (OUTLIER) cc_final: 0.6420 (tt0) REVERT: H 230 MET cc_start: 0.7216 (ttp) cc_final: 0.6954 (ttp) REVERT: H 234 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6648 (mt-10) REVERT: R 1 MET cc_start: 0.2539 (mtm) cc_final: 0.1663 (tpt) REVERT: R 25 PHE cc_start: 0.6335 (t80) cc_final: 0.5906 (t80) REVERT: R 47 LEU cc_start: 0.2804 (pp) cc_final: 0.2397 (tp) REVERT: R 60 LYS cc_start: 0.5844 (OUTLIER) cc_final: 0.5359 (mttp) REVERT: R 84 MET cc_start: 0.4802 (ttm) cc_final: 0.3839 (tpp) REVERT: R 100 CYS cc_start: 0.7265 (OUTLIER) cc_final: 0.6688 (t) REVERT: R 164 LYS cc_start: 0.5269 (mptp) cc_final: 0.4675 (mppt) REVERT: R 234 MET cc_start: 0.6504 (mmt) cc_final: 0.6012 (mtm) outliers start: 43 outliers final: 27 residues processed: 137 average time/residue: 0.9621 time to fit residues: 143.2313 Evaluate side-chains 134 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 61 MET 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 234 PHE 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 279 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 50 LEU 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 11 LEU Chi-restraints excluded: chain R residue 20 VAL 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 201 LEU Chi-restraints excluded: chain R residue 236 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 306 GLN A 346 ASN R 161 HIS ** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.220028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.168030 restraints weight = 9396.341| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 1.36 r_work: 0.3706 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9182 Z= 0.141 Angle : 0.585 9.250 12441 Z= 0.302 Chirality : 0.042 0.134 1405 Planarity : 0.004 0.051 1567 Dihedral : 4.654 24.142 1241 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.59 % Allowed : 23.25 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1135 helix: 1.85 (0.26), residues: 386 sheet: 0.43 (0.31), residues: 286 loop : -0.54 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.008 0.001 HIS R 161 PHE 0.019 0.002 PHE R 21 TYR 0.010 0.001 TYR A 290 ARG 0.007 0.001 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 427) hydrogen bonds : angle 4.65815 ( 1194) covalent geometry : bond 0.00314 ( 9182) covalent geometry : angle 0.58474 (12441) *********************** 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 148 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 104 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7717 (m-30) cc_final: 0.7483 (t70) REVERT: A 345 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7866 (mttm) REVERT: A 346 ASN cc_start: 0.7693 (m110) cc_final: 0.7418 (m-40) REVERT: B 294 CYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7274 (m) REVERT: G 21 MET cc_start: 0.1889 (mtp) cc_final: 0.1295 (pmm) REVERT: G 31 SER cc_start: 0.3641 (OUTLIER) cc_final: 0.3385 (t) REVERT: G 38 MET cc_start: 0.1919 (mpm) cc_final: 0.0616 (mpm) REVERT: H 30 SER cc_start: 0.7552 (p) cc_final: 0.7259 (p) REVERT: H 55 SER cc_start: 0.6692 (m) cc_final: 0.6095 (t) REVERT: H 78 THR cc_start: 0.5556 (m) cc_final: 0.5177 (t) REVERT: H 82 GLN cc_start: 0.6436 (tt0) cc_final: 0.6150 (mm-40) REVERT: H 93 MET cc_start: 0.7538 (ttt) cc_final: 0.6877 (tpp) REVERT: H 96 CYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7191 (p) REVERT: H 98 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7127 (ptt-90) REVERT: H 179 GLN cc_start: 0.6805 (OUTLIER) cc_final: 0.6497 (tt0) REVERT: H 230 MET cc_start: 0.7273 (ttp) cc_final: 0.6754 (ttp) REVERT: H 234 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6790 (mt-10) REVERT: R 1 MET cc_start: 0.2376 (mtm) cc_final: 0.1547 (tpt) REVERT: R 25 PHE cc_start: 0.6238 (t80) cc_final: 0.5875 (t80) REVERT: R 47 LEU cc_start: 0.2804 (pp) cc_final: 0.2414 (tp) REVERT: R 60 LYS cc_start: 0.5875 (OUTLIER) cc_final: 0.5402 (mttp) REVERT: R 84 MET cc_start: 0.4818 (ttm) cc_final: 0.3855 (tpp) REVERT: R 100 CYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6712 (t) REVERT: R 164 LYS cc_start: 0.5302 (mptp) cc_final: 0.4731 (mppt) REVERT: R 234 MET cc_start: 0.6534 (mmt) cc_final: 0.6040 (mtm) outliers start: 44 outliers final: 28 residues processed: 139 average time/residue: 1.0078 time to fit residues: 151.7881 Evaluate side-chains 135 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 61 MET 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 279 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 50 LEU 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 H residue 179 GLN Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 20 VAL 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 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 51 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 294 ASN A 306 GLN R 161 HIS R 170 GLN ** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.217023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 123)---------------| | r_work = 0.3891 r_free = 0.3891 target = 0.160932 restraints weight = 9312.233| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 1.64 r_work: 0.3654 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9182 Z= 0.192 Angle : 0.645 9.849 12441 Z= 0.336 Chirality : 0.044 0.143 1405 Planarity : 0.005 0.052 1567 Dihedral : 5.117 27.526 1241 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.69 % Allowed : 23.04 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.25), residues: 1135 helix: 1.58 (0.26), residues: 389 sheet: 0.25 (0.30), residues: 287 loop : -0.66 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.013 0.002 HIS R 223 PHE 0.028 0.002 PHE R 117 TYR 0.013 0.002 TYR A 290 ARG 0.006 0.001 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.04779 ( 427) hydrogen bonds : angle 4.92999 ( 1194) covalent geometry : bond 0.00437 ( 9182) covalent geometry : angle 0.64481 (12441) *********************** 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 148 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 103 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7665 (m-30) cc_final: 0.7464 (t70) REVERT: A 346 ASN cc_start: 0.7768 (m110) cc_final: 0.7496 (m-40) REVERT: G 21 MET cc_start: 0.1763 (mtp) cc_final: 0.1182 (pmm) REVERT: G 31 SER cc_start: 0.3887 (OUTLIER) cc_final: 0.3644 (t) REVERT: G 38 MET cc_start: 0.2374 (mpm) cc_final: 0.1128 (mpm) REVERT: H 30 SER cc_start: 0.7705 (p) cc_final: 0.7415 (p) REVERT: H 55 SER cc_start: 0.6742 (m) cc_final: 0.6169 (t) REVERT: H 82 GLN cc_start: 0.6410 (tt0) cc_final: 0.6053 (mm-40) REVERT: H 93 MET cc_start: 0.7574 (ttt) cc_final: 0.6991 (tpp) REVERT: H 96 CYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7235 (p) REVERT: H 98 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7090 (ptt-90) REVERT: H 179 GLN cc_start: 0.6800 (OUTLIER) cc_final: 0.6468 (tt0) REVERT: H 230 MET cc_start: 0.7312 (ttp) cc_final: 0.6761 (ttp) REVERT: H 234 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6845 (mt-10) REVERT: R 1 MET cc_start: 0.2356 (mtm) cc_final: 0.1560 (tpt) REVERT: R 25 PHE cc_start: 0.6271 (t80) cc_final: 0.5914 (t80) REVERT: R 47 LEU cc_start: 0.2676 (pp) cc_final: 0.2327 (tp) REVERT: R 60 LYS cc_start: 0.5892 (OUTLIER) cc_final: 0.5367 (mttp) REVERT: R 100 CYS cc_start: 0.7195 (OUTLIER) cc_final: 0.6635 (t) REVERT: R 164 LYS cc_start: 0.5397 (mptp) cc_final: 0.4776 (mppt) REVERT: R 227 LYS cc_start: 0.6615 (mttp) cc_final: 0.5860 (mtmt) REVERT: R 234 MET cc_start: 0.6588 (mmt) cc_final: 0.6083 (mtm) outliers start: 45 outliers final: 27 residues processed: 138 average time/residue: 0.9004 time to fit residues: 135.2576 Evaluate side-chains 128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 61 MET 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 279 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 VAL 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 174 LEU Chi-restraints excluded: chain H residue 179 GLN Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 20 VAL 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 283 THR 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 45 optimal weight: 0.9980 chunk 55 optimal weight: 0.0970 chunk 54 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 84 optimal weight: 0.0370 chunk 35 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.5856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 306 GLN R 161 HIS R 170 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.221385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.166562 restraints weight = 9330.676| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 1.59 r_work: 0.3727 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9182 Z= 0.118 Angle : 0.569 9.837 12441 Z= 0.292 Chirality : 0.041 0.136 1405 Planarity : 0.004 0.052 1567 Dihedral : 4.625 23.713 1241 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.55 % Allowed : 23.98 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1135 helix: 1.92 (0.26), residues: 389 sheet: 0.32 (0.31), residues: 286 loop : -0.62 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.009 0.001 HIS R 161 PHE 0.023 0.001 PHE R 117 TYR 0.008 0.001 TYR R 295 ARG 0.007 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 427) hydrogen bonds : angle 4.62520 ( 1194) covalent geometry : bond 0.00252 ( 9182) covalent geometry : angle 0.56877 (12441) ********************** 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 137 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7711 (m-30) cc_final: 0.7483 (t70) REVERT: A 346 ASN cc_start: 0.7743 (m110) cc_final: 0.7475 (m-40) REVERT: B 96 ARG cc_start: 0.7792 (mtt180) cc_final: 0.7087 (tpp-160) REVERT: G 21 MET cc_start: 0.1824 (mtp) cc_final: 0.1253 (pmm) REVERT: G 31 SER cc_start: 0.3874 (OUTLIER) cc_final: 0.3631 (t) REVERT: G 38 MET cc_start: 0.2416 (mpm) cc_final: 0.1032 (mpm) REVERT: H 30 SER cc_start: 0.7541 (p) cc_final: 0.7243 (p) REVERT: H 55 SER cc_start: 0.6678 (m) cc_final: 0.6081 (t) REVERT: H 82 GLN cc_start: 0.6420 (tt0) cc_final: 0.6063 (mm-40) REVERT: H 93 MET cc_start: 0.7521 (ttt) cc_final: 0.6898 (tpp) REVERT: H 96 CYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7333 (p) REVERT: H 98 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7033 (ptt-90) REVERT: H 179 GLN cc_start: 0.6826 (OUTLIER) cc_final: 0.6434 (tt0) REVERT: H 234 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6755 (mt-10) REVERT: R 1 MET cc_start: 0.2473 (mtm) cc_final: 0.1606 (tpt) REVERT: R 25 PHE cc_start: 0.6202 (t80) cc_final: 0.5849 (t80) REVERT: R 47 LEU cc_start: 0.2763 (pp) cc_final: 0.2485 (tp) REVERT: R 60 LYS cc_start: 0.5827 (OUTLIER) cc_final: 0.5251 (mttp) REVERT: R 84 MET cc_start: 0.4837 (ttm) cc_final: 0.3845 (tpp) REVERT: R 100 CYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6627 (t) REVERT: R 164 LYS cc_start: 0.5359 (mptp) cc_final: 0.4764 (mppt) REVERT: R 227 LYS cc_start: 0.6501 (mttp) cc_final: 0.5787 (mtmt) REVERT: R 234 MET cc_start: 0.6522 (mmt) cc_final: 0.6050 (mtm) outliers start: 34 outliers final: 19 residues processed: 129 average time/residue: 0.9951 time to fit residues: 138.8041 Evaluate side-chains 126 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR 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 279 SER Chi-restraints excluded: chain G residue 31 SER 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 11 LEU Chi-restraints excluded: chain R residue 20 VAL 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 120 VAL Chi-restraints excluded: chain R residue 170 GLN Chi-restraints excluded: chain R residue 283 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 294 ASN A 306 GLN R 133 HIS R 137 ASN R 161 HIS R 170 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.215249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3753 r_free = 0.3753 target = 0.151657 restraints weight = 9299.102| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.77 r_work: 0.3585 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9182 Z= 0.243 Angle : 0.711 9.795 12441 Z= 0.369 Chirality : 0.047 0.166 1405 Planarity : 0.005 0.050 1567 Dihedral : 5.363 27.610 1241 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.17 % Allowed : 23.36 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1135 helix: 1.39 (0.26), residues: 390 sheet: 0.14 (0.30), residues: 288 loop : -0.77 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.012 0.002 HIS R 223 PHE 0.042 0.003 PHE R 117 TYR 0.016 0.002 TYR A 290 ARG 0.009 0.001 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.05138 ( 427) hydrogen bonds : angle 5.07438 ( 1194) covalent geometry : bond 0.00562 ( 9182) covalent geometry : angle 0.71059 (12441) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8044.15 seconds wall clock time: 138 minutes 48.34 seconds (8328.34 seconds total)