Starting phenix.real_space_refine on Sat Aug 23 00:19:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ast_43825/08_2025/9ast_43825.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ast_43825/08_2025/9ast_43825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ast_43825/08_2025/9ast_43825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ast_43825/08_2025/9ast_43825.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ast_43825/08_2025/9ast_43825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ast_43825/08_2025/9ast_43825.map" } resolution = 3.07 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= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 5667 2.51 5 N 1496 2.21 5 O 1651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 8876 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1758 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "L" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 80 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "R" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 276} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 6, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 2578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2578 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "E" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Time building chain proxies: 2.16, per 1000 atoms: 0.24 Number of scatterers: 8876 At special positions: 0 Unit cell: (90.2, 124.64, 127.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1651 8.00 N 1496 7.00 C 5667 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 259 " distance=1.59 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 175 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 668.4 milliseconds Enol-peptide restraints added in 1.4 microseconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 38.3% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.803A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 removed outlier: 4.011A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.219A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.900A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.637A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.699A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'R' and resid 25 through 59 removed outlier: 4.648A pdb=" N PHE R 29 " --> pdb=" O GLN R 25 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU R 32 " --> pdb=" O VAL R 28 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N CYS R 39 " --> pdb=" O THR R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 84 Processing helix chain 'R' and resid 85 through 87 No H-bonds generated for 'chain 'R' and resid 85 through 87' Processing helix chain 'R' and resid 88 through 94 removed outlier: 3.934A pdb=" N HIS R 92 " --> pdb=" O ILE R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 133 Processing helix chain 'R' and resid 133 through 139 removed outlier: 3.634A pdb=" N THR R 137 " --> pdb=" O SER R 133 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG R 139 " --> pdb=" O LEU R 135 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 167 removed outlier: 3.842A pdb=" N ARG R 146 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL R 147 " --> pdb=" O LEU R 143 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU R 163 " --> pdb=" O LEU R 159 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASP R 164 " --> pdb=" O SER R 160 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE R 166 " --> pdb=" O ILE R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 215 removed outlier: 3.549A pdb=" N TYR R 183 " --> pdb=" O GLU R 179 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER R 215 " --> pdb=" O THR R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 253 removed outlier: 4.090A pdb=" N THR R 223 " --> pdb=" O ARG R 219 " (cutoff:3.500A) Proline residue: R 240 - end of helix removed outlier: 3.785A pdb=" N THR R 253 " --> pdb=" O THR R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 278 removed outlier: 3.677A pdb=" N LYS R 262 " --> pdb=" O SER R 258 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN R 263 " --> pdb=" O CYS R 259 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN R 264 " --> pdb=" O GLU R 260 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 288 Proline residue: R 284 - end of helix Processing helix chain 'R' and resid 291 through 303 removed outlier: 3.790A pdb=" N ARG R 303 " --> pdb=" O LYS R 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 10 through 21 removed outlier: 3.823A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.089A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 9 through 10 Processing sheet with id=AA3, first strand: chain 'R' and resid 169 through 170 removed outlier: 3.791A pdb=" N LYS R 169 " --> pdb=" O ASP R 176 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP R 176 " --> pdb=" O LYS R 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.613A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.622A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.845A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.786A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.872A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.513A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.819A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.698A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'E' and resid 182 through 183 removed outlier: 6.717A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.50 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2477 1.33 - 1.45: 1652 1.45 - 1.57: 4850 1.57 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 9064 Sorted by residual: bond pdb=" CA ASN B 237 " pdb=" C ASN B 237 " ideal model delta sigma weight residual 1.524 1.460 0.064 1.26e-02 6.30e+03 2.59e+01 bond pdb=" CA ILE G 28 " pdb=" C ILE G 28 " ideal model delta sigma weight residual 1.524 1.489 0.035 8.60e-03 1.35e+04 1.70e+01 bond pdb=" CA TYR G 40 " pdb=" C TYR G 40 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.26e-02 6.30e+03 1.15e+01 bond pdb=" N VAL A 225 " pdb=" CA VAL A 225 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.11e-02 8.12e+03 9.52e+00 bond pdb=" CA ALA G 33 " pdb=" CB ALA G 33 " ideal model delta sigma weight residual 1.530 1.483 0.046 1.56e-02 4.11e+03 8.81e+00 ... (remaining 9059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 12053 2.25 - 4.49: 197 4.49 - 6.74: 32 6.74 - 8.98: 5 8.98 - 11.23: 1 Bond angle restraints: 12288 Sorted by residual: angle pdb=" N ALA G 10 " pdb=" CA ALA G 10 " pdb=" C ALA G 10 " ideal model delta sigma weight residual 111.82 105.31 6.51 1.16e+00 7.43e-01 3.15e+01 angle pdb=" N GLN R 25 " pdb=" CA GLN R 25 " pdb=" C GLN R 25 " ideal model delta sigma weight residual 112.38 106.00 6.38 1.22e+00 6.72e-01 2.73e+01 angle pdb=" CB GLN B 9 " pdb=" CG GLN B 9 " pdb=" CD GLN B 9 " ideal model delta sigma weight residual 112.60 120.84 -8.24 1.70e+00 3.46e-01 2.35e+01 angle pdb=" N GLU G 22 " pdb=" CA GLU G 22 " pdb=" C GLU G 22 " ideal model delta sigma weight residual 111.33 116.96 -5.63 1.21e+00 6.83e-01 2.16e+01 angle pdb=" N LEU G 51 " pdb=" CA LEU G 51 " pdb=" C LEU G 51 " ideal model delta sigma weight residual 111.56 104.69 6.87 1.53e+00 4.27e-01 2.02e+01 ... (remaining 12283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4677 17.91 - 35.83: 527 35.83 - 53.74: 119 53.74 - 71.66: 27 71.66 - 89.57: 5 Dihedral angle restraints: 5355 sinusoidal: 2056 harmonic: 3299 Sorted by residual: dihedral pdb=" CB CYS R 102 " pdb=" SG CYS R 102 " pdb=" SG CYS R 175 " pdb=" CB CYS R 175 " ideal model delta sinusoidal sigma weight residual -86.00 -175.57 89.57 1 1.00e+01 1.00e-02 9.53e+01 dihedral pdb=" CB CYS R 22 " pdb=" SG CYS R 22 " pdb=" SG CYS R 259 " pdb=" CB CYS R 259 " ideal model delta sinusoidal sigma weight residual -86.00 -166.34 80.34 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" CA TYR E 101 " pdb=" C TYR E 101 " pdb=" N TYR E 102 " pdb=" CA TYR E 102 " ideal model delta harmonic sigma weight residual 180.00 163.05 16.95 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 5352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1173 0.056 - 0.112: 189 0.112 - 0.167: 39 0.167 - 0.223: 7 0.223 - 0.279: 3 Chirality restraints: 1411 Sorted by residual: chirality pdb=" CB VAL A 233 " pdb=" CA VAL A 233 " pdb=" CG1 VAL A 233 " pdb=" CG2 VAL A 233 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA LEU A 39 " pdb=" N LEU A 39 " pdb=" C LEU A 39 " pdb=" CB LEU A 39 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CG LEU R 37 " pdb=" CB LEU R 37 " pdb=" CD1 LEU R 37 " pdb=" CD2 LEU R 37 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1408 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " -0.052 5.00e-02 4.00e+02 7.90e-02 9.99e+00 pdb=" N PRO G 60 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.042 5.00e-02 4.00e+02 6.28e-02 6.30e+00 pdb=" N PRO G 49 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO G 53 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " 0.025 5.00e-02 4.00e+02 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 0.11 - 1.07: 3 1.07 - 2.03: 12 2.03 - 2.99: 4427 2.99 - 3.94: 22714 3.94 - 4.90: 43515 Warning: very small nonbonded interaction distances. Nonbonded interactions: 70671 Sorted by model distance: nonbonded pdb=" O SER G 57 " pdb=" CD GLN G 58 " model vdw 0.114 3.270 nonbonded pdb=" C SER G 57 " pdb=" NE2 GLN G 58 " model vdw 0.366 3.350 nonbonded pdb=" O ASN G 59 " pdb=" N PHE G 61 " model vdw 0.933 3.120 nonbonded pdb=" O GLN G 58 " pdb=" N PRO G 60 " model vdw 1.180 3.120 nonbonded pdb=" O SER G 57 " pdb=" OE1 GLN G 58 " model vdw 1.197 3.040 ... (remaining 70666 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.770 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 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 : 0.006 0.444 9067 Z= 0.363 Angle : 0.743 24.722 12294 Z= 0.449 Chirality : 0.047 0.279 1411 Planarity : 0.004 0.079 1539 Dihedral : 15.898 89.165 3214 Min Nonbonded Distance : 0.114 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.36 % Allowed : 2.42 % Favored : 97.22 % Rotamer: Outliers : 2.16 % Allowed : 20.33 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.26), residues: 1116 helix: 1.91 (0.27), residues: 375 sheet: 0.22 (0.32), residues: 282 loop : -1.12 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 9 TYR 0.018 0.001 TYR R 128 PHE 0.021 0.001 PHE R 167 TRP 0.012 0.001 TRP B 63 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 9064) covalent geometry : angle 0.69867 (12288) SS BOND : bond 0.25634 ( 3) SS BOND : angle 11.47491 ( 6) hydrogen bonds : bond 0.18417 ( 432) hydrogen bonds : angle 6.77550 ( 1236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 17 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.6824 (tt0) REVERT: G 22 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.5903 (mp0) outliers start: 21 outliers final: 13 residues processed: 158 average time/residue: 0.1216 time to fit residues: 24.9347 Evaluate side-chains 151 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain E residue 91 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN B 340 ASN E 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.163372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.132897 restraints weight = 12218.190| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.30 r_work: 0.3503 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9067 Z= 0.161 Angle : 0.531 6.936 12294 Z= 0.282 Chirality : 0.041 0.149 1411 Planarity : 0.004 0.065 1539 Dihedral : 7.471 66.940 1263 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.06 % Favored : 97.85 % Rotamer: Outliers : 3.18 % Allowed : 19.71 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.77 (0.26), residues: 1116 helix: 2.33 (0.27), residues: 375 sheet: 0.44 (0.31), residues: 283 loop : -1.01 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 137 TYR 0.017 0.002 TYR E 178 PHE 0.017 0.002 PHE R 167 TRP 0.022 0.002 TRP B 169 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9064) covalent geometry : angle 0.53079 (12288) SS BOND : bond 0.00427 ( 3) SS BOND : angle 0.79930 ( 6) hydrogen bonds : bond 0.04984 ( 432) hydrogen bonds : angle 4.91927 ( 1236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7609 (mtp) cc_final: 0.7384 (ttm) REVERT: B 150 ARG cc_start: 0.8631 (mmt-90) cc_final: 0.8282 (mmt180) REVERT: B 170 ASP cc_start: 0.8011 (t70) cc_final: 0.7720 (t70) REVERT: G 22 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.5902 (mp0) outliers start: 31 outliers final: 18 residues processed: 159 average time/residue: 0.1091 time to fit residues: 22.8468 Evaluate side-chains 152 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 106 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 GLN E 167 GLN E 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.164137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.133628 restraints weight = 12102.330| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.30 r_work: 0.3525 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9067 Z= 0.116 Angle : 0.480 7.081 12294 Z= 0.251 Chirality : 0.040 0.148 1411 Planarity : 0.003 0.052 1539 Dihedral : 5.903 62.222 1242 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.24 % Favored : 97.67 % Rotamer: Outliers : 3.08 % Allowed : 21.56 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.26), residues: 1116 helix: 2.65 (0.27), residues: 376 sheet: 0.54 (0.31), residues: 288 loop : -1.02 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 62 TYR 0.016 0.001 TYR E 178 PHE 0.014 0.001 PHE R 109 TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9064) covalent geometry : angle 0.47966 (12288) SS BOND : bond 0.00333 ( 3) SS BOND : angle 0.55403 ( 6) hydrogen bonds : bond 0.04161 ( 432) hydrogen bonds : angle 4.47838 ( 1236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7595 (mtp) cc_final: 0.7353 (ttm) REVERT: B 150 ARG cc_start: 0.8628 (mmt-90) cc_final: 0.8282 (mmt180) REVERT: G 22 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.5983 (mp0) outliers start: 30 outliers final: 18 residues processed: 155 average time/residue: 0.1072 time to fit residues: 21.8946 Evaluate side-chains 155 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 63 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.163976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.133305 restraints weight = 12214.099| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.32 r_work: 0.3511 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9067 Z= 0.124 Angle : 0.475 7.610 12294 Z= 0.250 Chirality : 0.040 0.140 1411 Planarity : 0.003 0.048 1539 Dihedral : 5.506 60.128 1240 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.33 % Favored : 97.58 % Rotamer: Outliers : 4.11 % Allowed : 20.94 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.26), residues: 1116 helix: 2.79 (0.27), residues: 375 sheet: 0.53 (0.31), residues: 288 loop : -1.00 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.016 0.001 TYR E 178 PHE 0.015 0.001 PHE R 109 TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9064) covalent geometry : angle 0.47457 (12288) SS BOND : bond 0.00339 ( 3) SS BOND : angle 0.57138 ( 6) hydrogen bonds : bond 0.04101 ( 432) hydrogen bonds : angle 4.34113 ( 1236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8423 (mmmm) cc_final: 0.7883 (mmmm) REVERT: A 37 LEU cc_start: 0.8436 (tt) cc_final: 0.8206 (tp) REVERT: A 349 LYS cc_start: 0.7877 (ttpp) cc_final: 0.7667 (ttpp) REVERT: R 37 LEU cc_start: 0.7989 (mm) cc_final: 0.7756 (mm) REVERT: R 171 LEU cc_start: 0.7023 (mp) cc_final: 0.6786 (mp) REVERT: B 150 ARG cc_start: 0.8626 (mmt-90) cc_final: 0.8295 (mmt180) REVERT: B 217 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7792 (ptp) REVERT: B 289 TYR cc_start: 0.8109 (m-80) cc_final: 0.7810 (m-80) REVERT: G 22 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.6050 (mp0) outliers start: 40 outliers final: 23 residues processed: 163 average time/residue: 0.1175 time to fit residues: 24.9978 Evaluate side-chains 163 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain L residue 4 GLU Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 70 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 57 optimal weight: 0.0170 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.164255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.133371 restraints weight = 12176.039| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.32 r_work: 0.3509 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9067 Z= 0.120 Angle : 0.474 7.763 12294 Z= 0.247 Chirality : 0.040 0.141 1411 Planarity : 0.003 0.045 1539 Dihedral : 5.266 61.744 1238 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.24 % Favored : 97.67 % Rotamer: Outliers : 3.70 % Allowed : 21.66 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.26), residues: 1116 helix: 2.84 (0.27), residues: 376 sheet: 0.50 (0.31), residues: 289 loop : -1.00 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.015 0.001 TYR E 178 PHE 0.015 0.001 PHE R 109 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9064) covalent geometry : angle 0.47419 (12288) SS BOND : bond 0.00321 ( 3) SS BOND : angle 0.55529 ( 6) hydrogen bonds : bond 0.04001 ( 432) hydrogen bonds : angle 4.25412 ( 1236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 LYS cc_start: 0.7891 (ttpp) cc_final: 0.7542 (ttpp) REVERT: R 37 LEU cc_start: 0.8020 (mm) cc_final: 0.7779 (mm) REVERT: R 171 LEU cc_start: 0.7110 (mp) cc_final: 0.6857 (mp) REVERT: B 150 ARG cc_start: 0.8613 (mmt-90) cc_final: 0.8301 (mmt180) REVERT: B 228 ASP cc_start: 0.7965 (m-30) cc_final: 0.7704 (m-30) REVERT: B 289 TYR cc_start: 0.8110 (m-80) cc_final: 0.7872 (m-80) REVERT: G 22 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.6047 (mp0) outliers start: 36 outliers final: 28 residues processed: 164 average time/residue: 0.1240 time to fit residues: 26.7035 Evaluate side-chains 167 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 82 optimal weight: 0.0370 chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.164046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.133233 restraints weight = 12112.452| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.32 r_work: 0.3510 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9067 Z= 0.129 Angle : 0.478 7.179 12294 Z= 0.249 Chirality : 0.040 0.140 1411 Planarity : 0.003 0.045 1539 Dihedral : 5.151 61.693 1238 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.51 % Favored : 97.40 % Rotamer: Outliers : 3.90 % Allowed : 21.46 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.26), residues: 1116 helix: 2.86 (0.27), residues: 376 sheet: 0.49 (0.31), residues: 285 loop : -1.02 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.015 0.001 TYR E 178 PHE 0.016 0.001 PHE R 109 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9064) covalent geometry : angle 0.47760 (12288) SS BOND : bond 0.00338 ( 3) SS BOND : angle 0.60525 ( 6) hydrogen bonds : bond 0.04099 ( 432) hydrogen bonds : angle 4.23451 ( 1236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8406 (tt) cc_final: 0.8189 (tp) REVERT: A 349 LYS cc_start: 0.7886 (ttpp) cc_final: 0.7520 (ttpp) REVERT: R 37 LEU cc_start: 0.8018 (mm) cc_final: 0.7759 (mm) REVERT: R 171 LEU cc_start: 0.7032 (mp) cc_final: 0.6774 (mp) REVERT: B 150 ARG cc_start: 0.8613 (mmt-90) cc_final: 0.8292 (mmt180) REVERT: B 228 ASP cc_start: 0.7994 (m-30) cc_final: 0.7636 (m-30) REVERT: B 237 ASN cc_start: 0.8110 (t0) cc_final: 0.7884 (t0) REVERT: B 289 TYR cc_start: 0.8110 (m-80) cc_final: 0.7889 (m-80) REVERT: G 22 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.6019 (mp0) outliers start: 38 outliers final: 29 residues processed: 164 average time/residue: 0.1183 time to fit residues: 25.5927 Evaluate side-chains 169 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain L residue 4 GLU Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 chunk 60 optimal weight: 0.0770 chunk 76 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 82 optimal weight: 0.4980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 49 ASN E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.164680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.133990 restraints weight = 12160.872| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.30 r_work: 0.3516 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9067 Z= 0.114 Angle : 0.466 7.034 12294 Z= 0.243 Chirality : 0.039 0.140 1411 Planarity : 0.003 0.043 1539 Dihedral : 5.056 63.307 1238 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.33 % Favored : 97.58 % Rotamer: Outliers : 3.49 % Allowed : 22.28 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.26), residues: 1116 helix: 2.94 (0.27), residues: 376 sheet: 0.50 (0.31), residues: 284 loop : -1.00 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 251 TYR 0.015 0.001 TYR E 178 PHE 0.015 0.001 PHE R 109 TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9064) covalent geometry : angle 0.46552 (12288) SS BOND : bond 0.00303 ( 3) SS BOND : angle 0.54088 ( 6) hydrogen bonds : bond 0.03879 ( 432) hydrogen bonds : angle 4.18540 ( 1236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8418 (tt) cc_final: 0.8176 (tp) REVERT: A 349 LYS cc_start: 0.7892 (ttpp) cc_final: 0.7532 (ttpp) REVERT: R 37 LEU cc_start: 0.8033 (mm) cc_final: 0.7784 (mm) REVERT: R 171 LEU cc_start: 0.7104 (mp) cc_final: 0.6867 (mp) REVERT: B 228 ASP cc_start: 0.7980 (m-30) cc_final: 0.7720 (m-30) REVERT: B 237 ASN cc_start: 0.8113 (t0) cc_final: 0.7857 (t0) REVERT: B 289 TYR cc_start: 0.8095 (m-80) cc_final: 0.7887 (m-80) REVERT: G 22 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.6012 (mp0) outliers start: 34 outliers final: 29 residues processed: 160 average time/residue: 0.1219 time to fit residues: 25.6557 Evaluate side-chains 165 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 50 optimal weight: 0.0980 chunk 49 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 83 optimal weight: 0.0030 chunk 78 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.165824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.135049 restraints weight = 12112.256| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.32 r_work: 0.3530 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9067 Z= 0.101 Angle : 0.461 6.775 12294 Z= 0.239 Chirality : 0.039 0.140 1411 Planarity : 0.003 0.039 1539 Dihedral : 4.956 63.691 1238 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.24 % Favored : 97.67 % Rotamer: Outliers : 3.08 % Allowed : 23.41 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.26), residues: 1116 helix: 3.01 (0.27), residues: 376 sheet: 0.51 (0.31), residues: 284 loop : -0.97 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.015 0.001 TYR E 178 PHE 0.014 0.001 PHE R 109 TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 9064) covalent geometry : angle 0.46121 (12288) SS BOND : bond 0.00276 ( 3) SS BOND : angle 0.47836 ( 6) hydrogen bonds : bond 0.03663 ( 432) hydrogen bonds : angle 4.11474 ( 1236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8412 (tt) cc_final: 0.8184 (tp) REVERT: A 349 LYS cc_start: 0.7860 (ttpp) cc_final: 0.7507 (ttpp) REVERT: R 37 LEU cc_start: 0.8030 (mm) cc_final: 0.7781 (mm) REVERT: R 171 LEU cc_start: 0.7088 (mp) cc_final: 0.6832 (mp) REVERT: B 197 ARG cc_start: 0.7698 (mmm160) cc_final: 0.7495 (mmm160) REVERT: B 228 ASP cc_start: 0.7974 (m-30) cc_final: 0.7702 (m-30) REVERT: G 22 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.6059 (mp0) outliers start: 30 outliers final: 29 residues processed: 152 average time/residue: 0.1154 time to fit residues: 22.8771 Evaluate side-chains 157 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 249 THR Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 0.0170 chunk 59 optimal weight: 0.0070 chunk 18 optimal weight: 0.4980 chunk 10 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 248 GLN B 239 ASN E 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.165859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.135371 restraints weight = 12071.818| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.29 r_work: 0.3537 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9067 Z= 0.097 Angle : 0.466 6.687 12294 Z= 0.239 Chirality : 0.039 0.139 1411 Planarity : 0.003 0.038 1539 Dihedral : 4.910 64.423 1238 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.51 % Favored : 97.40 % Rotamer: Outliers : 3.18 % Allowed : 23.82 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.26), residues: 1116 helix: 3.02 (0.27), residues: 376 sheet: 0.48 (0.31), residues: 284 loop : -0.94 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.015 0.001 TYR E 178 PHE 0.015 0.001 PHE R 167 TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 9064) covalent geometry : angle 0.46561 (12288) SS BOND : bond 0.00268 ( 3) SS BOND : angle 0.47515 ( 6) hydrogen bonds : bond 0.03559 ( 432) hydrogen bonds : angle 4.07917 ( 1236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8393 (tt) cc_final: 0.8175 (tp) REVERT: A 349 LYS cc_start: 0.7843 (ttpp) cc_final: 0.7493 (ttpp) REVERT: R 37 LEU cc_start: 0.8011 (mm) cc_final: 0.7755 (mm) REVERT: R 56 LEU cc_start: 0.6677 (OUTLIER) cc_final: 0.6374 (mt) REVERT: R 171 LEU cc_start: 0.7064 (mp) cc_final: 0.6781 (mp) REVERT: B 228 ASP cc_start: 0.7952 (m-30) cc_final: 0.7663 (m-30) REVERT: B 237 ASN cc_start: 0.8074 (t0) cc_final: 0.7816 (t0) REVERT: G 22 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.6055 (mp0) outliers start: 31 outliers final: 27 residues processed: 155 average time/residue: 0.1122 time to fit residues: 22.8222 Evaluate side-chains 159 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 249 THR Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 0 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 82 optimal weight: 0.0370 chunk 10 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 263 GLN E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.163830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.133393 restraints weight = 12039.531| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.27 r_work: 0.3512 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9067 Z= 0.178 Angle : 0.523 7.311 12294 Z= 0.272 Chirality : 0.041 0.135 1411 Planarity : 0.003 0.041 1539 Dihedral : 5.114 63.914 1238 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.24 % Favored : 97.67 % Rotamer: Outliers : 2.98 % Allowed : 24.23 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.26), residues: 1116 helix: 2.87 (0.27), residues: 375 sheet: 0.40 (0.31), residues: 287 loop : -0.97 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.014 0.002 TYR A 320 PHE 0.023 0.002 PHE R 167 TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 9064) covalent geometry : angle 0.52296 (12288) SS BOND : bond 0.00385 ( 3) SS BOND : angle 0.74058 ( 6) hydrogen bonds : bond 0.04431 ( 432) hydrogen bonds : angle 4.29501 ( 1236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 349 LYS cc_start: 0.7858 (ttpp) cc_final: 0.7508 (ttpp) REVERT: R 37 LEU cc_start: 0.8029 (mm) cc_final: 0.7762 (mm) REVERT: R 171 LEU cc_start: 0.7005 (mp) cc_final: 0.6774 (mp) REVERT: B 197 ARG cc_start: 0.7383 (mmm160) cc_final: 0.7127 (mmm160) REVERT: B 228 ASP cc_start: 0.8005 (m-30) cc_final: 0.7593 (m-30) REVERT: B 289 TYR cc_start: 0.8129 (m-80) cc_final: 0.7224 (m-80) REVERT: G 22 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6015 (mp0) outliers start: 29 outliers final: 27 residues processed: 158 average time/residue: 0.1199 time to fit residues: 24.9239 Evaluate side-chains 165 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN B 295 ASN E 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.164846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.133810 restraints weight = 11868.796| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.31 r_work: 0.3517 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9067 Z= 0.151 Angle : 0.503 7.770 12294 Z= 0.261 Chirality : 0.041 0.138 1411 Planarity : 0.003 0.041 1539 Dihedral : 5.113 65.823 1238 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.60 % Favored : 97.31 % Rotamer: Outliers : 3.08 % Allowed : 24.33 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.26), residues: 1116 helix: 2.89 (0.27), residues: 375 sheet: 0.41 (0.31), residues: 287 loop : -1.00 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 197 TYR 0.014 0.001 TYR E 178 PHE 0.021 0.001 PHE R 167 TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9064) covalent geometry : angle 0.50302 (12288) SS BOND : bond 0.00354 ( 3) SS BOND : angle 0.66714 ( 6) hydrogen bonds : bond 0.04248 ( 432) hydrogen bonds : angle 4.28677 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2751.74 seconds wall clock time: 47 minutes 44.13 seconds (2864.13 seconds total)