Starting phenix.real_space_refine on Wed Feb 4 11:23:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xos_38539/02_2026/8xos_38539.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xos_38539/02_2026/8xos_38539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xos_38539/02_2026/8xos_38539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xos_38539/02_2026/8xos_38539.map" model { file = "/net/cci-nas-00/data/ceres_data/8xos_38539/02_2026/8xos_38539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xos_38539/02_2026/8xos_38539.cif" } resolution = 3.2 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= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1946 atoms to isotropic. 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 65 5.16 5 C 5713 2.51 5 N 1476 2.21 5 O 1665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8919 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1752 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2577 Classifications: {'peptide': 336} 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: "C" 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: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2335 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 11, 'TRANS': 285} Chain breaks: 2 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.62, per 1000 atoms: 0.18 Number of scatterers: 8919 At special positions: 0 Unit cell: (116.739, 94.248, 117.81, 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 65 16.00 O 1665 8.00 N 1476 7.00 C 5713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 175 " - pdb=" SG CYS R 254 " 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: 0.78 Conformation dependent library (CDL) restraints added in 350.9 milliseconds 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: 2134 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 38.4% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.511A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 207 through 218 removed outlier: 4.707A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) 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 242 through 255 Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.434A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 7 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.504A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'R' and resid 89 through 98 Processing helix chain 'R' and resid 103 through 127 Proline residue: R 118 - end of helix Processing helix chain 'R' and resid 135 through 154 removed outlier: 3.553A pdb=" N VAL R 154 " --> pdb=" O LEU R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 164 removed outlier: 3.872A pdb=" N LYS R 158 " --> pdb=" O VAL R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 206 Processing helix chain 'R' and resid 206 through 214 removed outlier: 3.618A pdb=" N LEU R 211 " --> pdb=" O PRO R 207 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER R 212 " --> pdb=" O MET R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 234 removed outlier: 3.653A pdb=" N VAL R 234 " --> pdb=" O ALA R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 234 through 240 Processing helix chain 'R' and resid 260 through 266 Processing helix chain 'R' and resid 266 through 279 Processing helix chain 'R' and resid 279 through 298 Processing helix chain 'R' and resid 308 through 325 Processing helix chain 'R' and resid 326 through 337 Processing helix chain 'R' and resid 342 through 361 removed outlier: 4.407A pdb=" N GLU R 347 " --> pdb=" O THR R 343 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ALA R 348 " --> pdb=" O SER R 344 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 372 Proline residue: R 368 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 9.071A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.531A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.578A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.916A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.543A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.427A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.686A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.772A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.513A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.513A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.152A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 87 through 88 446 hydrogen bonds defined for protein. 1224 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: 1.35 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2817 1.34 - 1.46: 2032 1.46 - 1.58: 4174 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 9114 Sorted by residual: bond pdb=" CD2 HIS E 232 " pdb=" NE2 HIS E 232 " ideal model delta sigma weight residual 1.374 1.397 -0.023 1.10e-02 8.26e+03 4.40e+00 bond pdb=" N SER A 6 " pdb=" CA SER A 6 " ideal model delta sigma weight residual 1.455 1.479 -0.024 1.27e-02 6.20e+03 3.62e+00 bond pdb=" C13 CLR R 601 " pdb=" C17 CLR R 601 " ideal model delta sigma weight residual 1.550 1.513 0.037 2.00e-02 2.50e+03 3.48e+00 bond pdb=" C13 CLR R 602 " pdb=" C17 CLR R 602 " ideal model delta sigma weight residual 1.550 1.514 0.036 2.00e-02 2.50e+03 3.27e+00 bond pdb=" CE1 HIS E 232 " pdb=" NE2 HIS E 232 " ideal model delta sigma weight residual 1.321 1.339 -0.018 1.00e-02 1.00e+04 3.22e+00 ... (remaining 9109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 11435 1.58 - 3.16: 786 3.16 - 4.73: 111 4.73 - 6.31: 18 6.31 - 7.89: 10 Bond angle restraints: 12360 Sorted by residual: angle pdb=" CB HIS E 35 " pdb=" CG HIS E 35 " pdb=" CD2 HIS E 35 " ideal model delta sigma weight residual 131.20 125.42 5.78 1.30e+00 5.92e-01 1.98e+01 angle pdb=" CB HIS E 167 " pdb=" CG HIS E 167 " pdb=" CD2 HIS E 167 " ideal model delta sigma weight residual 131.20 125.62 5.58 1.30e+00 5.92e-01 1.84e+01 angle pdb=" CB HIS E 232 " pdb=" CG HIS E 232 " pdb=" CD2 HIS E 232 " ideal model delta sigma weight residual 131.20 126.66 4.54 1.30e+00 5.92e-01 1.22e+01 angle pdb=" ND1 HIS E 167 " pdb=" CG HIS E 167 " pdb=" CD2 HIS E 167 " ideal model delta sigma weight residual 106.10 109.54 -3.44 1.00e+00 1.00e+00 1.19e+01 angle pdb=" CB ARG B 314 " pdb=" CG ARG B 314 " pdb=" CD ARG B 314 " ideal model delta sigma weight residual 111.30 103.41 7.89 2.30e+00 1.89e-01 1.18e+01 ... (remaining 12355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 5080 17.74 - 35.49: 324 35.49 - 53.23: 55 53.23 - 70.97: 18 70.97 - 88.72: 5 Dihedral angle restraints: 5482 sinusoidal: 2174 harmonic: 3308 Sorted by residual: dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA ALA E 92 " pdb=" C ALA E 92 " pdb=" N MET E 93 " pdb=" CA MET E 93 " ideal model delta harmonic sigma weight residual 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 152.32 27.68 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 5479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1129 0.068 - 0.135: 257 0.135 - 0.202: 24 0.202 - 0.270: 3 0.270 - 0.337: 2 Chirality restraints: 1415 Sorted by residual: chirality pdb=" C13 CLR R 601 " pdb=" C12 CLR R 601 " pdb=" C14 CLR R 601 " pdb=" C17 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.93 -2.59 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C13 CLR R 602 " pdb=" C12 CLR R 602 " pdb=" C14 CLR R 602 " pdb=" C17 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.93 -2.62 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 1412 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 59 " -0.081 2.00e-02 2.50e+03 4.15e-02 3.44e+01 pdb=" CG TYR E 59 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR E 59 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR E 59 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR E 59 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR E 59 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR E 59 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 59 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 101 " 0.059 2.00e-02 2.50e+03 3.09e-02 1.91e+01 pdb=" CG TYR E 101 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR E 101 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR E 101 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR E 101 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR E 101 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR E 101 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 101 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 191 " -0.090 9.50e-02 1.11e+02 5.24e-02 1.50e+01 pdb=" NE ARG E 191 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG E 191 " -0.064 2.00e-02 2.50e+03 pdb=" NH1 ARG E 191 " 0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG E 191 " 0.018 2.00e-02 2.50e+03 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 970 2.74 - 3.28: 9488 3.28 - 3.82: 14879 3.82 - 4.36: 18335 4.36 - 4.90: 31266 Nonbonded interactions: 74938 Sorted by model distance: nonbonded pdb=" CE1 PHE B 253 " pdb=" CG GLU B 260 " model vdw 2.197 3.740 nonbonded pdb=" CD2 TYR E 50 " pdb=" OH TYR E 235 " model vdw 2.236 3.340 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR A 230 " pdb=" OG SER A 281 " model vdw 2.255 3.040 nonbonded pdb=" O GLY R 165 " pdb=" OG SER R 166 " model vdw 2.289 3.040 ... (remaining 74933 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.710 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 : 0.008 0.060 9115 Z= 0.361 Angle : 0.902 7.888 12362 Z= 0.523 Chirality : 0.057 0.337 1415 Planarity : 0.007 0.052 1540 Dihedral : 12.894 88.719 3345 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.72 % Allowed : 4.42 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.24), residues: 1116 helix: -0.52 (0.25), residues: 377 sheet: 0.32 (0.30), residues: 269 loop : -0.91 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.065 0.009 ARG E 191 TYR 0.081 0.007 TYR E 59 PHE 0.040 0.003 PHE E 177 TRP 0.035 0.005 TRP E 47 HIS 0.011 0.002 HIS R 143 Details of bonding type rmsd covalent geometry : bond 0.00808 ( 9114) covalent geometry : angle 0.90013 (12360) SS BOND : bond 0.00132 ( 1) SS BOND : angle 4.50130 ( 2) hydrogen bonds : bond 0.14773 ( 442) hydrogen bonds : angle 7.08536 ( 1224) *********************** 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 207 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 200 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8393 (t70) cc_final: 0.8127 (t0) REVERT: A 204 GLN cc_start: 0.9165 (pp30) cc_final: 0.8878 (pp30) REVERT: B 12 GLU cc_start: 0.9425 (tp30) cc_final: 0.9176 (tp30) REVERT: B 17 GLN cc_start: 0.9594 (tm-30) cc_final: 0.9271 (tm-30) REVERT: B 32 GLN cc_start: 0.8902 (mt0) cc_final: 0.8662 (mt0) REVERT: B 220 GLN cc_start: 0.9068 (mt0) cc_final: 0.8776 (mt0) REVERT: C 58 GLU cc_start: 0.8248 (tp30) cc_final: 0.8010 (tp30) REVERT: E 73 ASP cc_start: 0.8323 (t0) cc_final: 0.8009 (t70) REVERT: E 120 SER cc_start: 0.8709 (t) cc_final: 0.8503 (p) REVERT: E 230 MET cc_start: 0.9003 (tmm) cc_final: 0.8432 (ttt) REVERT: R 167 ASP cc_start: 0.8660 (t0) cc_final: 0.8342 (t70) REVERT: R 193 MET cc_start: 0.8832 (mtm) cc_final: 0.8614 (mtt) REVERT: R 347 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8106 (mm-30) REVERT: R 367 ASP cc_start: 0.8635 (m-30) cc_final: 0.8434 (m-30) outliers start: 7 outliers final: 3 residues processed: 206 average time/residue: 0.1221 time to fit residues: 32.2397 Evaluate side-chains 130 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain R residue 215 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 295 ASN B 340 ASN C 24 ASN R 330 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.084325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.060377 restraints weight = 21572.650| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.29 r_work: 0.2780 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9115 Z= 0.143 Angle : 0.644 7.084 12362 Z= 0.344 Chirality : 0.044 0.211 1415 Planarity : 0.005 0.050 1540 Dihedral : 6.902 53.514 1359 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.06 % Allowed : 9.35 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.25), residues: 1116 helix: 1.19 (0.26), residues: 370 sheet: 0.30 (0.29), residues: 284 loop : -0.36 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 160 TYR 0.028 0.002 TYR E 235 PHE 0.022 0.001 PHE A 196 TRP 0.017 0.002 TRP B 339 HIS 0.004 0.001 HIS R 143 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9114) covalent geometry : angle 0.64332 (12360) SS BOND : bond 0.00359 ( 1) SS BOND : angle 1.95504 ( 2) hydrogen bonds : bond 0.04284 ( 442) hydrogen bonds : angle 5.34358 ( 1224) *********************** 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 165 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8745 (t70) cc_final: 0.8451 (t0) REVERT: A 204 GLN cc_start: 0.9267 (pp30) cc_final: 0.8678 (pp30) REVERT: A 243 MET cc_start: 0.8600 (tpp) cc_final: 0.7351 (tpp) REVERT: B 10 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8900 (mp0) REVERT: B 215 GLU cc_start: 0.9159 (mp0) cc_final: 0.8591 (mp0) REVERT: C 58 GLU cc_start: 0.8703 (tp30) cc_final: 0.8370 (tp30) REVERT: E 120 SER cc_start: 0.8658 (t) cc_final: 0.8421 (p) REVERT: E 223 ASP cc_start: 0.9214 (m-30) cc_final: 0.8818 (m-30) REVERT: E 244 LYS cc_start: 0.9230 (tttt) cc_final: 0.8938 (tptp) REVERT: E 246 GLU cc_start: 0.7308 (pm20) cc_final: 0.6985 (pm20) REVERT: R 167 ASP cc_start: 0.8732 (t0) cc_final: 0.8444 (t70) REVERT: R 193 MET cc_start: 0.9064 (mtm) cc_final: 0.8861 (mtt) REVERT: R 347 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8283 (mm-30) outliers start: 20 outliers final: 6 residues processed: 155 average time/residue: 0.0928 time to fit residues: 19.4126 Evaluate side-chains 131 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain R residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 59 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN B 176 GLN B 239 ASN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.082564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.058298 restraints weight = 21801.857| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.33 r_work: 0.2736 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9115 Z= 0.195 Angle : 0.633 7.207 12362 Z= 0.335 Chirality : 0.044 0.219 1415 Planarity : 0.004 0.052 1540 Dihedral : 6.136 54.034 1356 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.85 % Allowed : 11.51 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.25), residues: 1116 helix: 1.41 (0.27), residues: 370 sheet: 0.47 (0.30), residues: 280 loop : -0.36 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 214 TYR 0.025 0.002 TYR E 235 PHE 0.028 0.002 PHE E 68 TRP 0.008 0.002 TRP B 63 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 9114) covalent geometry : angle 0.63233 (12360) SS BOND : bond 0.00212 ( 1) SS BOND : angle 1.92177 ( 2) hydrogen bonds : bond 0.04178 ( 442) hydrogen bonds : angle 5.11426 ( 1224) *********************** 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 151 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8813 (t70) cc_final: 0.8489 (t0) REVERT: A 204 GLN cc_start: 0.9221 (pp30) cc_final: 0.8607 (pp30) REVERT: A 243 MET cc_start: 0.8541 (tpp) cc_final: 0.7596 (tpp) REVERT: B 307 VAL cc_start: 0.9222 (OUTLIER) cc_final: 0.8980 (t) REVERT: C 17 GLU cc_start: 0.9563 (mm-30) cc_final: 0.9299 (tm-30) REVERT: C 20 LYS cc_start: 0.9433 (pptt) cc_final: 0.9169 (pptt) REVERT: C 22 GLU cc_start: 0.8180 (tp30) cc_final: 0.7812 (tt0) REVERT: C 30 VAL cc_start: 0.8576 (t) cc_final: 0.8221 (p) REVERT: C 58 GLU cc_start: 0.8661 (tp30) cc_final: 0.8291 (tp30) REVERT: E 73 ASP cc_start: 0.8059 (t0) cc_final: 0.7625 (t70) REVERT: E 93 MET cc_start: 0.8808 (tpp) cc_final: 0.8598 (tpp) REVERT: E 120 SER cc_start: 0.8721 (t) cc_final: 0.8497 (p) REVERT: E 220 GLU cc_start: 0.8452 (mp0) cc_final: 0.7911 (mp0) REVERT: E 223 ASP cc_start: 0.9252 (m-30) cc_final: 0.8288 (m-30) REVERT: E 230 MET cc_start: 0.8946 (tmm) cc_final: 0.8658 (ttt) REVERT: E 244 LYS cc_start: 0.9247 (tttt) cc_final: 0.8977 (tptp) REVERT: E 246 GLU cc_start: 0.7405 (pm20) cc_final: 0.7134 (pm20) REVERT: R 167 ASP cc_start: 0.8677 (t0) cc_final: 0.8407 (t70) REVERT: R 347 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8281 (mm-30) outliers start: 18 outliers final: 13 residues processed: 148 average time/residue: 0.0978 time to fit residues: 20.1434 Evaluate side-chains 139 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 355 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 72 optimal weight: 20.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.082548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.058357 restraints weight = 22041.829| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.33 r_work: 0.2741 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9115 Z= 0.171 Angle : 0.610 7.102 12362 Z= 0.319 Chirality : 0.043 0.230 1415 Planarity : 0.004 0.053 1540 Dihedral : 5.738 51.444 1356 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.95 % Allowed : 13.67 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.26), residues: 1116 helix: 1.49 (0.27), residues: 376 sheet: 0.57 (0.30), residues: 278 loop : -0.37 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 214 TYR 0.022 0.002 TYR E 235 PHE 0.017 0.001 PHE A 196 TRP 0.008 0.001 TRP B 339 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 9114) covalent geometry : angle 0.60936 (12360) SS BOND : bond 0.00176 ( 1) SS BOND : angle 1.95273 ( 2) hydrogen bonds : bond 0.03934 ( 442) hydrogen bonds : angle 4.94603 ( 1224) *********************** 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 148 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8784 (t70) cc_final: 0.8454 (t0) REVERT: A 22 ASN cc_start: 0.8994 (m-40) cc_final: 0.8773 (t0) REVERT: A 204 GLN cc_start: 0.9241 (pp30) cc_final: 0.8600 (pp30) REVERT: B 10 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8776 (mp0) REVERT: B 14 LEU cc_start: 0.9122 (mm) cc_final: 0.8890 (mt) REVERT: B 32 GLN cc_start: 0.8849 (mt0) cc_final: 0.8608 (mt0) REVERT: B 307 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.8980 (t) REVERT: C 17 GLU cc_start: 0.9556 (mm-30) cc_final: 0.9187 (tm-30) REVERT: C 19 LEU cc_start: 0.8690 (mm) cc_final: 0.8443 (mm) REVERT: C 22 GLU cc_start: 0.8147 (tp30) cc_final: 0.7735 (tt0) REVERT: C 30 VAL cc_start: 0.8387 (t) cc_final: 0.8094 (p) REVERT: C 58 GLU cc_start: 0.8717 (tp30) cc_final: 0.8324 (tp30) REVERT: E 73 ASP cc_start: 0.7977 (t0) cc_final: 0.7199 (t70) REVERT: E 76 LYS cc_start: 0.9175 (mtpp) cc_final: 0.8780 (mtmm) REVERT: E 90 ASP cc_start: 0.8547 (m-30) cc_final: 0.8111 (m-30) REVERT: E 93 MET cc_start: 0.8804 (tpp) cc_final: 0.8558 (tpp) REVERT: E 120 SER cc_start: 0.8712 (t) cc_final: 0.8471 (p) REVERT: E 183 GLN cc_start: 0.8903 (mt0) cc_final: 0.8569 (pt0) REVERT: E 220 GLU cc_start: 0.8403 (mp0) cc_final: 0.8074 (mp0) REVERT: E 222 GLU cc_start: 0.8714 (pm20) cc_final: 0.8501 (pm20) REVERT: E 223 ASP cc_start: 0.9162 (m-30) cc_final: 0.8113 (m-30) REVERT: E 230 MET cc_start: 0.8932 (tmm) cc_final: 0.8602 (ttt) REVERT: R 167 ASP cc_start: 0.8652 (t0) cc_final: 0.8381 (t70) REVERT: R 347 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8258 (mm-30) outliers start: 19 outliers final: 14 residues processed: 144 average time/residue: 0.0793 time to fit residues: 15.9086 Evaluate side-chains 138 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 355 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.081849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.057534 restraints weight = 21910.335| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.34 r_work: 0.2703 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9115 Z= 0.230 Angle : 0.639 7.223 12362 Z= 0.336 Chirality : 0.044 0.212 1415 Planarity : 0.004 0.054 1540 Dihedral : 5.733 51.914 1356 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.77 % Allowed : 13.46 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.26), residues: 1116 helix: 1.67 (0.28), residues: 364 sheet: 0.41 (0.31), residues: 280 loop : -0.38 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.027 0.002 TYR E 235 PHE 0.039 0.002 PHE E 68 TRP 0.008 0.001 TRP R 100 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00524 ( 9114) covalent geometry : angle 0.63877 (12360) SS BOND : bond 0.00547 ( 1) SS BOND : angle 1.72993 ( 2) hydrogen bonds : bond 0.04071 ( 442) hydrogen bonds : angle 4.97884 ( 1224) *********************** 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 150 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8849 (t70) cc_final: 0.8495 (t0) REVERT: A 306 GLN cc_start: 0.9347 (mm-40) cc_final: 0.8968 (mm-40) REVERT: B 10 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8772 (mp0) REVERT: B 14 LEU cc_start: 0.8977 (mm) cc_final: 0.8771 (mt) REVERT: B 307 VAL cc_start: 0.9232 (OUTLIER) cc_final: 0.8957 (t) REVERT: C 19 LEU cc_start: 0.8771 (mm) cc_final: 0.8531 (mm) REVERT: C 22 GLU cc_start: 0.8248 (tp30) cc_final: 0.7641 (tt0) REVERT: C 30 VAL cc_start: 0.8421 (t) cc_final: 0.8158 (p) REVERT: C 58 GLU cc_start: 0.8803 (tp30) cc_final: 0.8407 (tp30) REVERT: E 73 ASP cc_start: 0.7958 (t0) cc_final: 0.7165 (t70) REVERT: E 76 LYS cc_start: 0.9176 (mtpp) cc_final: 0.8845 (mtmm) REVERT: E 93 MET cc_start: 0.8835 (tpp) cc_final: 0.8566 (tpp) REVERT: E 120 SER cc_start: 0.8735 (t) cc_final: 0.8481 (p) REVERT: E 183 GLN cc_start: 0.8919 (mt0) cc_final: 0.8598 (pt0) REVERT: E 220 GLU cc_start: 0.8358 (mp0) cc_final: 0.7958 (mp0) REVERT: E 222 GLU cc_start: 0.8742 (pm20) cc_final: 0.8440 (pm20) REVERT: E 223 ASP cc_start: 0.9091 (m-30) cc_final: 0.8023 (m-30) REVERT: E 230 MET cc_start: 0.8943 (tmm) cc_final: 0.8616 (ttt) REVERT: E 244 LYS cc_start: 0.9055 (tttp) cc_final: 0.8531 (tptp) REVERT: E 246 GLU cc_start: 0.7624 (pm20) cc_final: 0.7262 (pm20) REVERT: R 167 ASP cc_start: 0.8696 (t0) cc_final: 0.8443 (t70) REVERT: R 347 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8206 (mm-30) outliers start: 27 outliers final: 17 residues processed: 144 average time/residue: 0.0958 time to fit residues: 19.0751 Evaluate side-chains 135 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 355 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 98 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.084011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.059930 restraints weight = 21411.530| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.31 r_work: 0.2770 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9115 Z= 0.124 Angle : 0.587 7.649 12362 Z= 0.308 Chirality : 0.042 0.172 1415 Planarity : 0.004 0.052 1540 Dihedral : 5.282 49.980 1356 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.95 % Allowed : 15.11 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.26), residues: 1116 helix: 1.51 (0.27), residues: 377 sheet: 0.50 (0.31), residues: 278 loop : -0.30 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 87 TYR 0.018 0.001 TYR E 235 PHE 0.023 0.001 PHE E 68 TRP 0.012 0.001 TRP B 339 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9114) covalent geometry : angle 0.58656 (12360) SS BOND : bond 0.00129 ( 1) SS BOND : angle 1.73002 ( 2) hydrogen bonds : bond 0.03584 ( 442) hydrogen bonds : angle 4.75525 ( 1224) *********************** 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 152 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8783 (t70) cc_final: 0.8475 (t0) REVERT: A 32 ARG cc_start: 0.8596 (ttp-110) cc_final: 0.8387 (ttm-80) REVERT: B 12 GLU cc_start: 0.9193 (tp30) cc_final: 0.8792 (tp30) REVERT: B 14 LEU cc_start: 0.9021 (mm) cc_final: 0.8789 (mt) REVERT: C 58 GLU cc_start: 0.8797 (tp30) cc_final: 0.8415 (tp30) REVERT: E 73 ASP cc_start: 0.8016 (t0) cc_final: 0.7623 (t70) REVERT: E 82 GLN cc_start: 0.8640 (tp-100) cc_final: 0.8436 (tp-100) REVERT: E 93 MET cc_start: 0.8796 (tpp) cc_final: 0.8520 (tpp) REVERT: E 120 SER cc_start: 0.8667 (t) cc_final: 0.8440 (p) REVERT: E 183 GLN cc_start: 0.8912 (mt0) cc_final: 0.8692 (pt0) REVERT: E 223 ASP cc_start: 0.9085 (m-30) cc_final: 0.8258 (m-30) REVERT: E 230 MET cc_start: 0.8894 (tmm) cc_final: 0.8510 (ttt) REVERT: E 244 LYS cc_start: 0.9059 (tttp) cc_final: 0.8545 (tptp) REVERT: E 246 GLU cc_start: 0.7679 (pm20) cc_final: 0.7316 (pm20) REVERT: R 132 LYS cc_start: 0.8133 (mmmt) cc_final: 0.7919 (mmtt) REVERT: R 158 LYS cc_start: 0.9411 (mttm) cc_final: 0.9202 (mttt) REVERT: R 167 ASP cc_start: 0.8560 (t0) cc_final: 0.8294 (t70) REVERT: R 258 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7894 (mp) REVERT: R 260 GLU cc_start: 0.8430 (pm20) cc_final: 0.8196 (pm20) REVERT: R 347 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8173 (mm-30) outliers start: 19 outliers final: 11 residues processed: 146 average time/residue: 0.1033 time to fit residues: 20.6853 Evaluate side-chains 136 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 355 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 0.0770 chunk 11 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 6 optimal weight: 0.0870 chunk 22 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.0118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.084278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.059987 restraints weight = 21523.177| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.36 r_work: 0.2775 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9115 Z= 0.125 Angle : 0.591 7.690 12362 Z= 0.307 Chirality : 0.041 0.164 1415 Planarity : 0.004 0.051 1540 Dihedral : 5.133 49.169 1356 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.75 % Allowed : 16.14 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.26), residues: 1116 helix: 1.52 (0.27), residues: 378 sheet: 0.51 (0.31), residues: 278 loop : -0.33 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.023 0.001 TYR E 235 PHE 0.016 0.001 PHE E 68 TRP 0.009 0.001 TRP B 339 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9114) covalent geometry : angle 0.59102 (12360) SS BOND : bond 0.00132 ( 1) SS BOND : angle 1.60869 ( 2) hydrogen bonds : bond 0.03515 ( 442) hydrogen bonds : angle 4.67675 ( 1224) *********************** 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 150 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8785 (t70) cc_final: 0.8472 (t0) REVERT: A 32 ARG cc_start: 0.8576 (ttp-110) cc_final: 0.8331 (ttm-80) REVERT: A 53 MET cc_start: 0.9199 (mpp) cc_final: 0.8970 (mpp) REVERT: B 12 GLU cc_start: 0.9216 (tp30) cc_final: 0.8984 (tp30) REVERT: B 14 LEU cc_start: 0.9051 (mm) cc_final: 0.8831 (mt) REVERT: B 32 GLN cc_start: 0.8902 (mt0) cc_final: 0.8658 (mt0) REVERT: C 22 GLU cc_start: 0.8069 (tp30) cc_final: 0.7335 (tt0) REVERT: C 58 GLU cc_start: 0.8807 (tp30) cc_final: 0.8419 (tp30) REVERT: E 73 ASP cc_start: 0.8178 (t0) cc_final: 0.7712 (t70) REVERT: E 76 LYS cc_start: 0.9203 (mtmm) cc_final: 0.8994 (mtmm) REVERT: E 82 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8348 (tp-100) REVERT: E 93 MET cc_start: 0.8831 (tpp) cc_final: 0.8557 (tpp) REVERT: E 120 SER cc_start: 0.8663 (t) cc_final: 0.8372 (p) REVERT: E 153 GLU cc_start: 0.8689 (pt0) cc_final: 0.8285 (pm20) REVERT: E 183 GLN cc_start: 0.8907 (mt0) cc_final: 0.8702 (pt0) REVERT: E 223 ASP cc_start: 0.8961 (m-30) cc_final: 0.8486 (m-30) REVERT: E 230 MET cc_start: 0.8878 (tmm) cc_final: 0.8515 (ttt) REVERT: R 258 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8034 (mp) REVERT: R 347 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8221 (mm-30) outliers start: 17 outliers final: 11 residues processed: 145 average time/residue: 0.0916 time to fit residues: 18.2049 Evaluate side-chains 137 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 355 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 0.0670 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.082768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.058693 restraints weight = 21572.118| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.31 r_work: 0.2745 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9115 Z= 0.168 Angle : 0.630 7.801 12362 Z= 0.329 Chirality : 0.042 0.171 1415 Planarity : 0.004 0.053 1540 Dihedral : 5.224 50.629 1356 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.85 % Allowed : 16.44 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.26), residues: 1116 helix: 1.50 (0.27), residues: 379 sheet: 0.47 (0.31), residues: 284 loop : -0.31 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 87 TYR 0.026 0.001 TYR E 235 PHE 0.024 0.001 PHE E 68 TRP 0.008 0.001 TRP B 169 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9114) covalent geometry : angle 0.62945 (12360) SS BOND : bond 0.00127 ( 1) SS BOND : angle 1.53339 ( 2) hydrogen bonds : bond 0.03711 ( 442) hydrogen bonds : angle 4.70860 ( 1224) *********************** 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 144 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8833 (t70) cc_final: 0.8477 (t0) REVERT: A 22 ASN cc_start: 0.9079 (m-40) cc_final: 0.8869 (t0) REVERT: B 32 GLN cc_start: 0.8887 (mt0) cc_final: 0.8662 (mt0) REVERT: B 259 GLN cc_start: 0.8166 (tt0) cc_final: 0.7721 (mt0) REVERT: C 22 GLU cc_start: 0.8028 (tp30) cc_final: 0.7266 (tt0) REVERT: C 58 GLU cc_start: 0.8840 (tp30) cc_final: 0.8452 (tp30) REVERT: E 73 ASP cc_start: 0.8202 (t0) cc_final: 0.7681 (t70) REVERT: E 93 MET cc_start: 0.8857 (tpp) cc_final: 0.8577 (tpp) REVERT: E 120 SER cc_start: 0.8679 (t) cc_final: 0.8391 (p) REVERT: E 183 GLN cc_start: 0.8909 (mt0) cc_final: 0.8705 (pt0) REVERT: E 223 ASP cc_start: 0.8963 (m-30) cc_final: 0.8726 (m-30) REVERT: E 230 MET cc_start: 0.8878 (tmm) cc_final: 0.8558 (ttt) REVERT: R 141 MET cc_start: 0.9141 (mmm) cc_final: 0.8685 (mmm) REVERT: R 167 ASP cc_start: 0.8423 (t0) cc_final: 0.8025 (t70) REVERT: R 258 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8190 (mp) REVERT: R 347 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8265 (mm-30) outliers start: 18 outliers final: 12 residues processed: 140 average time/residue: 0.0834 time to fit residues: 16.2056 Evaluate side-chains 134 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 324 ILE Chi-restraints excluded: chain R residue 355 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 20 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.083155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.058848 restraints weight = 21575.654| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.34 r_work: 0.2746 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9115 Z= 0.166 Angle : 0.651 14.111 12362 Z= 0.335 Chirality : 0.043 0.344 1415 Planarity : 0.004 0.054 1540 Dihedral : 5.222 50.776 1356 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.06 % Allowed : 16.55 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.26), residues: 1116 helix: 1.48 (0.27), residues: 385 sheet: 0.38 (0.31), residues: 287 loop : -0.39 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 87 TYR 0.023 0.001 TYR E 235 PHE 0.025 0.001 PHE E 68 TRP 0.007 0.001 TRP A 211 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9114) covalent geometry : angle 0.65089 (12360) SS BOND : bond 0.00115 ( 1) SS BOND : angle 1.53251 ( 2) hydrogen bonds : bond 0.03657 ( 442) hydrogen bonds : angle 4.68468 ( 1224) *********************** 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 145 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8839 (t70) cc_final: 0.8470 (t0) REVERT: A 22 ASN cc_start: 0.9091 (m-40) cc_final: 0.8871 (t0) REVERT: B 32 GLN cc_start: 0.8874 (mt0) cc_final: 0.8671 (mt0) REVERT: B 259 GLN cc_start: 0.8192 (tt0) cc_final: 0.7699 (mt0) REVERT: C 58 GLU cc_start: 0.8842 (tp30) cc_final: 0.8455 (tp30) REVERT: E 73 ASP cc_start: 0.8307 (t0) cc_final: 0.7931 (t70) REVERT: E 93 MET cc_start: 0.8873 (tpp) cc_final: 0.8598 (tpp) REVERT: E 120 SER cc_start: 0.8716 (t) cc_final: 0.8432 (p) REVERT: E 153 GLU cc_start: 0.8777 (pt0) cc_final: 0.8333 (pm20) REVERT: E 223 ASP cc_start: 0.8838 (m-30) cc_final: 0.8548 (m-30) REVERT: E 230 MET cc_start: 0.8890 (tmm) cc_final: 0.8572 (ttt) REVERT: E 244 LYS cc_start: 0.9231 (tttm) cc_final: 0.8297 (tptp) REVERT: E 246 GLU cc_start: 0.7999 (pm20) cc_final: 0.7029 (pm20) REVERT: R 141 MET cc_start: 0.9149 (mmm) cc_final: 0.8738 (mmm) REVERT: R 167 ASP cc_start: 0.8449 (t0) cc_final: 0.8064 (t70) REVERT: R 258 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8291 (mp) REVERT: R 347 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8359 (mm-30) outliers start: 20 outliers final: 14 residues processed: 141 average time/residue: 0.0855 time to fit residues: 16.6418 Evaluate side-chains 134 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 324 ILE Chi-restraints excluded: chain R residue 355 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.082842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.058595 restraints weight = 21640.274| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.37 r_work: 0.2742 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9115 Z= 0.166 Angle : 0.668 12.211 12362 Z= 0.342 Chirality : 0.044 0.309 1415 Planarity : 0.004 0.054 1540 Dihedral : 5.228 50.583 1356 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.85 % Allowed : 16.14 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.26), residues: 1116 helix: 1.61 (0.27), residues: 379 sheet: 0.40 (0.31), residues: 287 loop : -0.34 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 87 TYR 0.022 0.001 TYR E 235 PHE 0.024 0.001 PHE E 68 TRP 0.008 0.001 TRP B 99 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9114) covalent geometry : angle 0.66812 (12360) SS BOND : bond 0.00105 ( 1) SS BOND : angle 1.54476 ( 2) hydrogen bonds : bond 0.03637 ( 442) hydrogen bonds : angle 4.71338 ( 1224) ********************** 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 143 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8849 (t70) cc_final: 0.8482 (t0) REVERT: A 22 ASN cc_start: 0.9097 (m-40) cc_final: 0.8887 (t0) REVERT: B 259 GLN cc_start: 0.8218 (tt0) cc_final: 0.7793 (mt0) REVERT: C 22 GLU cc_start: 0.7714 (tp30) cc_final: 0.7109 (tt0) REVERT: C 58 GLU cc_start: 0.8845 (tp30) cc_final: 0.8460 (tp30) REVERT: E 73 ASP cc_start: 0.8371 (t0) cc_final: 0.7946 (t70) REVERT: E 93 MET cc_start: 0.8882 (tpp) cc_final: 0.8611 (tpp) REVERT: E 120 SER cc_start: 0.8729 (t) cc_final: 0.8454 (p) REVERT: E 223 ASP cc_start: 0.8883 (m-30) cc_final: 0.8636 (m-30) REVERT: E 230 MET cc_start: 0.8884 (tmm) cc_final: 0.8576 (ttt) REVERT: E 244 LYS cc_start: 0.9243 (tttm) cc_final: 0.8650 (tptp) REVERT: E 246 GLU cc_start: 0.7895 (pm20) cc_final: 0.7484 (pm20) REVERT: R 141 MET cc_start: 0.9138 (mmm) cc_final: 0.8726 (mmm) REVERT: R 167 ASP cc_start: 0.8452 (t0) cc_final: 0.8062 (t70) REVERT: R 258 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8285 (mp) REVERT: R 347 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8372 (mm-30) outliers start: 18 outliers final: 16 residues processed: 138 average time/residue: 0.0961 time to fit residues: 18.4015 Evaluate side-chains 134 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 324 ILE Chi-restraints excluded: chain R residue 355 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.083197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.059121 restraints weight = 21390.983| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.32 r_work: 0.2750 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9115 Z= 0.157 Angle : 0.654 11.623 12362 Z= 0.335 Chirality : 0.043 0.311 1415 Planarity : 0.004 0.051 1540 Dihedral : 5.189 49.857 1356 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.95 % Allowed : 16.14 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.26), residues: 1116 helix: 1.51 (0.27), residues: 386 sheet: 0.41 (0.31), residues: 287 loop : -0.40 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 87 TYR 0.026 0.001 TYR E 235 PHE 0.020 0.001 PHE E 68 TRP 0.008 0.001 TRP B 99 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9114) covalent geometry : angle 0.65400 (12360) SS BOND : bond 0.00112 ( 1) SS BOND : angle 1.47783 ( 2) hydrogen bonds : bond 0.03589 ( 442) hydrogen bonds : angle 4.68057 ( 1224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1989.85 seconds wall clock time: 34 minutes 54.62 seconds (2094.62 seconds total)