Starting phenix.real_space_refine on Sun Aug 24 04:34:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u4w_63857/08_2025/9u4w_63857_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u4w_63857/08_2025/9u4w_63857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u4w_63857/08_2025/9u4w_63857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u4w_63857/08_2025/9u4w_63857.map" model { file = "/net/cci-nas-00/data/ceres_data/9u4w_63857/08_2025/9u4w_63857_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u4w_63857/08_2025/9u4w_63857_neut.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.050 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 55 5.16 5 C 5628 2.51 5 N 1506 2.21 5 O 1620 1.98 5 H 8492 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17301 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3455 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 5048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5048 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 90 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 830 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "R" Number of atoms: 4448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 4448 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 257} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3429 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 3.54, per 1000 atoms: 0.20 Number of scatterers: 17301 At special positions: 0 Unit cell: (111.69, 114.61, 127.75, 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) S 55 16.00 O 1620 8.00 N 1506 7.00 C 5628 6.00 H 8492 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 528.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 13 sheets defined 38.4% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.636A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.996A pdb=" N ARG A 248 " --> pdb=" O ARG A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 296 through 316 Processing helix chain 'A' and resid 335 through 357 Processing helix chain 'B' and resid 9 through 30 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.805A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 32 through 62 removed outlier: 3.822A pdb=" N LYS R 36 " --> pdb=" O THR R 32 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE R 37 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG R 38 " --> pdb=" O SER R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 104 removed outlier: 3.866A pdb=" N MET R 95 " --> pdb=" O THR R 91 " (cutoff:3.500A) Proline residue: R 96 - end of helix Processing helix chain 'R' and resid 110 through 145 removed outlier: 3.916A pdb=" N LEU R 122 " --> pdb=" O SER R 118 " (cutoff:3.500A) Proline residue: R 128 - end of helix Processing helix chain 'R' and resid 145 through 150 Processing helix chain 'R' and resid 151 through 153 No H-bonds generated for 'chain 'R' and resid 151 through 153' Processing helix chain 'R' and resid 154 through 172 removed outlier: 4.327A pdb=" N ILE R 160 " --> pdb=" O GLY R 156 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP R 164 " --> pdb=" O ILE R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 178 removed outlier: 3.751A pdb=" N ILE R 177 " --> pdb=" O PRO R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 220 Processing helix chain 'R' and resid 220 through 243 Processing helix chain 'R' and resid 257 through 293 Proline residue: R 282 - end of helix Processing helix chain 'R' and resid 294 through 298 removed outlier: 3.937A pdb=" N VAL R 297 " --> pdb=" O PRO R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 308 removed outlier: 3.860A pdb=" N PHE R 308 " --> pdb=" O VAL R 304 " (cutoff:3.500A) Processing helix chain 'R' and resid 309 through 312 removed outlier: 4.055A pdb=" N ALA R 312 " --> pdb=" O PHE R 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 309 through 312' Processing helix chain 'R' and resid 313 through 327 removed outlier: 3.751A pdb=" N CYS R 317 " --> pdb=" O PHE R 313 " (cutoff:3.500A) Proline residue: R 320 - end of helix Processing helix chain 'S' and resid 27 through 31 Processing helix chain 'S' and resid 52 through 55 removed outlier: 4.235A pdb=" N GLY S 55 " --> pdb=" O SER S 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 52 through 55' Processing helix chain 'S' and resid 86 through 90 Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.511A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 189 removed outlier: 6.948A pdb=" N ARG A 35 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU A 37 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N VAL A 222 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU A 39 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N ASP A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE A 219 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE A 255 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE A 221 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN A 257 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL A 223 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 254 " --> pdb=" O TYR A 325 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 6.701A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA B 333 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU B 323 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLY B 335 " --> pdb=" O SER B 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.527A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 75 " --> pdb=" O TRP B 87 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS B 96 " --> pdb=" O ILE B 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 110 removed outlier: 3.629A pdb=" N GLY B 120 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER B 127 " --> pdb=" O CYS B 119 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG B 142 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 158 removed outlier: 6.485A pdb=" N SER B 165 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N CYS B 154 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL B 163 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N PHE B 156 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N GLN B 161 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 162 " --> pdb=" O TRP B 174 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN B 180 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 7.137A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 237 removed outlier: 3.648A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 281 through 283 removed outlier: 3.525A pdb=" N GLY B 311 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 180 through 182 Processing sheet with id=AB1, first strand: chain 'S' and resid 2 through 6 removed outlier: 3.774A pdb=" N LEU S 19 " --> pdb=" O LEU S 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 9 through 11 removed outlier: 3.620A pdb=" N GLY S 9 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN S 38 " --> pdb=" O MET S 92 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N MET S 33 " --> pdb=" O TYR S 49 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N TYR S 49 " --> pdb=" O MET S 33 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP S 35 " --> pdb=" O VAL S 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 4.062A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR S 243 " --> pdb=" O TYR S 227 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL S 226 " --> pdb=" O GLN S 179 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1155 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: 4.35 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.02: 8460 1.02 - 1.22: 33 1.22 - 1.42: 3880 1.42 - 1.62: 5048 1.62 - 1.82: 81 Bond restraints: 17502 Sorted by residual: bond pdb=" N PCA F 1 " pdb=" H PCA F 1 " ideal model delta sigma weight residual 0.860 1.009 -0.149 2.00e-02 2.50e+03 5.54e+01 bond pdb=" SG CYS B 238 " pdb=" HG CYS B 238 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" CA PCA F 1 " pdb=" HA PCA F 1 " ideal model delta sigma weight residual 0.970 1.100 -0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" ND2 ASN R 305 " pdb="HD22 ASN R 305 " ideal model delta sigma weight residual 0.860 0.982 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" CG PCA F 1 " pdb=" HG3 PCA F 1 " ideal model delta sigma weight residual 0.970 1.092 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 17497 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.93: 31394 6.93 - 13.86: 2 13.86 - 20.79: 0 20.79 - 27.72: 1 27.72 - 34.65: 2 Bond angle restraints: 31399 Sorted by residual: angle pdb=" N GLU A 274 " pdb=" CA GLU A 274 " pdb=" HA GLU A 274 " ideal model delta sigma weight residual 110.00 75.35 34.65 3.00e+00 1.11e-01 1.33e+02 angle pdb=" C GLU A 274 " pdb=" CA GLU A 274 " pdb=" HA GLU A 274 " ideal model delta sigma weight residual 109.00 76.46 32.54 3.00e+00 1.11e-01 1.18e+02 angle pdb=" CB GLU A 274 " pdb=" CA GLU A 274 " pdb=" HA GLU A 274 " ideal model delta sigma weight residual 109.00 82.94 26.06 3.00e+00 1.11e-01 7.54e+01 angle pdb=" N GLU A 274 " pdb=" CA GLU A 274 " pdb=" C GLU A 274 " ideal model delta sigma weight residual 110.80 119.34 -8.54 2.13e+00 2.20e-01 1.61e+01 angle pdb=" N ILE R 226 " pdb=" CA ILE R 226 " pdb=" CB ILE R 226 " ideal model delta sigma weight residual 110.58 116.58 -6.00 1.50e+00 4.44e-01 1.60e+01 ... (remaining 31394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.74: 8045 31.74 - 63.48: 248 63.48 - 95.22: 20 95.22 - 126.95: 0 126.95 - 158.69: 1 Dihedral angle restraints: 8314 sinusoidal: 4365 harmonic: 3949 Sorted by residual: dihedral pdb=" N GLU A 274 " pdb=" C GLU A 274 " pdb=" CA GLU A 274 " pdb=" CB GLU A 274 " ideal model delta harmonic sigma weight residual 122.80 140.41 -17.61 0 2.50e+00 1.60e-01 4.96e+01 dihedral pdb=" C GLU A 274 " pdb=" N GLU A 274 " pdb=" CA GLU A 274 " pdb=" CB GLU A 274 " ideal model delta harmonic sigma weight residual -122.60 -139.60 17.00 0 2.50e+00 1.60e-01 4.63e+01 dihedral pdb=" N PCA F 1 " pdb=" CA PCA F 1 " pdb=" CB PCA F 1 " pdb=" HB3 PCA F 1 " ideal model delta sinusoidal sigma weight residual 273.91 115.22 158.69 1 3.00e+01 1.11e-03 2.06e+01 ... (remaining 8311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 1370 0.146 - 0.292: 1 0.292 - 0.437: 0 0.437 - 0.583: 0 0.583 - 0.729: 1 Chirality restraints: 1372 Sorted by residual: chirality pdb=" CA GLU A 274 " pdb=" N GLU A 274 " pdb=" C GLU A 274 " pdb=" CB GLU A 274 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CA ILE S 189 " pdb=" N ILE S 189 " pdb=" C ILE S 189 " pdb=" CB ILE S 189 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA PRO R 29 " pdb=" N PRO R 29 " pdb=" C PRO R 29 " pdb=" CB PRO R 29 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 1369 not shown) Planarity restraints: 2614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN R 305 " -0.284 2.00e-02 2.50e+03 4.46e-01 2.98e+03 pdb=" CG ASN R 305 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN R 305 " 0.274 2.00e-02 2.50e+03 pdb=" ND2 ASN R 305 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN R 305 " 0.709 2.00e-02 2.50e+03 pdb="HD22 ASN R 305 " -0.730 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 102 " -0.147 2.00e-02 2.50e+03 1.44e-01 3.09e+02 pdb=" CG ASN R 102 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN R 102 " 0.135 2.00e-02 2.50e+03 pdb=" ND2 ASN R 102 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN R 102 " 0.201 2.00e-02 2.50e+03 pdb="HD22 ASN R 102 " -0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 124 " -0.082 2.00e-02 2.50e+03 7.85e-02 9.26e+01 pdb=" CG ASN B 124 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN B 124 " 0.073 2.00e-02 2.50e+03 pdb=" ND2 ASN B 124 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN B 124 " 0.108 2.00e-02 2.50e+03 pdb="HD22 ASN B 124 " -0.115 2.00e-02 2.50e+03 ... (remaining 2611 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 845 2.18 - 2.79: 34875 2.79 - 3.39: 47701 3.39 - 4.00: 61499 4.00 - 4.60: 95154 Nonbonded interactions: 240074 Sorted by model distance: nonbonded pdb=" OE1 GLU A 287 " pdb=" H GLU A 287 " model vdw 1.577 2.450 nonbonded pdb=" O ILE B 63 " pdb=" HG SER B 321 " model vdw 1.626 2.450 nonbonded pdb=" HE ARG S 180 " pdb=" O GLU S 222 " model vdw 1.648 2.450 nonbonded pdb=" OE1 GLU S 5 " pdb=" H GLY S 113 " model vdw 1.657 2.450 nonbonded pdb="HH21 ARG B 256 " pdb=" OE2 GLU B 265 " model vdw 1.659 2.450 ... (remaining 240069 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 0.110 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.120 Find NCS groups from input model: 0.070 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 9012 Z= 0.209 Angle : 0.565 8.536 12225 Z= 0.320 Chirality : 0.044 0.729 1372 Planarity : 0.004 0.039 1552 Dihedral : 13.614 87.815 3185 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.11 % Allowed : 1.81 % Favored : 98.09 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.26), residues: 1102 helix: 2.29 (0.27), residues: 370 sheet: -0.91 (0.31), residues: 277 loop : -1.19 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 66 TYR 0.019 0.001 TYR R 283 PHE 0.014 0.001 PHE R 276 TRP 0.019 0.001 TRP R 291 HIS 0.005 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9010) covalent geometry : angle 0.56397 (12223) SS BOND : bond 0.00146 ( 1) SS BOND : angle 2.39721 ( 2) hydrogen bonds : bond 0.18797 ( 414) hydrogen bonds : angle 7.64423 ( 1155) Misc. bond : bond 0.10171 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue MET 192 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue THR 238 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 TYR cc_start: 0.7164 (t80) cc_final: 0.6912 (t80) REVERT: B 202 ARG cc_start: 0.7803 (mmm160) cc_final: 0.7544 (tpp80) REVERT: B 326 THR cc_start: 0.7648 (p) cc_final: 0.7300 (p) REVERT: R 175 LEU cc_start: 0.7247 (mm) cc_final: 0.7029 (mt) REVERT: R 212 ASN cc_start: 0.6870 (m-40) cc_final: 0.6551 (m-40) REVERT: S 226 VAL cc_start: 0.8284 (t) cc_final: 0.7910 (p) outliers start: 1 outliers final: 1 residues processed: 267 average time/residue: 0.2962 time to fit residues: 100.8580 Evaluate side-chains 183 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 179 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN B 18 GLN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN R 102 ASN R 208 GLN ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.183346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.148295 restraints weight = 34778.595| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.75 r_work: 0.3790 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9012 Z= 0.129 Angle : 0.529 6.591 12225 Z= 0.286 Chirality : 0.042 0.409 1372 Planarity : 0.004 0.040 1552 Dihedral : 4.746 47.293 1225 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.17 % Allowed : 7.66 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.26), residues: 1102 helix: 2.47 (0.26), residues: 380 sheet: -0.84 (0.30), residues: 308 loop : -0.89 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 97 TYR 0.011 0.001 TYR S 190 PHE 0.016 0.001 PHE A 187 TRP 0.016 0.001 TRP F 3 HIS 0.006 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9010) covalent geometry : angle 0.52841 (12223) SS BOND : bond 0.00184 ( 1) SS BOND : angle 2.41293 ( 2) hydrogen bonds : bond 0.04613 ( 414) hydrogen bonds : angle 5.59712 ( 1155) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue MET 192 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue THR 238 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 187 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 PHE cc_start: 0.7430 (p90) cc_final: 0.5039 (t80) REVERT: A 283 TYR cc_start: 0.7463 (t80) cc_final: 0.7202 (t80) REVERT: B 326 THR cc_start: 0.7754 (p) cc_final: 0.7404 (p) outliers start: 11 outliers final: 11 residues processed: 196 average time/residue: 0.2798 time to fit residues: 71.0532 Evaluate side-chains 172 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain R residue 179 ARG Chi-restraints excluded: chain R residue 181 ILE Chi-restraints excluded: chain R residue 213 PHE Chi-restraints excluded: chain R residue 327 SER Chi-restraints excluded: chain S residue 16 SER Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN ** R 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 GLN ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.175330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.142453 restraints weight = 35559.496| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.53 r_work: 0.3685 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9012 Z= 0.209 Angle : 0.568 6.733 12225 Z= 0.306 Chirality : 0.043 0.418 1372 Planarity : 0.004 0.040 1552 Dihedral : 4.872 44.788 1225 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.70 % Allowed : 10.21 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.27), residues: 1102 helix: 2.37 (0.26), residues: 375 sheet: -1.01 (0.30), residues: 301 loop : -0.83 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 31 TYR 0.018 0.002 TYR R 283 PHE 0.015 0.002 PHE B 204 TRP 0.011 0.002 TRP R 291 HIS 0.008 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 9010) covalent geometry : angle 0.56731 (12223) SS BOND : bond 0.00356 ( 1) SS BOND : angle 2.63660 ( 2) hydrogen bonds : bond 0.04493 ( 414) hydrogen bonds : angle 5.15686 ( 1155) Misc. bond : bond 0.00242 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue MET 192 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue THR 238 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 PHE cc_start: 0.7811 (p90) cc_final: 0.4889 (t80) REVERT: B 37 GLN cc_start: 0.8466 (mt0) cc_final: 0.7896 (mp10) REVERT: B 202 ARG cc_start: 0.8580 (ttm110) cc_final: 0.8146 (tpt-90) REVERT: B 264 GLN cc_start: 0.7555 (mm110) cc_final: 0.7300 (tt0) REVERT: B 267 MET cc_start: 0.7852 (mmm) cc_final: 0.7527 (mmm) REVERT: B 326 THR cc_start: 0.7863 (p) cc_final: 0.7558 (p) REVERT: R 264 ARG cc_start: 0.7316 (mtp85) cc_final: 0.7010 (ttt90) REVERT: S 6 SER cc_start: 0.7964 (t) cc_final: 0.7763 (p) REVERT: S 244 LYS cc_start: 0.8021 (tptt) cc_final: 0.7660 (tptt) outliers start: 16 outliers final: 15 residues processed: 192 average time/residue: 0.2494 time to fit residues: 62.9204 Evaluate side-chains 183 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 179 ARG Chi-restraints excluded: chain R residue 181 ILE Chi-restraints excluded: chain R residue 213 PHE Chi-restraints excluded: chain R residue 327 SER Chi-restraints excluded: chain S residue 16 SER Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN R 195 GLN R 208 GLN R 305 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.177799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.143401 restraints weight = 35121.501| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.79 r_work: 0.3707 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9012 Z= 0.124 Angle : 0.503 6.705 12225 Z= 0.268 Chirality : 0.041 0.413 1372 Planarity : 0.004 0.038 1552 Dihedral : 4.675 46.214 1225 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.81 % Allowed : 11.28 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.27), residues: 1102 helix: 2.40 (0.26), residues: 382 sheet: -1.15 (0.30), residues: 303 loop : -0.61 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 66 TYR 0.013 0.001 TYR R 283 PHE 0.013 0.001 PHE R 308 TRP 0.012 0.001 TRP R 291 HIS 0.007 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9010) covalent geometry : angle 0.50246 (12223) SS BOND : bond 0.00317 ( 1) SS BOND : angle 1.80233 ( 2) hydrogen bonds : bond 0.03837 ( 414) hydrogen bonds : angle 4.87175 ( 1155) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue MET 192 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue THR 238 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 PHE cc_start: 0.7752 (p90) cc_final: 0.4822 (t80) REVERT: B 264 GLN cc_start: 0.7468 (mm110) cc_final: 0.7245 (tt0) REVERT: R 152 ASN cc_start: 0.6927 (m-40) cc_final: 0.6680 (t0) REVERT: R 326 PHE cc_start: 0.8058 (m-80) cc_final: 0.7837 (m-80) outliers start: 17 outliers final: 14 residues processed: 189 average time/residue: 0.2464 time to fit residues: 62.0961 Evaluate side-chains 176 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 179 ARG Chi-restraints excluded: chain R residue 181 ILE Chi-restraints excluded: chain R residue 327 SER Chi-restraints excluded: chain S residue 16 SER Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 41 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.172266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.138917 restraints weight = 35506.391| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.65 r_work: 0.3628 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9012 Z= 0.254 Angle : 0.584 6.641 12225 Z= 0.317 Chirality : 0.044 0.417 1372 Planarity : 0.005 0.043 1552 Dihedral : 4.988 44.895 1225 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.98 % Allowed : 11.91 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.26), residues: 1102 helix: 2.16 (0.26), residues: 375 sheet: -1.25 (0.30), residues: 300 loop : -0.82 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 66 TYR 0.020 0.002 TYR R 283 PHE 0.015 0.002 PHE B 156 TRP 0.013 0.002 TRP B 302 HIS 0.009 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 9010) covalent geometry : angle 0.58310 (12223) SS BOND : bond 0.00414 ( 1) SS BOND : angle 1.87279 ( 2) hydrogen bonds : bond 0.04296 ( 414) hydrogen bonds : angle 4.96710 ( 1155) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue MET 192 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue THR 238 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 PHE cc_start: 0.7986 (p90) cc_final: 0.4949 (t80) REVERT: B 235 ASN cc_start: 0.8084 (m-40) cc_final: 0.7316 (t0) REVERT: R 152 ASN cc_start: 0.6971 (m-40) cc_final: 0.6748 (t0) REVERT: R 267 LYS cc_start: 0.7631 (mmtt) cc_final: 0.7159 (mtmt) REVERT: S 18 LYS cc_start: 0.8428 (ttpp) cc_final: 0.8022 (ttmt) outliers start: 28 outliers final: 24 residues processed: 184 average time/residue: 0.2517 time to fit residues: 62.2104 Evaluate side-chains 185 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain R residue 101 TRP Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 179 ARG Chi-restraints excluded: chain R residue 194 SER Chi-restraints excluded: chain R residue 327 SER Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 16 SER Chi-restraints excluded: chain S residue 20 SER Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 ASN ** S 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.171691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.132954 restraints weight = 35076.164| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.90 r_work: 0.3576 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9012 Z= 0.231 Angle : 0.563 6.597 12225 Z= 0.305 Chirality : 0.043 0.416 1372 Planarity : 0.004 0.044 1552 Dihedral : 4.993 45.885 1225 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.09 % Allowed : 12.98 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.26), residues: 1102 helix: 2.26 (0.26), residues: 367 sheet: -1.26 (0.30), residues: 297 loop : -0.82 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 66 TYR 0.018 0.002 TYR R 283 PHE 0.014 0.002 PHE R 276 TRP 0.011 0.002 TRP B 302 HIS 0.007 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 9010) covalent geometry : angle 0.56222 (12223) SS BOND : bond 0.00358 ( 1) SS BOND : angle 1.74366 ( 2) hydrogen bonds : bond 0.04134 ( 414) hydrogen bonds : angle 4.89320 ( 1155) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue MET 192 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue THR 238 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 PHE cc_start: 0.6969 (t80) cc_final: 0.6721 (t80) REVERT: B 235 ASN cc_start: 0.7900 (m-40) cc_final: 0.7104 (t0) REVERT: B 244 ASN cc_start: 0.7993 (m110) cc_final: 0.7684 (m110) REVERT: B 289 LEU cc_start: 0.6259 (OUTLIER) cc_final: 0.6033 (mp) REVERT: R 267 LYS cc_start: 0.7405 (mmtt) cc_final: 0.6898 (mtmt) REVERT: S 18 LYS cc_start: 0.8436 (ttpp) cc_final: 0.8013 (ttmt) outliers start: 29 outliers final: 24 residues processed: 185 average time/residue: 0.2214 time to fit residues: 56.0350 Evaluate side-chains 185 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain R residue 101 TRP Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 179 ARG Chi-restraints excluded: chain R residue 181 ILE Chi-restraints excluded: chain R residue 194 SER Chi-restraints excluded: chain R residue 212 ASN Chi-restraints excluded: chain R residue 327 SER Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 16 SER Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 109 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 ASN ** S 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.173654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.135525 restraints weight = 34947.846| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.86 r_work: 0.3614 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9012 Z= 0.144 Angle : 0.517 6.646 12225 Z= 0.277 Chirality : 0.042 0.414 1372 Planarity : 0.004 0.041 1552 Dihedral : 4.819 47.284 1225 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.45 % Allowed : 14.15 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.27), residues: 1102 helix: 2.36 (0.26), residues: 372 sheet: -1.23 (0.30), residues: 299 loop : -0.71 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 27 TYR 0.015 0.001 TYR R 283 PHE 0.012 0.001 PHE B 246 TRP 0.008 0.001 TRP S 46 HIS 0.006 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9010) covalent geometry : angle 0.51711 (12223) SS BOND : bond 0.00355 ( 1) SS BOND : angle 1.53390 ( 2) hydrogen bonds : bond 0.03836 ( 414) hydrogen bonds : angle 4.73538 ( 1155) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue MET 192 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue THR 238 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 PHE cc_start: 0.7878 (p90) cc_final: 0.4907 (t80) REVERT: B 235 ASN cc_start: 0.7856 (m-40) cc_final: 0.7066 (t0) REVERT: B 244 ASN cc_start: 0.8007 (m110) cc_final: 0.7715 (m110) REVERT: B 267 MET cc_start: 0.7613 (mmm) cc_final: 0.7328 (mmm) REVERT: B 289 LEU cc_start: 0.6229 (OUTLIER) cc_final: 0.5997 (mp) REVERT: R 267 LYS cc_start: 0.7397 (mmtt) cc_final: 0.6931 (mtmt) REVERT: S 18 LYS cc_start: 0.8443 (ttpp) cc_final: 0.8046 (ttmt) outliers start: 23 outliers final: 20 residues processed: 181 average time/residue: 0.1863 time to fit residues: 46.1768 Evaluate side-chains 182 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain R residue 101 TRP Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 179 ARG Chi-restraints excluded: chain R residue 181 ILE Chi-restraints excluded: chain R residue 194 SER Chi-restraints excluded: chain R residue 327 SER Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 16 SER Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 ASN ** S 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.172156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133166 restraints weight = 34957.092| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.97 r_work: 0.3574 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9012 Z= 0.189 Angle : 0.532 6.597 12225 Z= 0.286 Chirality : 0.042 0.415 1372 Planarity : 0.004 0.042 1552 Dihedral : 4.838 47.390 1225 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.98 % Allowed : 14.26 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.27), residues: 1102 helix: 2.30 (0.26), residues: 372 sheet: -1.21 (0.31), residues: 294 loop : -0.71 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 160 TYR 0.018 0.002 TYR R 283 PHE 0.012 0.001 PHE R 276 TRP 0.010 0.002 TRP B 302 HIS 0.006 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 9010) covalent geometry : angle 0.53163 (12223) SS BOND : bond 0.00343 ( 1) SS BOND : angle 1.55082 ( 2) hydrogen bonds : bond 0.03869 ( 414) hydrogen bonds : angle 4.71436 ( 1155) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue MET 192 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue THR 238 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 LEU cc_start: 0.8253 (tp) cc_final: 0.8015 (tt) REVERT: B 235 ASN cc_start: 0.7853 (m-40) cc_final: 0.7071 (t0) REVERT: B 244 ASN cc_start: 0.8038 (m110) cc_final: 0.7704 (m110) REVERT: B 289 LEU cc_start: 0.6294 (OUTLIER) cc_final: 0.6020 (mp) REVERT: R 267 LYS cc_start: 0.7358 (mmtt) cc_final: 0.6820 (mtmt) REVERT: S 18 LYS cc_start: 0.8423 (ttpp) cc_final: 0.7973 (ttmt) outliers start: 28 outliers final: 24 residues processed: 181 average time/residue: 0.2046 time to fit residues: 50.8727 Evaluate side-chains 182 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain R residue 101 TRP Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 179 ARG Chi-restraints excluded: chain R residue 194 SER Chi-restraints excluded: chain R residue 327 SER Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 16 SER Chi-restraints excluded: chain S residue 20 SER Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 31 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.174550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.135714 restraints weight = 34981.030| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.99 r_work: 0.3613 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9012 Z= 0.122 Angle : 0.510 8.027 12225 Z= 0.272 Chirality : 0.041 0.413 1372 Planarity : 0.004 0.041 1552 Dihedral : 4.657 48.591 1225 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.34 % Allowed : 14.79 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.27), residues: 1102 helix: 2.49 (0.26), residues: 373 sheet: -1.15 (0.31), residues: 294 loop : -0.61 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 160 TYR 0.013 0.001 TYR R 283 PHE 0.012 0.001 PHE R 178 TRP 0.007 0.001 TRP B 87 HIS 0.005 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9010) covalent geometry : angle 0.51006 (12223) SS BOND : bond 0.00293 ( 1) SS BOND : angle 1.48314 ( 2) hydrogen bonds : bond 0.03580 ( 414) hydrogen bonds : angle 4.55536 ( 1155) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue MET 192 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue THR 238 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 ASN cc_start: 0.7899 (m-40) cc_final: 0.7070 (t0) REVERT: B 244 ASN cc_start: 0.8011 (m110) cc_final: 0.7683 (m110) REVERT: B 289 LEU cc_start: 0.6211 (OUTLIER) cc_final: 0.5958 (mp) REVERT: G 42 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8133 (mm-30) REVERT: R 267 LYS cc_start: 0.7315 (mmtt) cc_final: 0.6778 (mtmt) outliers start: 22 outliers final: 21 residues processed: 175 average time/residue: 0.2000 time to fit residues: 47.2080 Evaluate side-chains 178 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain R residue 101 TRP Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 179 ARG Chi-restraints excluded: chain R residue 181 ILE Chi-restraints excluded: chain R residue 194 SER Chi-restraints excluded: chain R residue 327 SER Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 20 SER Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 63 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 11 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.178994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.145166 restraints weight = 35345.732| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.77 r_work: 0.3696 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9012 Z= 0.109 Angle : 0.493 6.884 12225 Z= 0.261 Chirality : 0.041 0.412 1372 Planarity : 0.004 0.038 1552 Dihedral : 4.500 49.663 1225 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.91 % Allowed : 15.53 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.27), residues: 1102 helix: 2.65 (0.26), residues: 373 sheet: -1.04 (0.31), residues: 294 loop : -0.52 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 160 TYR 0.012 0.001 TYR R 283 PHE 0.012 0.001 PHE R 178 TRP 0.008 0.001 TRP S 46 HIS 0.005 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9010) covalent geometry : angle 0.49302 (12223) SS BOND : bond 0.00258 ( 1) SS BOND : angle 1.47534 ( 2) hydrogen bonds : bond 0.03371 ( 414) hydrogen bonds : angle 4.43025 ( 1155) Misc. bond : bond 0.00001 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 149 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue MET 192 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue THR 238 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 PHE cc_start: 0.7093 (t80) cc_final: 0.6827 (t80) REVERT: B 235 ASN cc_start: 0.7853 (m-40) cc_final: 0.7015 (t0) REVERT: B 289 LEU cc_start: 0.6238 (OUTLIER) cc_final: 0.5966 (mp) REVERT: G 42 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8047 (mm-30) REVERT: R 212 ASN cc_start: 0.7805 (m-40) cc_final: 0.7541 (m-40) REVERT: R 267 LYS cc_start: 0.7450 (mmtt) cc_final: 0.6977 (mtmt) REVERT: S 220 GLU cc_start: 0.6956 (mp0) cc_final: 0.6621 (mp0) outliers start: 18 outliers final: 17 residues processed: 181 average time/residue: 0.2067 time to fit residues: 50.7235 Evaluate side-chains 176 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain R residue 101 TRP Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 179 ARG Chi-restraints excluded: chain R residue 327 SER Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 20 SER Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.177171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.143182 restraints weight = 35938.732| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.76 r_work: 0.3660 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9012 Z= 0.164 Angle : 0.525 6.636 12225 Z= 0.279 Chirality : 0.042 0.414 1372 Planarity : 0.004 0.040 1552 Dihedral : 4.587 48.915 1225 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.66 % Allowed : 15.11 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.27), residues: 1102 helix: 2.68 (0.26), residues: 366 sheet: -1.06 (0.31), residues: 294 loop : -0.57 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 160 TYR 0.016 0.001 TYR R 283 PHE 0.016 0.001 PHE B 246 TRP 0.008 0.001 TRP S 46 HIS 0.006 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 9010) covalent geometry : angle 0.52454 (12223) SS BOND : bond 0.00296 ( 1) SS BOND : angle 1.50415 ( 2) hydrogen bonds : bond 0.03574 ( 414) hydrogen bonds : angle 4.48835 ( 1155) Misc. bond : bond 0.00001 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4796.54 seconds wall clock time: 82 minutes 9.39 seconds (4929.39 seconds total)