Starting phenix.real_space_refine on Fri Nov 15 13:53:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6j_36006/11_2024/8j6j_36006.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6j_36006/11_2024/8j6j_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6j_36006/11_2024/8j6j_36006.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6j_36006/11_2024/8j6j_36006.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6j_36006/11_2024/8j6j_36006.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6j_36006/11_2024/8j6j_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-5513/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: 5.38, 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: 2.63 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.08 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: 2.71 Time building geometry restraints manager: 3.00 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: 0.810 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.140 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.690 ------------------------------------------------------------------------------- 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= 0.243 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 *********************** 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 : 0.981 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: 1.1498 time to fit residues: 200.1523 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 : 1.027 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 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= 0.206 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 *********************** 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 : 1.014 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.5731 (mttt) cc_final: 0.5364 (mmtt) REVERT: A 35 LYS cc_start: 0.7400 (mtmm) cc_final: 0.7027 (mtpp) REVERT: A 207 GLU cc_start: 0.6006 (tt0) cc_final: 0.5758 (tt0) REVERT: A 247 MET cc_start: 0.7361 (mtp) cc_final: 0.7018 (mtp) REVERT: A 248 LYS cc_start: 0.7370 (ttmm) cc_final: 0.7118 (pttp) REVERT: A 305 CYS cc_start: 0.7178 (m) cc_final: 0.6822 (t) REVERT: A 309 ASP cc_start: 0.6519 (m-30) cc_final: 0.6246 (t70) REVERT: A 313 ARG cc_start: 0.5772 (OUTLIER) cc_final: 0.5516 (ptp-170) REVERT: A 346 ASN cc_start: 0.6355 (m-40) cc_final: 0.6053 (m-40) REVERT: B 45 MET cc_start: 0.8463 (mtt) cc_final: 0.8159 (mmm) REVERT: B 46 ARG cc_start: 0.7063 (mmm-85) cc_final: 0.6563 (mmp80) REVERT: B 96 ARG cc_start: 0.6486 (tpt170) cc_final: 0.6047 (mtt180) REVERT: B 146 LEU cc_start: 0.8049 (tp) cc_final: 0.7785 (mm) REVERT: B 195 ASP cc_start: 0.7175 (p0) cc_final: 0.6922 (p0) REVERT: B 217 MET cc_start: 0.7589 (pmt) cc_final: 0.7073 (pmm) REVERT: B 220 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7410 (mt0) REVERT: B 254 ASP cc_start: 0.7313 (t0) cc_final: 0.6946 (t0) REVERT: B 298 ASP cc_start: 0.7784 (t0) cc_final: 0.7394 (t0) REVERT: B 325 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7606 (tpp) REVERT: B 336 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7361 (mt) REVERT: G 21 MET cc_start: 0.1766 (mtp) cc_final: 0.1302 (pmm) REVERT: G 38 MET cc_start: 0.2420 (mpm) cc_final: 0.0301 (mpm) REVERT: G 50 LEU cc_start: 0.1330 (OUTLIER) cc_final: 0.0858 (tt) REVERT: H 30 SER cc_start: 0.6816 (p) cc_final: 0.6534 (p) REVERT: H 55 SER cc_start: 0.6353 (m) cc_final: 0.6024 (m) REVERT: H 71 SER cc_start: 0.5775 (p) cc_final: 0.5344 (t) REVERT: H 93 MET cc_start: 0.7286 (ttm) cc_final: 0.7072 (ttt) REVERT: H 234 GLU cc_start: 0.6048 (mt-10) cc_final: 0.5149 (mm-30) REVERT: R 50 TRP cc_start: 0.3080 (m-10) cc_final: 0.2526 (m-10) REVERT: R 164 LYS cc_start: 0.5491 (mptp) cc_final: 0.4810 (mppt) REVERT: R 183 CYS cc_start: 0.7977 (t) cc_final: 0.7748 (m) REVERT: R 234 MET cc_start: 0.5914 (mmt) cc_final: 0.5265 (mtp) REVERT: R 253 ARG cc_start: 0.4960 (ttt180) cc_final: 0.4730 (tpt-90) REVERT: R 288 MET cc_start: 0.5581 (OUTLIER) cc_final: 0.4955 (tmm) outliers start: 51 outliers final: 11 residues processed: 162 average time/residue: 0.9562 time to fit residues: 168.4142 Evaluate side-chains 123 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU 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 56 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 34 optimal weight: 0.1980 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 H 82 GLN R 112 GLN R 161 HIS ** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9182 Z= 0.203 Angle : 0.590 7.351 12441 Z= 0.305 Chirality : 0.042 0.147 1405 Planarity : 0.004 0.050 1567 Dihedral : 4.335 21.101 1241 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.21 % Allowed : 20.23 % Favored : 74.56 % 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: 1.03 (0.26), residues: 1135 helix: 1.86 (0.26), residues: 396 sheet: 0.88 (0.31), residues: 284 loop : -0.47 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 59 HIS 0.008 0.001 HIS R 161 PHE 0.018 0.002 PHE R 21 TYR 0.016 0.002 TYR B 85 ARG 0.004 0.001 ARG B 49 *********************** 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 160 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 110 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.5740 (mttt) cc_final: 0.5284 (mmtt) REVERT: A 35 LYS cc_start: 0.7375 (mtmm) cc_final: 0.7034 (mtpp) REVERT: A 247 MET cc_start: 0.7480 (mtp) cc_final: 0.7193 (mtp) REVERT: A 248 LYS cc_start: 0.7397 (ttmm) cc_final: 0.7121 (pttp) REVERT: A 305 CYS cc_start: 0.7196 (m) cc_final: 0.6954 (t) REVERT: A 309 ASP cc_start: 0.6598 (m-30) cc_final: 0.6287 (t70) REVERT: A 313 ARG cc_start: 0.5818 (OUTLIER) cc_final: 0.5438 (ptp-170) REVERT: A 331 ASN cc_start: 0.7220 (t0) cc_final: 0.6241 (m-40) REVERT: A 346 ASN cc_start: 0.6440 (m-40) cc_final: 0.6111 (m-40) REVERT: B 45 MET cc_start: 0.8587 (mtt) cc_final: 0.8277 (mtm) REVERT: B 46 ARG cc_start: 0.7133 (mmm-85) cc_final: 0.6679 (mpt180) REVERT: B 96 ARG cc_start: 0.6547 (tpt170) cc_final: 0.6193 (mpt-90) REVERT: B 97 SER cc_start: 0.7666 (OUTLIER) cc_final: 0.7464 (t) REVERT: B 146 LEU cc_start: 0.8058 (tp) cc_final: 0.7795 (mm) REVERT: B 195 ASP cc_start: 0.7194 (p0) cc_final: 0.6927 (p0) REVERT: B 217 MET cc_start: 0.7679 (pmt) cc_final: 0.7255 (pmm) REVERT: B 254 ASP cc_start: 0.7249 (t0) cc_final: 0.6918 (t0) REVERT: B 294 CYS cc_start: 0.7671 (OUTLIER) cc_final: 0.6694 (m) REVERT: B 304 ARG cc_start: 0.6869 (mtp-110) cc_final: 0.6612 (mtp180) REVERT: B 325 MET cc_start: 0.7796 (tpt) cc_final: 0.7567 (mmm) REVERT: B 336 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7494 (mt) REVERT: G 21 MET cc_start: 0.1841 (mtp) cc_final: 0.1287 (pmm) REVERT: G 38 MET cc_start: 0.2642 (mpm) cc_final: 0.0542 (mpm) REVERT: H 30 SER cc_start: 0.7025 (p) cc_final: 0.6752 (p) REVERT: H 55 SER cc_start: 0.6441 (m) cc_final: 0.6142 (m) REVERT: H 71 SER cc_start: 0.6209 (p) cc_final: 0.5669 (t) REVERT: H 96 CYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7224 (p) REVERT: H 230 MET cc_start: 0.6449 (tmm) cc_final: 0.5879 (ttp) REVERT: H 234 GLU cc_start: 0.6367 (mt-10) cc_final: 0.6079 (mt-10) REVERT: R 47 LEU cc_start: 0.2786 (pp) cc_final: 0.2323 (tp) REVERT: R 60 LYS cc_start: 0.4010 (OUTLIER) cc_final: 0.3643 (ptpt) REVERT: R 164 LYS cc_start: 0.5505 (mptp) cc_final: 0.4863 (mppt) REVERT: R 234 MET cc_start: 0.5928 (mmt) cc_final: 0.5346 (mtp) REVERT: R 253 ARG cc_start: 0.5040 (ttt180) cc_final: 0.4797 (tpt-90) REVERT: R 288 MET cc_start: 0.5341 (OUTLIER) cc_final: 0.4966 (tmm) outliers start: 50 outliers final: 15 residues processed: 149 average time/residue: 1.0758 time to fit residues: 172.6903 Evaluate side-chains 128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 A residue 313 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 31 SER 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 60 LYS 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 76 optimal weight: 0.3980 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 96 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 75 GLN B 268 ASN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9182 Z= 0.171 Angle : 0.554 8.721 12441 Z= 0.286 Chirality : 0.041 0.142 1405 Planarity : 0.004 0.049 1567 Dihedral : 4.249 20.444 1241 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.07 % Allowed : 21.38 % Favored : 74.56 % 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: 1.15 (0.26), residues: 1135 helix: 2.23 (0.26), residues: 384 sheet: 0.84 (0.31), residues: 277 loop : -0.50 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.008 0.001 HIS R 161 PHE 0.015 0.001 PHE R 232 TYR 0.011 0.001 TYR B 85 ARG 0.003 0.000 ARG B 49 *********************** 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 153 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.5675 (mttt) cc_final: 0.5213 (mmtt) REVERT: A 35 LYS cc_start: 0.7285 (mtmm) cc_final: 0.6945 (mtpp) REVERT: A 51 LYS cc_start: 0.7350 (mmtm) cc_final: 0.7118 (mmtm) REVERT: A 247 MET cc_start: 0.7446 (mtp) cc_final: 0.7162 (mtp) REVERT: A 248 LYS cc_start: 0.7375 (ttmm) cc_final: 0.7073 (pttp) REVERT: A 281 SER cc_start: 0.6696 (m) cc_final: 0.6336 (t) REVERT: A 309 ASP cc_start: 0.6518 (m-30) cc_final: 0.6245 (t70) REVERT: A 313 ARG cc_start: 0.5806 (OUTLIER) cc_final: 0.5409 (ptp-170) REVERT: A 331 ASN cc_start: 0.7235 (t0) cc_final: 0.6465 (m-40) REVERT: A 346 ASN cc_start: 0.6415 (m-40) cc_final: 0.6087 (m-40) REVERT: B 45 MET cc_start: 0.8565 (mtt) cc_final: 0.8226 (mtm) REVERT: B 46 ARG cc_start: 0.7144 (mmm-85) cc_final: 0.6691 (mpt180) REVERT: B 96 ARG cc_start: 0.6494 (tpt170) cc_final: 0.6108 (mtt180) REVERT: B 195 ASP cc_start: 0.7142 (p0) cc_final: 0.6859 (p0) REVERT: B 219 ARG cc_start: 0.7441 (mmm160) cc_final: 0.6689 (ttm-80) REVERT: B 234 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.6794 (t80) REVERT: B 254 ASP cc_start: 0.7242 (t0) cc_final: 0.6929 (t0) REVERT: B 304 ARG cc_start: 0.6930 (mtp-110) cc_final: 0.6658 (mtp180) REVERT: G 21 MET cc_start: 0.1765 (mtp) cc_final: 0.1226 (pmm) REVERT: G 38 MET cc_start: 0.2500 (mpm) cc_final: 0.0488 (mpm) REVERT: H 30 SER cc_start: 0.7068 (p) cc_final: 0.6779 (p) REVERT: H 55 SER cc_start: 0.6481 (m) cc_final: 0.6185 (m) REVERT: H 71 SER cc_start: 0.6402 (p) cc_final: 0.5821 (t) REVERT: H 96 CYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7282 (p) REVERT: H 230 MET cc_start: 0.6585 (tmm) cc_final: 0.5886 (ttp) REVERT: H 234 GLU cc_start: 0.6418 (mt-10) cc_final: 0.6123 (mt-10) REVERT: R 1 MET cc_start: 0.2291 (mtm) cc_final: 0.1461 (tpt) REVERT: R 47 LEU cc_start: 0.2766 (pp) cc_final: 0.2286 (tp) REVERT: R 164 LYS cc_start: 0.5436 (mptp) cc_final: 0.4853 (mppt) REVERT: R 234 MET cc_start: 0.5947 (mmt) cc_final: 0.5355 (mtm) REVERT: R 253 ARG cc_start: 0.5032 (ttt180) cc_final: 0.4794 (tpt-90) outliers start: 39 outliers final: 16 residues processed: 142 average time/residue: 1.1097 time to fit residues: 170.0498 Evaluate side-chains 122 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 142 GLN Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 217 GLN Chi-restraints excluded: chain R residue 236 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 B 268 ASN R 161 HIS R 170 GLN ** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9182 Z= 0.224 Angle : 0.590 8.775 12441 Z= 0.306 Chirality : 0.042 0.145 1405 Planarity : 0.004 0.049 1567 Dihedral : 4.614 23.120 1241 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.21 % Allowed : 20.96 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.02 (0.25), residues: 1135 helix: 2.02 (0.26), residues: 387 sheet: 0.83 (0.31), residues: 279 loop : -0.55 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.008 0.001 HIS R 161 PHE 0.023 0.002 PHE R 21 TYR 0.015 0.002 TYR B 105 ARG 0.006 0.001 ARG B 137 *********************** 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 167 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 117 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.6495 (OUTLIER) cc_final: 0.6237 (ttt90) REVERT: A 17 LYS cc_start: 0.5783 (mttt) cc_final: 0.5434 (mtmm) REVERT: A 35 LYS cc_start: 0.7490 (mtmm) cc_final: 0.7133 (mtpp) REVERT: A 247 MET cc_start: 0.7467 (mtp) cc_final: 0.7098 (mtp) REVERT: A 248 LYS cc_start: 0.7436 (ttmm) cc_final: 0.7065 (pttp) REVERT: A 281 SER cc_start: 0.6774 (m) cc_final: 0.6506 (t) REVERT: A 309 ASP cc_start: 0.6563 (m-30) cc_final: 0.6337 (t70) REVERT: A 313 ARG cc_start: 0.5846 (OUTLIER) cc_final: 0.5641 (mpt-90) REVERT: A 331 ASN cc_start: 0.7267 (t0) cc_final: 0.6757 (m110) REVERT: A 346 ASN cc_start: 0.6615 (m-40) cc_final: 0.6315 (m-40) REVERT: B 45 MET cc_start: 0.8568 (mtt) cc_final: 0.8255 (mtm) REVERT: B 46 ARG cc_start: 0.7197 (mmm-85) cc_final: 0.6707 (mpt90) REVERT: B 96 ARG cc_start: 0.6591 (tpt170) cc_final: 0.6241 (mpt-90) REVERT: B 195 ASP cc_start: 0.7225 (p0) cc_final: 0.6953 (p0) REVERT: B 219 ARG cc_start: 0.7540 (mmm160) cc_final: 0.6832 (ttm-80) REVERT: B 294 CYS cc_start: 0.7671 (OUTLIER) cc_final: 0.6901 (m) REVERT: B 304 ARG cc_start: 0.6901 (mtp-110) cc_final: 0.6574 (mtp180) REVERT: G 21 MET cc_start: 0.1645 (mtp) cc_final: 0.1124 (pmm) REVERT: G 38 MET cc_start: 0.2531 (mpm) cc_final: 0.2277 (mpm) REVERT: H 30 SER cc_start: 0.7224 (p) cc_final: 0.6918 (p) REVERT: H 55 SER cc_start: 0.6478 (m) cc_final: 0.6177 (m) REVERT: H 96 CYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7378 (p) REVERT: H 98 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.7029 (ptt-90) REVERT: H 230 MET cc_start: 0.6846 (tmm) cc_final: 0.6021 (ttp) REVERT: H 234 GLU cc_start: 0.6757 (mt-10) cc_final: 0.6444 (mt-10) REVERT: R 1 MET cc_start: 0.2473 (mtm) cc_final: 0.1601 (tpt) REVERT: R 47 LEU cc_start: 0.2816 (pp) cc_final: 0.2266 (tp) REVERT: R 91 TRP cc_start: 0.5399 (OUTLIER) cc_final: 0.3943 (m100) REVERT: R 164 LYS cc_start: 0.5303 (mptp) cc_final: 0.4725 (mppt) REVERT: R 234 MET cc_start: 0.6071 (mmt) cc_final: 0.5511 (mtm) REVERT: R 253 ARG cc_start: 0.5048 (ttt180) cc_final: 0.4593 (tpt-90) outliers start: 50 outliers final: 28 residues processed: 155 average time/residue: 1.1073 time to fit residues: 184.8599 Evaluate side-chains 147 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 350 ASP 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 H residue 63 THR Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 91 TRP Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 238 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 294 ASN B 75 GLN B 268 ASN R 133 HIS R 137 ASN R 161 HIS R 170 GLN ** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 9182 Z= 0.466 Angle : 0.767 9.583 12441 Z= 0.405 Chirality : 0.050 0.161 1405 Planarity : 0.006 0.050 1567 Dihedral : 5.706 30.186 1241 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 6.26 % Allowed : 20.13 % 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: 0.26 (0.25), residues: 1135 helix: 1.08 (0.26), residues: 387 sheet: 0.42 (0.30), residues: 302 loop : -0.75 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 82 HIS 0.010 0.002 HIS B 54 PHE 0.034 0.003 PHE R 21 TYR 0.019 0.003 TYR A 290 ARG 0.006 0.001 ARG R 218 *********************** 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 175 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 115 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.6586 (OUTLIER) cc_final: 0.6234 (ttt90) REVERT: A 17 LYS cc_start: 0.5911 (mttt) cc_final: 0.5493 (mtmp) REVERT: A 21 ARG cc_start: 0.6150 (ttm-80) cc_final: 0.5798 (ttm-80) REVERT: A 22 ASN cc_start: 0.6591 (m-40) cc_final: 0.6305 (m-40) REVERT: A 24 ARG cc_start: 0.5763 (tpp-160) cc_final: 0.5347 (mtm-85) REVERT: A 35 LYS cc_start: 0.7797 (mtmm) cc_final: 0.7015 (mttt) REVERT: A 247 MET cc_start: 0.7444 (mtp) cc_final: 0.7065 (mtp) REVERT: A 248 LYS cc_start: 0.7604 (ttmm) cc_final: 0.7148 (ttpp) REVERT: A 305 CYS cc_start: 0.7784 (t) cc_final: 0.7038 (m) REVERT: A 331 ASN cc_start: 0.7382 (t0) cc_final: 0.6908 (m110) REVERT: A 345 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7138 (mtmt) REVERT: A 346 ASN cc_start: 0.6917 (m-40) cc_final: 0.6614 (m-40) REVERT: B 46 ARG cc_start: 0.7286 (mmm-85) cc_final: 0.6751 (mpt180) REVERT: B 96 ARG cc_start: 0.6484 (tpt170) cc_final: 0.6128 (mpt-90) REVERT: B 101 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8126 (ptp) REVERT: B 195 ASP cc_start: 0.7148 (p0) cc_final: 0.6906 (p0) REVERT: B 219 ARG cc_start: 0.7618 (mmm160) cc_final: 0.6894 (ttm-80) REVERT: B 254 ASP cc_start: 0.7374 (t0) cc_final: 0.7174 (t0) REVERT: B 294 CYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7212 (m) REVERT: G 21 MET cc_start: 0.1226 (mtp) cc_final: 0.0802 (pmm) REVERT: G 31 SER cc_start: 0.4021 (OUTLIER) cc_final: 0.3758 (t) REVERT: G 38 MET cc_start: 0.2299 (mpm) cc_final: 0.1918 (mpm) REVERT: H 30 SER cc_start: 0.7629 (p) cc_final: 0.7296 (p) REVERT: H 55 SER cc_start: 0.6785 (m) cc_final: 0.6166 (t) REVERT: H 93 MET cc_start: 0.7625 (ttt) cc_final: 0.7062 (tpp) REVERT: H 96 CYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7437 (p) REVERT: H 98 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.6732 (ptt-90) REVERT: H 234 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6564 (mt-10) REVERT: R 1 MET cc_start: 0.2266 (mtm) cc_final: 0.1526 (tpt) REVERT: R 47 LEU cc_start: 0.2811 (pp) cc_final: 0.2285 (tp) REVERT: R 90 ARG cc_start: 0.6194 (OUTLIER) cc_final: 0.5981 (tpt-90) REVERT: R 91 TRP cc_start: 0.5590 (OUTLIER) cc_final: 0.3844 (m100) REVERT: R 234 MET cc_start: 0.6079 (mmt) cc_final: 0.5549 (mtm) REVERT: R 253 ARG cc_start: 0.5255 (ttt180) cc_final: 0.4836 (tpt-90) outliers start: 60 outliers final: 29 residues processed: 161 average time/residue: 1.1683 time to fit residues: 202.4752 Evaluate side-chains 146 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU 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 A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 101 MET 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 279 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 31 SER 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 184 SER Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain R residue 91 TRP Chi-restraints excluded: chain R residue 97 ASP Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 288 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 91 optimal weight: 0.4980 chunk 60 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 294 ASN R 161 HIS R 170 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9182 Z= 0.209 Angle : 0.617 10.632 12441 Z= 0.320 Chirality : 0.043 0.154 1405 Planarity : 0.005 0.051 1567 Dihedral : 5.090 25.011 1241 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.96 % Allowed : 22.84 % Favored : 73.20 % 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: 0.50 (0.25), residues: 1135 helix: 1.40 (0.26), residues: 396 sheet: 0.41 (0.30), residues: 291 loop : -0.63 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 99 HIS 0.012 0.001 HIS R 223 PHE 0.021 0.002 PHE R 117 TYR 0.011 0.001 TYR A 290 ARG 0.009 0.001 ARG A 205 *********************** 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 147 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.6010 (tt0) REVERT: A 15 ARG cc_start: 0.6578 (OUTLIER) cc_final: 0.6290 (ttt90) REVERT: A 17 LYS cc_start: 0.5839 (mttt) cc_final: 0.5436 (mtmm) REVERT: A 22 ASN cc_start: 0.6478 (m-40) cc_final: 0.6235 (m-40) REVERT: A 24 ARG cc_start: 0.5820 (tpp-160) cc_final: 0.5463 (mtm-85) REVERT: A 35 LYS cc_start: 0.7663 (mtmm) cc_final: 0.6899 (mttt) REVERT: A 247 MET cc_start: 0.7435 (mtp) cc_final: 0.7018 (mtp) REVERT: A 248 LYS cc_start: 0.7456 (ttmm) cc_final: 0.7047 (pttp) REVERT: A 313 ARG cc_start: 0.5678 (OUTLIER) cc_final: 0.5432 (mpt-90) REVERT: A 346 ASN cc_start: 0.6877 (m-40) cc_final: 0.6591 (m-40) REVERT: B 46 ARG cc_start: 0.7165 (mmm-85) cc_final: 0.6754 (mpt180) REVERT: B 96 ARG cc_start: 0.6510 (tpt170) cc_final: 0.6154 (mpt-90) REVERT: B 195 ASP cc_start: 0.7363 (p0) cc_final: 0.7126 (p0) REVERT: B 219 ARG cc_start: 0.7615 (mmm160) cc_final: 0.6937 (ttm-80) REVERT: B 228 ASP cc_start: 0.7446 (p0) cc_final: 0.6286 (p0) REVERT: B 254 ASP cc_start: 0.7342 (t0) cc_final: 0.7030 (t0) REVERT: B 294 CYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7141 (m) REVERT: G 21 MET cc_start: 0.1476 (mtp) cc_final: 0.1042 (pmm) REVERT: G 31 SER cc_start: 0.4006 (OUTLIER) cc_final: 0.3745 (t) REVERT: G 38 MET cc_start: 0.2208 (mpm) cc_final: 0.1993 (mpm) REVERT: H 30 SER cc_start: 0.7631 (p) cc_final: 0.7308 (p) REVERT: H 55 SER cc_start: 0.6660 (m) cc_final: 0.6076 (t) REVERT: H 93 MET cc_start: 0.7695 (ttt) cc_final: 0.7127 (tpp) REVERT: H 96 CYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7566 (p) REVERT: H 98 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7323 (ptt-90) REVERT: H 230 MET cc_start: 0.7359 (ttp) cc_final: 0.6229 (ttp) REVERT: H 234 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6642 (mt-10) REVERT: R 1 MET cc_start: 0.2315 (mtm) cc_final: 0.1517 (tpt) REVERT: R 47 LEU cc_start: 0.2752 (pp) cc_final: 0.2437 (tp) REVERT: R 164 LYS cc_start: 0.5189 (mptp) cc_final: 0.4436 (mppt) REVERT: R 227 LYS cc_start: 0.5519 (mttp) cc_final: 0.4761 (mtmt) REVERT: R 234 MET cc_start: 0.6043 (mmt) cc_final: 0.5506 (mtm) REVERT: R 253 ARG cc_start: 0.5214 (ttt180) cc_final: 0.4765 (tpt-90) outliers start: 38 outliers final: 18 residues processed: 137 average time/residue: 1.1234 time to fit residues: 165.4470 Evaluate side-chains 128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 15 ARG 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 313 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 283 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 0.0970 chunk 98 optimal weight: 0.0870 chunk 103 optimal weight: 1.9990 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 294 ASN R 161 HIS R 170 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.4810 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= 0.220 Angle : 0.603 9.027 12441 Z= 0.314 Chirality : 0.042 0.138 1405 Planarity : 0.005 0.053 1567 Dihedral : 4.968 24.071 1241 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.07 % Allowed : 22.84 % Favored : 73.10 % 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: 0.56 (0.25), residues: 1135 helix: 1.52 (0.26), residues: 396 sheet: 0.34 (0.30), residues: 293 loop : -0.59 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 99 HIS 0.007 0.001 HIS R 161 PHE 0.026 0.002 PHE R 117 TYR 0.011 0.002 TYR A 290 ARG 0.006 0.001 ARG A 205 *********************** 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 145 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 106 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.6292 (OUTLIER) cc_final: 0.6005 (tt0) REVERT: A 15 ARG cc_start: 0.6538 (OUTLIER) cc_final: 0.6133 (ttt90) REVERT: A 17 LYS cc_start: 0.5858 (mttt) cc_final: 0.5470 (mtmm) REVERT: A 22 ASN cc_start: 0.6475 (m-40) cc_final: 0.6230 (m-40) REVERT: A 24 ARG cc_start: 0.5782 (tpp-160) cc_final: 0.5531 (mtm-85) REVERT: A 35 LYS cc_start: 0.7631 (mtmm) cc_final: 0.6854 (mttt) REVERT: A 205 ARG cc_start: 0.5778 (ttp-110) cc_final: 0.5230 (mtm110) REVERT: A 247 MET cc_start: 0.7496 (mtp) cc_final: 0.7069 (mtp) REVERT: A 248 LYS cc_start: 0.7473 (ttmm) cc_final: 0.7066 (pttp) REVERT: A 309 ASP cc_start: 0.6931 (t70) cc_final: 0.6642 (t70) REVERT: A 313 ARG cc_start: 0.5734 (OUTLIER) cc_final: 0.5477 (mpt-90) REVERT: A 346 ASN cc_start: 0.6822 (m-40) cc_final: 0.6550 (m-40) REVERT: B 46 ARG cc_start: 0.7198 (mmm-85) cc_final: 0.6746 (mpt180) REVERT: B 96 ARG cc_start: 0.6504 (tpt170) cc_final: 0.6146 (mpt-90) REVERT: B 219 ARG cc_start: 0.7560 (mmm160) cc_final: 0.6927 (ttm-80) REVERT: B 228 ASP cc_start: 0.7439 (p0) cc_final: 0.6320 (p0) REVERT: B 294 CYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7144 (m) REVERT: G 21 MET cc_start: 0.1569 (mtp) cc_final: 0.1078 (pmm) REVERT: G 31 SER cc_start: 0.3986 (OUTLIER) cc_final: 0.3716 (t) REVERT: G 38 MET cc_start: 0.2368 (mpm) cc_final: 0.2144 (mpm) REVERT: H 30 SER cc_start: 0.7627 (p) cc_final: 0.7301 (p) REVERT: H 55 SER cc_start: 0.6652 (m) cc_final: 0.6065 (t) REVERT: H 93 MET cc_start: 0.7715 (ttt) cc_final: 0.7134 (tpp) REVERT: H 96 CYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7573 (p) REVERT: H 98 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7322 (ptt-90) REVERT: H 230 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.7170 (ttp) REVERT: H 234 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6622 (mt-10) REVERT: R 1 MET cc_start: 0.2339 (mtm) cc_final: 0.1531 (tpt) REVERT: R 25 PHE cc_start: 0.6477 (t80) cc_final: 0.6128 (t80) REVERT: R 47 LEU cc_start: 0.2729 (pp) cc_final: 0.2412 (tp) REVERT: R 60 LYS cc_start: 0.5295 (OUTLIER) cc_final: 0.4805 (mttp) REVERT: R 84 MET cc_start: 0.4754 (ttm) cc_final: 0.3945 (tpp) REVERT: R 100 CYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6698 (t) REVERT: R 164 LYS cc_start: 0.5239 (mptp) cc_final: 0.4628 (mppt) REVERT: R 227 LYS cc_start: 0.5538 (mttp) cc_final: 0.4795 (mtmt) REVERT: R 234 MET cc_start: 0.6022 (mmt) cc_final: 0.5493 (mtm) REVERT: R 253 ARG cc_start: 0.5250 (ttt180) cc_final: 0.4810 (tpt-90) outliers start: 39 outliers final: 19 residues processed: 135 average time/residue: 1.2359 time to fit residues: 178.3196 Evaluate side-chains 133 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 15 ARG 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 313 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 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 H residue 82 GLN Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 230 MET 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 100 CYS Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 201 LEU 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 94 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.0370 chunk 66 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 294 ASN H 194 ASN R 137 ASN R 161 HIS R 170 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.4855 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= 0.193 Angle : 0.585 10.017 12441 Z= 0.302 Chirality : 0.042 0.134 1405 Planarity : 0.004 0.051 1567 Dihedral : 4.756 22.707 1241 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.65 % Allowed : 23.57 % Favored : 72.78 % 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: 0.65 (0.25), residues: 1135 helix: 1.64 (0.26), residues: 397 sheet: 0.38 (0.30), residues: 291 loop : -0.58 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.008 0.001 HIS R 161 PHE 0.022 0.002 PHE R 117 TYR 0.009 0.001 TYR A 290 ARG 0.006 0.001 ARG A 205 *********************** 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 144 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.6325 (ttt90) REVERT: A 17 LYS cc_start: 0.5889 (mttt) cc_final: 0.5253 (mmtt) REVERT: A 22 ASN cc_start: 0.6447 (m-40) cc_final: 0.6198 (m-40) REVERT: A 24 ARG cc_start: 0.5812 (tpp-160) cc_final: 0.5588 (mtm-85) REVERT: A 35 LYS cc_start: 0.7599 (mtmm) cc_final: 0.6819 (mttt) REVERT: A 205 ARG cc_start: 0.5974 (ttp-110) cc_final: 0.5458 (mtm110) REVERT: A 247 MET cc_start: 0.7454 (mtp) cc_final: 0.7000 (mtp) REVERT: A 248 LYS cc_start: 0.7471 (ttmm) cc_final: 0.7062 (pttp) REVERT: A 309 ASP cc_start: 0.6915 (t70) cc_final: 0.6634 (t70) REVERT: A 346 ASN cc_start: 0.6791 (m-40) cc_final: 0.6551 (m-40) REVERT: B 46 ARG cc_start: 0.7185 (mmm-85) cc_final: 0.6639 (mmp80) REVERT: B 96 ARG cc_start: 0.6558 (tpt170) cc_final: 0.6232 (mpt-90) REVERT: B 219 ARG cc_start: 0.7557 (mmm160) cc_final: 0.6922 (ttm-80) REVERT: B 294 CYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7032 (m) REVERT: G 21 MET cc_start: 0.1671 (mtp) cc_final: 0.1156 (pmm) REVERT: G 31 SER cc_start: 0.4051 (OUTLIER) cc_final: 0.3772 (t) REVERT: G 38 MET cc_start: 0.2343 (mpm) cc_final: 0.2125 (mpm) REVERT: H 30 SER cc_start: 0.7491 (p) cc_final: 0.7169 (p) REVERT: H 55 SER cc_start: 0.6637 (m) cc_final: 0.6049 (t) REVERT: H 93 MET cc_start: 0.7743 (ttt) cc_final: 0.7153 (tpp) REVERT: H 96 CYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7594 (p) REVERT: H 98 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7245 (ptt-90) REVERT: H 230 MET cc_start: 0.7377 (ttp) cc_final: 0.6613 (ttp) REVERT: H 234 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6596 (mt-10) REVERT: R 1 MET cc_start: 0.2435 (mtm) cc_final: 0.1564 (tpt) REVERT: R 25 PHE cc_start: 0.6363 (t80) cc_final: 0.6034 (t80) REVERT: R 47 LEU cc_start: 0.2743 (pp) cc_final: 0.2439 (tp) REVERT: R 60 LYS cc_start: 0.5095 (OUTLIER) cc_final: 0.4593 (mttp) REVERT: R 84 MET cc_start: 0.4763 (ttm) cc_final: 0.3929 (tpp) REVERT: R 100 CYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6639 (t) REVERT: R 164 LYS cc_start: 0.5195 (mptp) cc_final: 0.4586 (mppt) REVERT: R 178 SER cc_start: 0.7347 (p) cc_final: 0.6628 (m) REVERT: R 227 LYS cc_start: 0.5502 (mttp) cc_final: 0.4765 (mtmt) REVERT: R 234 MET cc_start: 0.6053 (mmt) cc_final: 0.5517 (mtm) REVERT: R 253 ARG cc_start: 0.5255 (ttt180) cc_final: 0.4812 (tpt-90) outliers start: 35 outliers final: 21 residues processed: 138 average time/residue: 1.2151 time to fit residues: 179.5456 Evaluate side-chains 132 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 15 ARG 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 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 H residue 82 GLN Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain R residue 11 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 120 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 111 optimal weight: 0.2980 chunk 102 optimal weight: 0.9980 chunk 88 optimal weight: 0.3980 chunk 9 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 294 ASN R 161 HIS R 170 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9182 Z= 0.171 Angle : 0.570 10.191 12441 Z= 0.295 Chirality : 0.041 0.130 1405 Planarity : 0.004 0.052 1567 Dihedral : 4.601 22.115 1241 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.13 % Allowed : 23.98 % 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: 0.74 (0.25), residues: 1135 helix: 1.77 (0.26), residues: 397 sheet: 0.50 (0.31), residues: 284 loop : -0.63 (0.29), 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 0.019 0.001 PHE R 117 TYR 0.010 0.001 TYR R 269 ARG 0.007 0.000 ARG B 137 ********************** 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: 30 poor density : 107 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.5857 (mttt) cc_final: 0.5264 (mmtt) REVERT: A 22 ASN cc_start: 0.6446 (m-40) cc_final: 0.6202 (m-40) REVERT: A 24 ARG cc_start: 0.5812 (tpp-160) cc_final: 0.5549 (mtm-85) REVERT: A 35 LYS cc_start: 0.7537 (mtmm) cc_final: 0.6753 (mttt) REVERT: A 205 ARG cc_start: 0.6035 (ttp-110) cc_final: 0.5496 (mtm110) REVERT: A 247 MET cc_start: 0.7469 (mtp) cc_final: 0.7035 (mtp) REVERT: A 248 LYS cc_start: 0.7459 (ttmm) cc_final: 0.7057 (pttp) REVERT: A 309 ASP cc_start: 0.6891 (t70) cc_final: 0.6631 (t70) REVERT: B 46 ARG cc_start: 0.7168 (mmm-85) cc_final: 0.6608 (mmp80) REVERT: B 96 ARG cc_start: 0.6556 (tpt170) cc_final: 0.6228 (mpt-90) REVERT: B 219 ARG cc_start: 0.7536 (mmm160) cc_final: 0.6890 (ttm-80) REVERT: B 294 CYS cc_start: 0.7677 (OUTLIER) cc_final: 0.6968 (m) REVERT: B 298 ASP cc_start: 0.7859 (t0) cc_final: 0.7352 (t0) REVERT: G 21 MET cc_start: 0.1676 (mtp) cc_final: 0.1172 (pmm) REVERT: G 31 SER cc_start: 0.4064 (OUTLIER) cc_final: 0.3780 (t) REVERT: G 38 MET cc_start: 0.2322 (mpm) cc_final: 0.2119 (mpm) REVERT: H 30 SER cc_start: 0.7367 (p) cc_final: 0.7026 (p) REVERT: H 55 SER cc_start: 0.6587 (m) cc_final: 0.5987 (t) REVERT: H 93 MET cc_start: 0.7714 (ttt) cc_final: 0.7100 (tpp) REVERT: H 98 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7210 (ptt-90) REVERT: H 230 MET cc_start: 0.7417 (ttp) cc_final: 0.6442 (ttp) REVERT: H 234 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6560 (mt-10) REVERT: R 1 MET cc_start: 0.2416 (mtm) cc_final: 0.1536 (tpt) REVERT: R 25 PHE cc_start: 0.6314 (t80) cc_final: 0.5605 (t80) REVERT: R 47 LEU cc_start: 0.2720 (pp) cc_final: 0.2424 (tp) REVERT: R 60 LYS cc_start: 0.5095 (OUTLIER) cc_final: 0.4566 (mttp) REVERT: R 84 MET cc_start: 0.4892 (ttm) cc_final: 0.3925 (tpt) REVERT: R 100 CYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6626 (t) REVERT: R 164 LYS cc_start: 0.5296 (mptp) cc_final: 0.4708 (mppt) REVERT: R 178 SER cc_start: 0.7243 (p) cc_final: 0.6498 (m) REVERT: R 227 LYS cc_start: 0.5512 (mttp) cc_final: 0.4768 (mtmt) REVERT: R 234 MET cc_start: 0.6047 (mmt) cc_final: 0.5505 (mtm) REVERT: R 253 ARG cc_start: 0.5262 (ttt180) cc_final: 0.4873 (tpt-90) outliers start: 30 outliers final: 19 residues processed: 131 average time/residue: 1.2097 time to fit residues: 169.7073 Evaluate side-chains 127 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain R residue 11 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 170 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 0.0770 chunk 5 optimal weight: 4.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 294 ASN ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.220939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.172646 restraints weight = 9207.332| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 1.34 r_work: 0.3729 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 9182 Z= 0.201 Angle : 0.961 59.198 12441 Z= 0.542 Chirality : 0.042 0.410 1405 Planarity : 0.004 0.052 1567 Dihedral : 4.614 22.104 1241 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.02 % Allowed : 24.30 % Favored : 72.68 % Cbeta Deviations : 0.09 % 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 (0.25), residues: 1135 helix: 1.77 (0.26), residues: 397 sheet: 0.51 (0.31), residues: 284 loop : -0.66 (0.29), residues: 454 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 0.001 PHE R 117 TYR 0.010 0.001 TYR R 269 ARG 0.006 0.000 ARG B 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3576.74 seconds wall clock time: 65 minutes 7.98 seconds (3907.98 seconds total)