Starting phenix.real_space_refine on Fri Aug 22 23:50:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x17_37986/08_2025/8x17_37986.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x17_37986/08_2025/8x17_37986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x17_37986/08_2025/8x17_37986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x17_37986/08_2025/8x17_37986.map" model { file = "/net/cci-nas-00/data/ceres_data/8x17_37986/08_2025/8x17_37986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x17_37986/08_2025/8x17_37986.cif" } resolution = 3.19 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= 0.007 sd= 0.087 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: 6 Type Number sf(0) Gaussians I 1 10.91 5 S 68 5.16 5 Cl 1 4.86 5 C 5615 2.51 5 N 1469 2.21 5 O 1599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8753 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "R" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2269 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 404 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1736 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1753 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'XS0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.23, per 1000 atoms: 0.25 Number of scatterers: 8753 At special positions: 0 Unit cell: (116.184, 88.992, 135.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) I 1 52.95 Cl 1 17.00 S 68 16.00 O 1599 8.00 N 1469 7.00 C 5615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 83 " - pdb=" SG CYS R 166 " distance=2.04 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: 0.89 Conformation dependent library (CDL) restraints added in 345.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 39.5% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.599A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.738A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 40 removed outlier: 3.597A pdb=" N ASN R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 44 Processing helix chain 'R' and resid 45 through 75 removed outlier: 3.501A pdb=" N PHE R 50 " --> pdb=" O THR R 46 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N MET R 66 " --> pdb=" O GLY R 62 " (cutoff:3.500A) Proline residue: R 67 - end of helix Processing helix chain 'R' and resid 79 through 114 removed outlier: 3.507A pdb=" N THR R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 122 Processing helix chain 'R' and resid 123 through 143 Processing helix chain 'R' and resid 150 through 154 Processing helix chain 'R' and resid 157 through 161 Processing helix chain 'R' and resid 167 through 172 Processing helix chain 'R' and resid 173 through 180 Processing helix chain 'R' and resid 180 through 186 Processing helix chain 'R' and resid 186 through 209 Processing helix chain 'R' and resid 224 through 253 removed outlier: 3.586A pdb=" N PHE R 239 " --> pdb=" O VAL R 235 " (cutoff:3.500A) Proline residue: R 245 - end of helix Processing helix chain 'R' and resid 260 through 273 Processing helix chain 'R' and resid 273 through 283 Proline residue: R 279 - end of helix Processing helix chain 'R' and resid 286 through 300 Processing helix chain 'C' and resid 12 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.595A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.509A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 53 removed outlier: 3.676A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.777A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.832A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.753A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 352 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.832A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.825A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.811A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.984A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.156A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.096A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.515A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.746A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 141 through 142 removed outlier: 3.941A pdb=" N VAL H 155 " --> pdb=" O ILE H 216 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS H 159 " --> pdb=" O PHE H 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.526A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE H 189 " --> pdb=" O TRP H 176 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.872A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1221 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: 1.34 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 3333 1.38 - 1.57: 5498 1.57 - 1.75: 3 1.75 - 1.93: 102 1.93 - 2.11: 1 Bond restraints: 8937 Sorted by residual: bond pdb=" C06 XS0 R 401 " pdb=" C07 XS0 R 401 " ideal model delta sigma weight residual 1.533 1.289 0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C16 XS0 R 401 " pdb="CL19 XS0 R 401 " ideal model delta sigma weight residual 1.737 1.889 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" C03 XS0 R 401 " pdb=" N02 XS0 R 401 " ideal model delta sigma weight residual 1.334 1.471 -0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" C05 XS0 R 401 " pdb=" O09 XS0 R 401 " ideal model delta sigma weight residual 1.411 1.527 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" C07 XS0 R 401 " pdb=" C08 XS0 R 401 " ideal model delta sigma weight residual 1.529 1.640 -0.111 2.00e-02 2.50e+03 3.09e+01 ... (remaining 8932 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 12033 2.66 - 5.33: 73 5.33 - 7.99: 8 7.99 - 10.66: 3 10.66 - 13.32: 2 Bond angle restraints: 12119 Sorted by residual: angle pdb=" N ILE R 248 " pdb=" CA ILE R 248 " pdb=" C ILE R 248 " ideal model delta sigma weight residual 111.45 105.38 6.07 9.30e-01 1.16e+00 4.26e+01 angle pdb=" C LEU R 84 " pdb=" N PHE R 85 " pdb=" CA PHE R 85 " ideal model delta sigma weight residual 120.31 113.51 6.80 1.52e+00 4.33e-01 2.00e+01 angle pdb=" N10 XS0 R 401 " pdb=" C08 XS0 R 401 " pdb=" O09 XS0 R 401 " ideal model delta sigma weight residual 109.29 95.97 13.32 3.00e+00 1.11e-01 1.97e+01 angle pdb=" C07 XS0 R 401 " pdb=" C08 XS0 R 401 " pdb=" N10 XS0 R 401 " ideal model delta sigma weight residual 112.51 124.11 -11.60 3.00e+00 1.11e-01 1.50e+01 angle pdb=" C SER R 165 " pdb=" N CYS R 166 " pdb=" CA CYS R 166 " ideal model delta sigma weight residual 122.84 117.87 4.97 1.30e+00 5.92e-01 1.46e+01 ... (remaining 12114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 4865 17.35 - 34.71: 335 34.71 - 52.06: 69 52.06 - 69.41: 11 69.41 - 86.76: 5 Dihedral angle restraints: 5285 sinusoidal: 2009 harmonic: 3276 Sorted by residual: dihedral pdb=" CB CYS R 83 " pdb=" SG CYS R 83 " pdb=" SG CYS R 166 " pdb=" CB CYS R 166 " ideal model delta sinusoidal sigma weight residual -86.00 -136.59 50.59 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CA ASP A 261 " pdb=" CB ASP A 261 " pdb=" CG ASP A 261 " pdb=" OD1 ASP A 261 " ideal model delta sinusoidal sigma weight residual -30.00 -88.10 58.10 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" N LYS B 15 " pdb=" CA LYS B 15 " pdb=" CB LYS B 15 " pdb=" CG LYS B 15 " ideal model delta sinusoidal sigma weight residual -60.00 -117.05 57.05 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 5282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1333 0.093 - 0.186: 68 0.186 - 0.280: 0 0.280 - 0.373: 0 0.373 - 0.466: 3 Chirality restraints: 1404 Sorted by residual: chirality pdb=" C05 XS0 R 401 " pdb=" C03 XS0 R 401 " pdb=" C06 XS0 R 401 " pdb=" O09 XS0 R 401 " both_signs ideal model delta sigma weight residual False 2.57 3.04 -0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" C07 XS0 R 401 " pdb=" C06 XS0 R 401 " pdb=" C08 XS0 R 401 " pdb=" O29 XS0 R 401 " both_signs ideal model delta sigma weight residual False 2.75 2.29 0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" C06 XS0 R 401 " pdb=" C05 XS0 R 401 " pdb=" C07 XS0 R 401 " pdb=" O30 XS0 R 401 " both_signs ideal model delta sigma weight residual False 2.59 2.21 0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 1401 not shown) Planarity restraints: 1507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR R 81 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C TYR R 81 " -0.047 2.00e-02 2.50e+03 pdb=" O TYR R 81 " 0.018 2.00e-02 2.50e+03 pdb=" N SER R 82 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 250 " -0.010 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C ASN R 250 " 0.037 2.00e-02 2.50e+03 pdb=" O ASN R 250 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS R 251 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR H 235 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO H 236 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO H 236 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 236 " 0.026 5.00e-02 4.00e+02 ... (remaining 1504 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.63: 116 2.63 - 3.22: 8488 3.22 - 3.80: 14248 3.80 - 4.38: 20078 4.38 - 4.96: 33618 Nonbonded interactions: 76548 Sorted by model distance: nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.053 3.040 nonbonded pdb=" ND2 ASN B 155 " pdb=" OD1 ASP B 170 " model vdw 2.227 3.120 nonbonded pdb=" OE1 GLU A 318 " pdb=" NZ LYS A 345 " model vdw 2.259 3.120 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.264 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.269 3.040 ... (remaining 76543 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.820 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 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 : 0.005 0.244 8938 Z= 0.270 Angle : 0.557 13.321 12121 Z= 0.322 Chirality : 0.043 0.466 1404 Planarity : 0.003 0.047 1507 Dihedral : 12.618 86.763 3168 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.32 % Allowed : 4.37 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.25), residues: 1109 helix: 0.15 (0.25), residues: 406 sheet: -0.91 (0.29), residues: 273 loop : -1.05 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 13 TYR 0.005 0.000 TYR H 190 PHE 0.006 0.000 PHE R 48 TRP 0.003 0.000 TRP B 339 HIS 0.002 0.000 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 8937) covalent geometry : angle 0.55503 (12119) SS BOND : bond 0.00945 ( 1) SS BOND : angle 3.60344 ( 2) hydrogen bonds : bond 0.18499 ( 441) hydrogen bonds : angle 6.58835 ( 1221) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 239 time to evaluate : 0.340 Fit side-chains REVERT: B 243 THR cc_start: 0.7925 (p) cc_final: 0.7542 (p) REVERT: R 99 MET cc_start: 0.8433 (mmm) cc_final: 0.8219 (mmm) REVERT: R 288 LYS cc_start: 0.8121 (ttpt) cc_final: 0.7847 (tttp) REVERT: H 59 TYR cc_start: 0.5904 (m-80) cc_final: 0.5632 (m-80) REVERT: H 94 TYR cc_start: 0.8419 (m-80) cc_final: 0.7989 (m-80) REVERT: H 106 SER cc_start: 0.8681 (t) cc_final: 0.8374 (p) REVERT: A 305 CYS cc_start: 0.8386 (m) cc_final: 0.7989 (m) outliers start: 3 outliers final: 1 residues processed: 242 average time/residue: 0.1136 time to fit residues: 36.7885 Evaluate side-chains 159 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 247 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 142 HIS B 230 ASN R 12 ASN R 158 HIS R 256 ASN C 24 ASN H 179 GLN A 244 HIS A 255 ASN A 294 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.149755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.108591 restraints weight = 9271.542| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.22 r_work: 0.3039 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 8938 Z= 0.251 Angle : 0.633 9.230 12121 Z= 0.337 Chirality : 0.047 0.191 1404 Planarity : 0.005 0.056 1507 Dihedral : 5.177 55.213 1241 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.09 % Allowed : 12.69 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.25), residues: 1109 helix: 0.97 (0.26), residues: 411 sheet: -0.41 (0.30), residues: 274 loop : -0.56 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 18 TYR 0.014 0.002 TYR B 105 PHE 0.038 0.002 PHE R 147 TRP 0.015 0.002 TRP B 169 HIS 0.005 0.002 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00588 ( 8937) covalent geometry : angle 0.63308 (12119) SS BOND : bond 0.00121 ( 1) SS BOND : angle 1.20425 ( 2) hydrogen bonds : bond 0.04371 ( 441) hydrogen bonds : angle 4.87794 ( 1221) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.374 Fit side-chains REVERT: B 261 LEU cc_start: 0.8826 (mm) cc_final: 0.8588 (mt) REVERT: B 312 ASP cc_start: 0.8422 (p0) cc_final: 0.8060 (p0) REVERT: R 244 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7557 (mp) REVERT: R 288 LYS cc_start: 0.8200 (ttpt) cc_final: 0.7910 (tttp) REVERT: C 42 GLU cc_start: 0.8448 (pp20) cc_final: 0.8104 (pp20) REVERT: H 77 ASN cc_start: 0.8275 (t0) cc_final: 0.8033 (t0) REVERT: H 183 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8388 (mm-40) REVERT: H 234 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7586 (mt-10) REVERT: A 251 ASP cc_start: 0.8756 (t70) cc_final: 0.8439 (t0) REVERT: A 269 ASN cc_start: 0.8790 (m-40) cc_final: 0.8475 (m110) REVERT: A 305 CYS cc_start: 0.8466 (m) cc_final: 0.8103 (m) REVERT: A 349 LYS cc_start: 0.8503 (mtmm) cc_final: 0.8069 (mttt) outliers start: 29 outliers final: 17 residues processed: 171 average time/residue: 0.1026 time to fit residues: 24.1689 Evaluate side-chains 148 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 206 ASN Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain A residue 327 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 31 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 8 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 230 ASN B 266 HIS H 39 GLN A 244 HIS A 311 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.154699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.113534 restraints weight = 9139.194| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.23 r_work: 0.3202 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8938 Z= 0.110 Angle : 0.485 6.834 12121 Z= 0.259 Chirality : 0.041 0.129 1404 Planarity : 0.004 0.053 1507 Dihedral : 4.649 55.011 1240 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.92 % Allowed : 15.35 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.26), residues: 1109 helix: 1.46 (0.26), residues: 416 sheet: -0.34 (0.30), residues: 270 loop : -0.25 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 313 TYR 0.017 0.001 TYR H 190 PHE 0.031 0.001 PHE R 147 TRP 0.013 0.001 TRP R 185 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8937) covalent geometry : angle 0.48532 (12119) SS BOND : bond 0.00022 ( 1) SS BOND : angle 0.72130 ( 2) hydrogen bonds : bond 0.03570 ( 441) hydrogen bonds : angle 4.41013 ( 1221) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.260 Fit side-chains REVERT: B 20 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.8588 (m-30) REVERT: R 44 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7921 (mm-40) REVERT: R 288 LYS cc_start: 0.8248 (ttpt) cc_final: 0.7977 (tttp) REVERT: C 42 GLU cc_start: 0.8341 (pp20) cc_final: 0.8003 (pp20) REVERT: H 18 ARG cc_start: 0.7880 (tpp80) cc_final: 0.7524 (mmm-85) REVERT: H 77 ASN cc_start: 0.8151 (t0) cc_final: 0.7900 (t0) REVERT: H 141 THR cc_start: 0.7965 (m) cc_final: 0.7605 (t) REVERT: A 231 ASP cc_start: 0.6919 (m-30) cc_final: 0.6595 (m-30) REVERT: A 269 ASN cc_start: 0.8819 (m-40) cc_final: 0.8576 (m110) REVERT: A 305 CYS cc_start: 0.8498 (m) cc_final: 0.8133 (m) REVERT: A 327 THR cc_start: 0.7453 (OUTLIER) cc_final: 0.7215 (p) REVERT: A 351 CYS cc_start: 0.7878 (p) cc_final: 0.7504 (p) outliers start: 18 outliers final: 11 residues processed: 156 average time/residue: 0.1002 time to fit residues: 21.3586 Evaluate side-chains 144 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 327 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 30 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 3 optimal weight: 0.1980 chunk 88 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS H 39 GLN A 244 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.151165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.109303 restraints weight = 9280.628| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.24 r_work: 0.3146 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8938 Z= 0.175 Angle : 0.526 7.237 12121 Z= 0.279 Chirality : 0.043 0.157 1404 Planarity : 0.004 0.056 1507 Dihedral : 4.769 53.143 1240 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.35 % Allowed : 17.27 % Favored : 80.38 % 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 aren not related in a simple way. whole: 0.56 (0.26), residues: 1109 helix: 1.60 (0.26), residues: 413 sheet: -0.17 (0.29), residues: 279 loop : -0.37 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 19 TYR 0.014 0.001 TYR H 190 PHE 0.036 0.002 PHE R 147 TRP 0.013 0.001 TRP R 185 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 8937) covalent geometry : angle 0.52614 (12119) SS BOND : bond 0.00033 ( 1) SS BOND : angle 0.81221 ( 2) hydrogen bonds : bond 0.03766 ( 441) hydrogen bonds : angle 4.43790 ( 1221) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: B 20 ASP cc_start: 0.8858 (OUTLIER) cc_final: 0.8536 (m-30) REVERT: R 56 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7456 (mp) REVERT: R 288 LYS cc_start: 0.8224 (ttpt) cc_final: 0.7931 (tttp) REVERT: C 42 GLU cc_start: 0.8443 (pp20) cc_final: 0.8102 (pp20) REVERT: C 46 LYS cc_start: 0.9100 (mmmt) cc_final: 0.8882 (mmtt) REVERT: H 18 ARG cc_start: 0.8044 (tpp80) cc_final: 0.7097 (mmm-85) REVERT: H 77 ASN cc_start: 0.8184 (t0) cc_final: 0.7901 (t0) REVERT: A 231 ASP cc_start: 0.6947 (m-30) cc_final: 0.6570 (m-30) REVERT: A 269 ASN cc_start: 0.8857 (m-40) cc_final: 0.8600 (m110) REVERT: A 305 CYS cc_start: 0.8513 (m) cc_final: 0.8155 (m) REVERT: A 327 THR cc_start: 0.7468 (OUTLIER) cc_final: 0.7213 (p) REVERT: A 351 CYS cc_start: 0.8033 (p) cc_final: 0.7654 (p) outliers start: 22 outliers final: 15 residues processed: 147 average time/residue: 0.0957 time to fit residues: 19.3896 Evaluate side-chains 145 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 327 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 57 optimal weight: 0.0010 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS H 39 GLN A 244 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.153583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.112393 restraints weight = 8395.462| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.16 r_work: 0.3131 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8938 Z= 0.106 Angle : 0.472 5.840 12121 Z= 0.253 Chirality : 0.040 0.140 1404 Planarity : 0.004 0.052 1507 Dihedral : 4.615 53.605 1240 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.45 % Allowed : 18.44 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.26), residues: 1109 helix: 1.79 (0.27), residues: 414 sheet: -0.05 (0.30), residues: 279 loop : -0.34 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 32 TYR 0.015 0.001 TYR H 190 PHE 0.034 0.001 PHE R 147 TRP 0.017 0.001 TRP R 185 HIS 0.006 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8937) covalent geometry : angle 0.47198 (12119) SS BOND : bond 0.00029 ( 1) SS BOND : angle 0.59995 ( 2) hydrogen bonds : bond 0.03421 ( 441) hydrogen bonds : angle 4.26659 ( 1221) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.354 Fit side-chains REVERT: B 20 ASP cc_start: 0.8840 (OUTLIER) cc_final: 0.8524 (m-30) REVERT: R 44 GLN cc_start: 0.8337 (mm-40) cc_final: 0.8049 (mm-40) REVERT: R 56 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7331 (mp) REVERT: R 172 MET cc_start: 0.7532 (tpp) cc_final: 0.6909 (tpp) REVERT: R 288 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7917 (tttp) REVERT: C 42 GLU cc_start: 0.8399 (pp20) cc_final: 0.8047 (pp20) REVERT: H 18 ARG cc_start: 0.7999 (tpp80) cc_final: 0.7570 (mmm-85) REVERT: H 77 ASN cc_start: 0.8032 (t0) cc_final: 0.7781 (t0) REVERT: A 231 ASP cc_start: 0.6842 (m-30) cc_final: 0.6426 (m-30) REVERT: A 269 ASN cc_start: 0.8830 (m-40) cc_final: 0.8536 (m110) REVERT: A 305 CYS cc_start: 0.8421 (m) cc_final: 0.8061 (m) REVERT: A 351 CYS cc_start: 0.7859 (p) cc_final: 0.7463 (p) outliers start: 23 outliers final: 12 residues processed: 147 average time/residue: 0.0927 time to fit residues: 18.8497 Evaluate side-chains 142 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 chunk 83 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN A 244 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.155132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.114653 restraints weight = 8696.883| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.09 r_work: 0.3209 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8938 Z= 0.101 Angle : 0.465 6.349 12121 Z= 0.249 Chirality : 0.040 0.136 1404 Planarity : 0.003 0.055 1507 Dihedral : 4.511 53.366 1240 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.56 % Allowed : 19.30 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.26), residues: 1109 helix: 1.90 (0.27), residues: 414 sheet: 0.08 (0.30), residues: 271 loop : -0.38 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 32 TYR 0.014 0.001 TYR H 190 PHE 0.013 0.001 PHE A 189 TRP 0.019 0.001 TRP R 185 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 8937) covalent geometry : angle 0.46457 (12119) SS BOND : bond 0.00054 ( 1) SS BOND : angle 0.59664 ( 2) hydrogen bonds : bond 0.03259 ( 441) hydrogen bonds : angle 4.18069 ( 1221) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.336 Fit side-chains REVERT: B 20 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8522 (m-30) REVERT: R 44 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7992 (mm-40) REVERT: R 56 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7361 (mp) REVERT: R 172 MET cc_start: 0.7445 (tpp) cc_final: 0.6889 (tpp) REVERT: R 238 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7603 (mp) REVERT: R 288 LYS cc_start: 0.8163 (ttpt) cc_final: 0.7880 (tttp) REVERT: H 18 ARG cc_start: 0.7979 (tpp80) cc_final: 0.7582 (mmm-85) REVERT: H 77 ASN cc_start: 0.7959 (t0) cc_final: 0.7678 (t0) REVERT: A 231 ASP cc_start: 0.6858 (m-30) cc_final: 0.6443 (m-30) REVERT: A 269 ASN cc_start: 0.8831 (m-40) cc_final: 0.8544 (m110) REVERT: A 305 CYS cc_start: 0.8396 (m) cc_final: 0.8052 (m) REVERT: A 351 CYS cc_start: 0.7773 (p) cc_final: 0.7399 (p) outliers start: 24 outliers final: 16 residues processed: 151 average time/residue: 0.0978 time to fit residues: 20.1095 Evaluate side-chains 145 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 69 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 67 optimal weight: 0.0060 chunk 24 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.154644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.113689 restraints weight = 9046.120| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.14 r_work: 0.3160 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8938 Z= 0.112 Angle : 0.477 6.561 12121 Z= 0.253 Chirality : 0.040 0.140 1404 Planarity : 0.003 0.053 1507 Dihedral : 4.659 60.238 1240 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.67 % Allowed : 19.62 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.26), residues: 1109 helix: 1.93 (0.27), residues: 414 sheet: 0.15 (0.30), residues: 271 loop : -0.32 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.013 0.001 TYR H 190 PHE 0.037 0.001 PHE R 147 TRP 0.020 0.001 TRP R 185 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8937) covalent geometry : angle 0.47700 (12119) SS BOND : bond 0.00000 ( 1) SS BOND : angle 0.55774 ( 2) hydrogen bonds : bond 0.03261 ( 441) hydrogen bonds : angle 4.16392 ( 1221) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.343 Fit side-chains REVERT: B 20 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8599 (m-30) REVERT: R 44 GLN cc_start: 0.8311 (mm-40) cc_final: 0.8013 (mm-40) REVERT: R 56 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7354 (mp) REVERT: R 147 PHE cc_start: 0.5467 (p90) cc_final: 0.4862 (m-80) REVERT: R 172 MET cc_start: 0.7520 (tpp) cc_final: 0.7001 (tpp) REVERT: R 238 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7623 (mp) REVERT: R 288 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7849 (tttp) REVERT: H 18 ARG cc_start: 0.7939 (tpp80) cc_final: 0.7535 (mmm-85) REVERT: H 77 ASN cc_start: 0.7920 (t0) cc_final: 0.7616 (t0) REVERT: A 231 ASP cc_start: 0.6852 (m-30) cc_final: 0.6368 (m-30) REVERT: A 305 CYS cc_start: 0.8407 (m) cc_final: 0.8071 (m) REVERT: A 351 CYS cc_start: 0.7874 (p) cc_final: 0.7478 (p) outliers start: 25 outliers final: 17 residues processed: 147 average time/residue: 0.0909 time to fit residues: 18.3569 Evaluate side-chains 145 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 91 optimal weight: 0.2980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.155255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114441 restraints weight = 9016.685| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.14 r_work: 0.3207 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8938 Z= 0.102 Angle : 0.463 5.700 12121 Z= 0.247 Chirality : 0.040 0.139 1404 Planarity : 0.003 0.054 1507 Dihedral : 4.583 58.814 1240 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.56 % Allowed : 20.15 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.26), residues: 1109 helix: 2.01 (0.27), residues: 414 sheet: 0.23 (0.31), residues: 271 loop : -0.26 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.013 0.001 TYR H 190 PHE 0.026 0.001 PHE R 147 TRP 0.022 0.001 TRP R 185 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 8937) covalent geometry : angle 0.46326 (12119) SS BOND : bond 0.00010 ( 1) SS BOND : angle 0.39577 ( 2) hydrogen bonds : bond 0.03157 ( 441) hydrogen bonds : angle 4.12071 ( 1221) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.348 Fit side-chains REVERT: B 20 ASP cc_start: 0.8870 (OUTLIER) cc_final: 0.8557 (m-30) REVERT: B 188 MET cc_start: 0.8984 (mmm) cc_final: 0.8770 (mmm) REVERT: R 28 VAL cc_start: 0.8573 (t) cc_final: 0.8354 (p) REVERT: R 44 GLN cc_start: 0.8276 (mm-40) cc_final: 0.7982 (mm-40) REVERT: R 56 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7452 (mp) REVERT: R 172 MET cc_start: 0.7627 (tpp) cc_final: 0.7202 (tpp) REVERT: R 179 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7604 (m-10) REVERT: R 238 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7699 (mp) REVERT: R 288 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7883 (tttp) REVERT: H 77 ASN cc_start: 0.7894 (t0) cc_final: 0.7595 (t0) REVERT: A 231 ASP cc_start: 0.6767 (m-30) cc_final: 0.6294 (m-30) REVERT: A 305 CYS cc_start: 0.8494 (m) cc_final: 0.8161 (m) REVERT: A 351 CYS cc_start: 0.7817 (p) cc_final: 0.7450 (p) outliers start: 24 outliers final: 16 residues processed: 147 average time/residue: 0.0931 time to fit residues: 18.8790 Evaluate side-chains 145 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 179 TYR Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN A 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.151585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110116 restraints weight = 8839.637| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.13 r_work: 0.3084 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8938 Z= 0.157 Angle : 0.511 6.587 12121 Z= 0.272 Chirality : 0.042 0.176 1404 Planarity : 0.004 0.055 1507 Dihedral : 4.766 59.744 1240 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.45 % Allowed : 20.15 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.26), residues: 1109 helix: 1.93 (0.27), residues: 414 sheet: 0.15 (0.30), residues: 276 loop : -0.25 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 18 TYR 0.012 0.001 TYR H 190 PHE 0.032 0.001 PHE R 147 TRP 0.016 0.001 TRP R 185 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8937) covalent geometry : angle 0.51051 (12119) SS BOND : bond 0.00015 ( 1) SS BOND : angle 0.67170 ( 2) hydrogen bonds : bond 0.03527 ( 441) hydrogen bonds : angle 4.23459 ( 1221) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.312 Fit side-chains REVERT: B 20 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8527 (m-30) REVERT: B 217 MET cc_start: 0.8193 (mmt) cc_final: 0.7857 (mmm) REVERT: R 28 VAL cc_start: 0.8560 (t) cc_final: 0.8358 (p) REVERT: R 32 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8248 (tt) REVERT: R 44 GLN cc_start: 0.8291 (mm-40) cc_final: 0.7933 (mm-40) REVERT: R 56 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7295 (mp) REVERT: R 172 MET cc_start: 0.7517 (tpp) cc_final: 0.7050 (tpp) REVERT: R 179 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.7541 (m-10) REVERT: R 238 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7624 (mp) REVERT: R 288 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7857 (tttp) REVERT: H 77 ASN cc_start: 0.7881 (t0) cc_final: 0.7544 (t0) REVERT: A 231 ASP cc_start: 0.6800 (m-30) cc_final: 0.6418 (m-30) REVERT: A 305 CYS cc_start: 0.8428 (m) cc_final: 0.8083 (m) REVERT: A 351 CYS cc_start: 0.8097 (p) cc_final: 0.7696 (p) outliers start: 23 outliers final: 16 residues processed: 144 average time/residue: 0.1007 time to fit residues: 19.7598 Evaluate side-chains 145 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 179 TYR Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 58 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 186 GLN A 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.154492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.113741 restraints weight = 8745.506| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.08 r_work: 0.3173 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8938 Z= 0.108 Angle : 0.481 6.106 12121 Z= 0.256 Chirality : 0.040 0.157 1404 Planarity : 0.004 0.051 1507 Dihedral : 4.615 59.996 1240 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.03 % Allowed : 20.47 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.27), residues: 1109 helix: 1.99 (0.27), residues: 420 sheet: 0.23 (0.31), residues: 276 loop : -0.26 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.014 0.001 TYR H 190 PHE 0.027 0.001 PHE R 147 TRP 0.019 0.001 TRP R 185 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8937) covalent geometry : angle 0.48129 (12119) SS BOND : bond 0.00009 ( 1) SS BOND : angle 0.35928 ( 2) hydrogen bonds : bond 0.03260 ( 441) hydrogen bonds : angle 4.17384 ( 1221) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.338 Fit side-chains REVERT: B 20 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8637 (m-30) REVERT: B 217 MET cc_start: 0.8251 (mmt) cc_final: 0.7918 (mmm) REVERT: R 44 GLN cc_start: 0.8299 (mm-40) cc_final: 0.7977 (mm-40) REVERT: R 56 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7358 (mp) REVERT: R 172 MET cc_start: 0.7584 (tpp) cc_final: 0.7128 (tpp) REVERT: R 238 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7694 (mp) REVERT: R 288 LYS cc_start: 0.8213 (ttpt) cc_final: 0.7926 (tttp) REVERT: H 77 ASN cc_start: 0.7840 (t0) cc_final: 0.7509 (t0) REVERT: A 231 ASP cc_start: 0.6651 (m-30) cc_final: 0.6243 (m-30) REVERT: A 305 CYS cc_start: 0.8451 (m) cc_final: 0.8106 (m) REVERT: A 351 CYS cc_start: 0.7981 (p) cc_final: 0.7607 (p) outliers start: 19 outliers final: 14 residues processed: 147 average time/residue: 0.0959 time to fit residues: 19.2676 Evaluate side-chains 147 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 88 optimal weight: 0.1980 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.152768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.111403 restraints weight = 8763.629| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.14 r_work: 0.3165 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8938 Z= 0.133 Angle : 0.498 5.976 12121 Z= 0.265 Chirality : 0.041 0.170 1404 Planarity : 0.004 0.055 1507 Dihedral : 4.636 58.792 1240 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.92 % Allowed : 20.58 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.27), residues: 1109 helix: 2.00 (0.27), residues: 420 sheet: 0.28 (0.31), residues: 281 loop : -0.21 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 19 TYR 0.013 0.001 TYR H 190 PHE 0.028 0.001 PHE R 147 TRP 0.033 0.001 TRP R 185 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8937) covalent geometry : angle 0.49792 (12119) SS BOND : bond 0.00010 ( 1) SS BOND : angle 0.52447 ( 2) hydrogen bonds : bond 0.03401 ( 441) hydrogen bonds : angle 4.21713 ( 1221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2461.57 seconds wall clock time: 42 minutes 53.83 seconds (2573.83 seconds total)