Starting phenix.real_space_refine on Sat Dec 28 15:40:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ast_43825/12_2024/9ast_43825.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ast_43825/12_2024/9ast_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ast_43825/12_2024/9ast_43825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ast_43825/12_2024/9ast_43825.map" model { file = "/net/cci-nas-00/data/ceres_data/9ast_43825/12_2024/9ast_43825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ast_43825/12_2024/9ast_43825.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 6, '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: 5.49, per 1000 atoms: 0.62 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: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.18 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: 2.70 Time building geometry restraints manager: 2.59 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.990 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.360 ------------------------------------------------------------------------------- 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 : 0.004 0.064 9064 Z= 0.281 Angle : 0.699 11.230 12288 Z= 0.433 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 : 6.75 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (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 TRP 0.012 0.001 TRP B 63 HIS 0.004 0.001 HIS G 44 PHE 0.021 0.001 PHE R 167 TYR 0.018 0.001 TYR R 128 ARG 0.004 0.000 ARG L 9 *********************** 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 : 1.013 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: 0.2854 time to fit residues: 58.7538 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 : 0.956 ------------------------------------------------------------------------------- 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 93 optimal weight: 0.0040 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 56 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9064 Z= 0.156 Angle : 0.499 6.774 12288 Z= 0.264 Chirality : 0.040 0.142 1411 Planarity : 0.004 0.062 1539 Dihedral : 7.183 65.848 1263 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.97 % Favored : 97.94 % Rotamer: Outliers : 2.87 % Allowed : 20.23 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.26), residues: 1116 helix: 2.58 (0.27), residues: 370 sheet: 0.43 (0.31), residues: 288 loop : -0.93 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 169 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE R 109 TYR 0.017 0.001 TYR E 178 ARG 0.003 0.000 ARG B 150 *********************** 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: 28 poor density : 143 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7497 (mtp) cc_final: 0.7270 (ttm) REVERT: A 243 MET cc_start: 0.7834 (tpp) cc_final: 0.7280 (mmm) REVERT: B 150 ARG cc_start: 0.8744 (mmt-90) cc_final: 0.8401 (mmt180) REVERT: G 22 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.6016 (mp0) outliers start: 28 outliers final: 17 residues processed: 158 average time/residue: 0.2667 time to fit residues: 55.0447 Evaluate side-chains 152 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 202 LEU Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU 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 E residue 91 THR Chi-restraints excluded: chain E residue 180 MET 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 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 0.0570 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.6704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN G 58 GLN E 167 GLN E 182 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 9064 Z= 0.178 Angle : 0.480 7.457 12288 Z= 0.252 Chirality : 0.040 0.135 1411 Planarity : 0.003 0.052 1539 Dihedral : 5.590 62.028 1239 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.51 % Favored : 97.40 % Rotamer: Outliers : 3.49 % Allowed : 21.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1116 helix: 2.70 (0.27), residues: 376 sheet: 0.56 (0.31), residues: 288 loop : -0.95 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.001 PHE R 109 TYR 0.015 0.001 TYR E 178 ARG 0.003 0.000 ARG B 49 *********************** 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 170 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7477 (mtp) cc_final: 0.7227 (ttm) REVERT: A 37 LEU cc_start: 0.8593 (tt) cc_final: 0.8333 (tp) REVERT: R 37 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7702 (mm) REVERT: G 22 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.6100 (mp0) outliers start: 34 outliers final: 22 residues processed: 158 average time/residue: 0.2526 time to fit residues: 53.0288 Evaluate side-chains 161 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 LEU 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 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 B residue 336 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET 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 192 SER Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 3.9990 chunk 52 optimal weight: 0.0770 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 0.0170 chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 60 optimal weight: 0.0010 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9064 Z= 0.153 Angle : 0.461 6.654 12288 Z= 0.242 Chirality : 0.039 0.139 1411 Planarity : 0.003 0.045 1539 Dihedral : 5.245 59.156 1237 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.15 % Favored : 97.76 % Rotamer: Outliers : 3.59 % Allowed : 21.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.26), residues: 1116 helix: 2.82 (0.27), residues: 376 sheet: 0.55 (0.31), residues: 287 loop : -0.97 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE R 109 TYR 0.015 0.001 TYR E 178 ARG 0.003 0.000 ARG B 137 *********************** 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 173 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 LYS cc_start: 0.7701 (ttpp) cc_final: 0.7444 (ttpp) REVERT: B 289 TYR cc_start: 0.8259 (m-80) cc_final: 0.8015 (m-80) REVERT: G 22 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6153 (mp0) outliers start: 35 outliers final: 25 residues processed: 158 average time/residue: 0.2667 time to fit residues: 55.5010 Evaluate side-chains 164 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 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 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 38 MET 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 E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 192 SER 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 1 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 0.0020 chunk 96 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 21 optimal weight: 0.0770 overall best weight: 0.6548 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9064 Z= 0.173 Angle : 0.482 8.122 12288 Z= 0.248 Chirality : 0.040 0.139 1411 Planarity : 0.003 0.043 1539 Dihedral : 5.080 59.791 1235 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.24 % Favored : 97.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.26), residues: 1116 helix: 2.87 (0.27), residues: 376 sheet: 0.55 (0.31), residues: 287 loop : -0.96 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS E 35 PHE 0.015 0.001 PHE R 109 TYR 0.015 0.001 TYR E 178 ARG 0.002 0.000 ARG B 49 *********************** 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 173 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8601 (tt) cc_final: 0.8349 (tp) REVERT: A 349 LYS cc_start: 0.7662 (ttpp) cc_final: 0.7302 (ttpp) REVERT: R 38 TYR cc_start: 0.7926 (m-80) cc_final: 0.7551 (m-80) REVERT: B 289 TYR cc_start: 0.8247 (m-80) cc_final: 0.8018 (m-80) REVERT: G 22 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.6157 (mp0) outliers start: 34 outliers final: 26 residues processed: 160 average time/residue: 0.2524 time to fit residues: 53.6305 Evaluate side-chains 167 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 LEU 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 B residue 336 LEU 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 38 MET 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 E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 192 SER 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 62 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 56 optimal weight: 0.7980 chunk 103 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9064 Z= 0.173 Angle : 0.475 6.949 12288 Z= 0.245 Chirality : 0.040 0.162 1411 Planarity : 0.003 0.043 1539 Dihedral : 4.992 61.588 1235 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.33 % Favored : 97.58 % Rotamer: Outliers : 4.11 % Allowed : 21.46 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.26), residues: 1116 helix: 2.88 (0.27), residues: 376 sheet: 0.56 (0.31), residues: 287 loop : -0.96 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS E 35 PHE 0.015 0.001 PHE R 109 TYR 0.015 0.001 TYR E 178 ARG 0.005 0.000 ARG B 137 *********************** 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 179 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8579 (tt) cc_final: 0.8341 (tp) REVERT: A 349 LYS cc_start: 0.7675 (ttpp) cc_final: 0.7301 (ttpp) REVERT: R 38 TYR cc_start: 0.7913 (m-80) cc_final: 0.7574 (m-80) REVERT: B 150 ARG cc_start: 0.8716 (mmt-90) cc_final: 0.8435 (mmt180) REVERT: G 22 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6196 (mp0) outliers start: 40 outliers final: 30 residues processed: 166 average time/residue: 0.2647 time to fit residues: 57.9776 Evaluate side-chains 168 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 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 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 74 SER 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 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET 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 E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 192 SER 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 78 optimal weight: 0.1980 chunk 60 optimal weight: 0.0370 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 0.0870 chunk 66 optimal weight: 0.2980 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.2836 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9064 Z= 0.115 Angle : 0.460 8.069 12288 Z= 0.233 Chirality : 0.039 0.151 1411 Planarity : 0.003 0.038 1539 Dihedral : 4.766 62.343 1235 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.33 % Favored : 97.58 % Rotamer: Outliers : 2.98 % Allowed : 22.90 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.26), residues: 1116 helix: 3.03 (0.27), residues: 376 sheet: 0.52 (0.31), residues: 276 loop : -0.96 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE R 109 TYR 0.015 0.001 TYR E 178 ARG 0.002 0.000 ARG B 137 *********************** 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 159 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8568 (tt) cc_final: 0.8340 (tp) REVERT: A 349 LYS cc_start: 0.7632 (ttpp) cc_final: 0.7290 (ttpp) REVERT: R 56 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6412 (mt) REVERT: B 246 ASP cc_start: 0.7870 (m-30) cc_final: 0.7519 (m-30) outliers start: 29 outliers final: 25 residues processed: 149 average time/residue: 0.2789 time to fit residues: 54.1199 Evaluate side-chains 153 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 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 318 LEU Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 38 MET 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 E residue 91 THR Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 203 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 0.0980 chunk 9 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN G 58 GLN E 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9064 Z= 0.194 Angle : 0.489 6.789 12288 Z= 0.251 Chirality : 0.040 0.151 1411 Planarity : 0.003 0.041 1539 Dihedral : 4.615 61.483 1232 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.42 % Favored : 97.49 % Rotamer: Outliers : 3.49 % Allowed : 22.90 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.26), residues: 1116 helix: 2.95 (0.27), residues: 376 sheet: 0.60 (0.31), residues: 288 loop : -0.92 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS E 35 PHE 0.017 0.001 PHE R 109 TYR 0.017 0.001 TYR R 38 ARG 0.004 0.000 ARG B 150 *********************** 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 169 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 349 LYS cc_start: 0.7654 (ttpp) cc_final: 0.7289 (ttpp) REVERT: R 56 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6448 (mt) outliers start: 34 outliers final: 30 residues processed: 159 average time/residue: 0.2511 time to fit residues: 53.2324 Evaluate side-chains 167 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 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 336 LEU Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET 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 192 SER Chi-restraints excluded: chain E residue 203 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 5.9990 chunk 60 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.2980 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 0.0170 chunk 99 optimal weight: 0.0670 chunk 65 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9064 Z= 0.116 Angle : 0.467 7.407 12288 Z= 0.237 Chirality : 0.039 0.147 1411 Planarity : 0.003 0.036 1539 Dihedral : 4.475 62.947 1232 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.33 % Favored : 97.58 % Rotamer: Outliers : 2.67 % Allowed : 23.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.26), residues: 1116 helix: 3.04 (0.27), residues: 376 sheet: 0.53 (0.31), residues: 281 loop : -0.90 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE R 109 TYR 0.015 0.001 TYR E 178 ARG 0.004 0.000 ARG B 197 *********************** 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 158 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8543 (tt) cc_final: 0.8318 (tp) REVERT: A 349 LYS cc_start: 0.7619 (ttpp) cc_final: 0.7308 (ttpp) REVERT: R 56 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6424 (mt) REVERT: B 197 ARG cc_start: 0.6873 (mmm160) cc_final: 0.6618 (mmm160) REVERT: B 237 ASN cc_start: 0.6912 (t0) cc_final: 0.6685 (t0) outliers start: 26 outliers final: 22 residues processed: 148 average time/residue: 0.2632 time to fit residues: 51.3885 Evaluate side-chains 154 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 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 G residue 11 GLN Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.0770 chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 0.0870 chunk 26 optimal weight: 0.0170 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 248 GLN B 230 ASN B 239 ASN G 58 GLN E 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9064 Z= 0.116 Angle : 0.464 7.475 12288 Z= 0.234 Chirality : 0.039 0.149 1411 Planarity : 0.003 0.035 1539 Dihedral : 3.728 52.689 1227 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.06 % Favored : 97.85 % Rotamer: Outliers : 2.57 % Allowed : 23.82 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.26), residues: 1116 helix: 3.11 (0.27), residues: 376 sheet: 0.42 (0.31), residues: 280 loop : -0.85 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE R 109 TYR 0.014 0.001 TYR E 178 ARG 0.003 0.000 ARG B 150 ********************** 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 159 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8412 (mttm) cc_final: 0.8199 (mtpp) REVERT: A 349 LYS cc_start: 0.7612 (ttpp) cc_final: 0.7296 (ttpp) REVERT: B 197 ARG cc_start: 0.6860 (mmm160) cc_final: 0.6598 (mmm160) REVERT: B 237 ASN cc_start: 0.6982 (t0) cc_final: 0.6776 (t0) outliers start: 25 outliers final: 23 residues processed: 149 average time/residue: 0.2683 time to fit residues: 53.3614 Evaluate side-chains 158 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 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 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 46 LYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.0010 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 63 optimal weight: 0.0170 overall best weight: 0.3024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 230 ASN G 58 GLN E 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.167260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.136617 restraints weight = 12016.445| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.30 r_work: 0.3554 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 9064 Z= 0.282 Angle : 0.881 59.188 12288 Z= 0.498 Chirality : 0.041 0.525 1411 Planarity : 0.003 0.035 1539 Dihedral : 3.770 52.672 1227 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.15 % Favored : 97.76 % Rotamer: Outliers : 2.36 % Allowed : 24.44 % Favored : 73.20 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.26), residues: 1116 helix: 3.11 (0.27), residues: 376 sheet: 0.43 (0.31), residues: 280 loop : -0.85 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE R 109 TYR 0.014 0.001 TYR E 178 ARG 0.005 0.000 ARG B 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2355.47 seconds wall clock time: 43 minutes 42.37 seconds (2622.37 seconds total)