Starting phenix.real_space_refine on Thu Jul 2 15:16:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sg1_40450/07_2026/8sg1_40450.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sg1_40450/07_2026/8sg1_40450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sg1_40450/07_2026/8sg1_40450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sg1_40450/07_2026/8sg1_40450.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8sg1_40450/07_2026/8sg1_40450.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sg1_40450/07_2026/8sg1_40450.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sg1_40450/07_2026/8sg1_40450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sg1_40450/07_2026/8sg1_40450.map" } resolution = 2.94 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= 0.001 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5669 2.51 5 N 1490 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8846 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2172 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "A" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1750 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 3 Chain: "L" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 77 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'CLR': 1, 'PLM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.74, per 1000 atoms: 0.20 Number of scatterers: 8846 At special positions: 0 Unit cell: (94.976, 119.568, 125.504, 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 66 16.00 O 1621 8.00 N 1490 7.00 C 5669 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 112 " - pdb=" SG CYS R 189 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " 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: 0.53 Conformation dependent library (CDL) restraints added in 291.3 milliseconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 36.2% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'R' and resid 36 through 65 removed outlier: 3.929A pdb=" N ILE R 41 " --> pdb=" O ARG R 37 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 92 removed outlier: 3.830A pdb=" N TRP R 77 " --> pdb=" O VAL R 73 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE R 88 " --> pdb=" O ALA R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 101 Processing helix chain 'R' and resid 108 through 112 Processing helix chain 'R' and resid 114 through 126 Processing helix chain 'R' and resid 127 through 143 removed outlier: 3.802A pdb=" N SER R 134 " --> pdb=" O LEU R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 150 removed outlier: 3.641A pdb=" N ASN R 149 " --> pdb=" O VAL R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 172 removed outlier: 3.648A pdb=" N ALA R 156 " --> pdb=" O SER R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 177 removed outlier: 3.921A pdb=" N VAL R 176 " --> pdb=" O SER R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 251 removed outlier: 5.043A pdb=" N VAL R 231 " --> pdb=" O CYS R 227 " (cutoff:3.500A) Proline residue: R 232 - end of helix Processing helix chain 'R' and resid 256 through 283 removed outlier: 3.617A pdb=" N ILE R 267 " --> pdb=" O VAL R 263 " (cutoff:3.500A) Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 284 through 286 No H-bonds generated for 'chain 'R' and resid 284 through 286' Processing helix chain 'R' and resid 291 through 307 removed outlier: 3.758A pdb=" N LEU R 296 " --> pdb=" O SER R 292 " (cutoff:3.500A) Proline residue: R 299 - end of helix removed outlier: 3.889A pdb=" N ALA R 307 " --> pdb=" O ALA R 303 " (cutoff:3.500A) Processing helix chain 'R' and resid 307 through 312 removed outlier: 3.692A pdb=" N MET R 311 " --> pdb=" O ALA R 307 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN R 312 " --> pdb=" O ASN R 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 307 through 312' Processing helix chain 'R' and resid 312 through 317 removed outlier: 3.522A pdb=" N VAL R 317 " --> pdb=" O PRO R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 327 removed outlier: 4.031A pdb=" N PHE R 326 " --> pdb=" O ASP R 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 25 removed outlier: 3.566A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 10 through 21 removed outlier: 4.235A pdb=" N MET G 21 " --> pdb=" O GLN G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'A' and resid 6 through 30 removed outlier: 3.853A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.197A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (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 270 through 279 removed outlier: 3.689A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.576A pdb=" N GLY A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 221 through 225 removed outlier: 4.121A pdb=" N VAL E 225 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 178 through 183 Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.403A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.678A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.910A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.962A 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 151 removed outlier: 3.645A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.005A 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: 3.611A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.580A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (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: 3.637A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.286A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 5.419A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 141 through 142 removed outlier: 3.714A pdb=" N VAL E 156 " --> pdb=" O ILE E 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 195 through 196 removed outlier: 6.674A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY E 226 " --> pdb=" O LEU E 246 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1143 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: 1.05 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1412 1.31 - 1.44: 2497 1.44 - 1.56: 5028 1.56 - 1.69: 2 1.69 - 1.81: 95 Bond restraints: 9034 Sorted by residual: bond pdb=" C CYS R 272 " pdb=" O CYS R 272 " ideal model delta sigma weight residual 1.236 1.325 -0.089 1.15e-02 7.56e+03 5.93e+01 bond pdb=" C THR R 268 " pdb=" O THR R 268 " ideal model delta sigma weight residual 1.236 1.304 -0.068 1.15e-02 7.56e+03 3.45e+01 bond pdb=" C TRP R 273 " pdb=" O TRP R 273 " ideal model delta sigma weight residual 1.237 1.189 0.047 1.19e-02 7.06e+03 1.58e+01 bond pdb=" C PHE R 270 " pdb=" O PHE R 270 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.16e-02 7.43e+03 1.47e+01 bond pdb=" C ILE R 266 " pdb=" O ILE R 266 " ideal model delta sigma weight residual 1.237 1.277 -0.041 1.12e-02 7.97e+03 1.33e+01 ... (remaining 9029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 12136 3.97 - 7.94: 85 7.94 - 11.91: 9 11.91 - 15.88: 0 15.88 - 19.85: 1 Bond angle restraints: 12231 Sorted by residual: angle pdb=" CA PRO R 275 " pdb=" N PRO R 275 " pdb=" CD PRO R 275 " ideal model delta sigma weight residual 112.00 92.15 19.85 1.40e+00 5.10e-01 2.01e+02 angle pdb=" N MET R 111 " pdb=" CA MET R 111 " pdb=" C MET R 111 " ideal model delta sigma weight residual 112.88 103.50 9.38 1.29e+00 6.01e-01 5.29e+01 angle pdb=" N VAL R 73 " pdb=" CA VAL R 73 " pdb=" C VAL R 73 " ideal model delta sigma weight residual 113.42 105.36 8.06 1.17e+00 7.31e-01 4.75e+01 angle pdb=" N CYS R 112 " pdb=" CA CYS R 112 " pdb=" C CYS R 112 " ideal model delta sigma weight residual 114.56 106.02 8.54 1.27e+00 6.20e-01 4.52e+01 angle pdb=" CA TYR E 236 " pdb=" CB TYR E 236 " pdb=" CG TYR E 236 " ideal model delta sigma weight residual 113.90 103.37 10.53 1.80e+00 3.09e-01 3.42e+01 ... (remaining 12226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 4827 17.47 - 34.94: 404 34.94 - 52.41: 89 52.41 - 69.88: 14 69.88 - 87.34: 7 Dihedral angle restraints: 5341 sinusoidal: 2075 harmonic: 3266 Sorted by residual: dihedral pdb=" C TYR E 236 " pdb=" N TYR E 236 " pdb=" CA TYR E 236 " pdb=" CB TYR E 236 " ideal model delta harmonic sigma weight residual -122.60 -145.35 22.75 0 2.50e+00 1.60e-01 8.28e+01 dihedral pdb=" N TYR E 236 " pdb=" C TYR E 236 " pdb=" CA TYR E 236 " pdb=" CB TYR E 236 " ideal model delta harmonic sigma weight residual 122.80 144.39 -21.59 0 2.50e+00 1.60e-01 7.46e+01 dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 230 " pdb=" CB CYS E 230 " ideal model delta sinusoidal sigma weight residual 93.00 138.69 -45.69 1 1.00e+01 1.00e-02 2.89e+01 ... (remaining 5338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.184: 1375 0.184 - 0.368: 19 0.368 - 0.552: 0 0.552 - 0.737: 0 0.737 - 0.921: 1 Chirality restraints: 1395 Sorted by residual: chirality pdb=" CA TYR E 236 " pdb=" N TYR E 236 " pdb=" C TYR E 236 " pdb=" CB TYR E 236 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.12e+01 chirality pdb=" CA MET R 101 " pdb=" N MET R 101 " pdb=" C MET R 101 " pdb=" CB MET R 101 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA MET R 111 " pdb=" N MET R 111 " pdb=" C MET R 111 " pdb=" CB MET R 111 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 1392 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS R 274 " -0.127 5.00e-02 4.00e+02 1.73e-01 4.78e+01 pdb=" N PRO R 275 " 0.298 5.00e-02 4.00e+02 pdb=" CA PRO R 275 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO R 275 " -0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 271 " 0.021 2.00e-02 2.50e+03 4.27e-02 1.82e+01 pdb=" C LEU R 271 " -0.074 2.00e-02 2.50e+03 pdb=" O LEU R 271 " 0.027 2.00e-02 2.50e+03 pdb=" N CYS R 272 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 275 " 0.021 2.00e-02 2.50e+03 4.21e-02 1.78e+01 pdb=" C PRO R 275 " -0.073 2.00e-02 2.50e+03 pdb=" O PRO R 275 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR R 276 " 0.025 2.00e-02 2.50e+03 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1528 2.77 - 3.30: 7933 3.30 - 3.83: 14018 3.83 - 4.37: 17055 4.37 - 4.90: 30530 Nonbonded interactions: 71064 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.235 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.246 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 176 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR E 151 " pdb=" OE1 GLU E 154 " model vdw 2.263 3.040 nonbonded pdb=" O THR E 145 " pdb=" OG1 THR E 244 " model vdw 2.265 3.040 ... (remaining 71059 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.160 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:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 0.089 9037 Z= 0.377 Angle : 0.890 19.854 12237 Z= 0.605 Chirality : 0.063 0.921 1395 Planarity : 0.007 0.173 1532 Dihedral : 13.773 87.345 3220 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.78 % Allowed : 17.49 % Favored : 80.73 % Cbeta Deviations : 0.19 % 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: 0.06 (0.25), residues: 1105 helix: 0.90 (0.30), residues: 351 sheet: 0.41 (0.31), residues: 281 loop : -0.79 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 314 TYR 0.061 0.002 TYR E 236 PHE 0.029 0.001 PHE L 154 TRP 0.041 0.002 TRP R 273 HIS 0.013 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.38 ( 9034) covalent geometry : angle 0.88963 / 0.61 (12231) SS BOND : bond 0.00273 / 0.13 ( 3) SS BOND : angle 0.59027 / 0.38 ( 6) hydrogen bonds : bond 0.19293 / 13.10 ( 401) hydrogen bonds : angle 6.68231 / 4.78 ( 1143) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 275 PRO cc_start: 0.6854 (OUTLIER) cc_final: 0.6601 (Cg_exo) REVERT: B 197 ARG cc_start: 0.7576 (mmt90) cc_final: 0.7074 (mpt180) REVERT: E 235 GLU cc_start: 0.7585 (mt-10) cc_final: 0.6745 (mm-30) outliers start: 17 outliers final: 15 residues processed: 128 average time/residue: 0.5492 time to fit residues: 75.3787 Evaluate side-chains 121 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 275 PRO Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 227 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.0010 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.0980 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 58 ASN R 74 ASN R 150 HIS B 175 GLN B 266 HIS B 340 ASN G 59 ASN A 331 ASN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.156967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109656 restraints weight = 10490.148| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.35 r_work: 0.3099 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9037 Z= 0.109 Angle : 0.533 7.251 12237 Z= 0.281 Chirality : 0.042 0.200 1395 Planarity : 0.004 0.052 1532 Dihedral : 5.638 59.507 1268 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.88 % Allowed : 17.28 % Favored : 80.84 % 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: 0.46 (0.25), residues: 1105 helix: 1.51 (0.29), residues: 362 sheet: 0.50 (0.30), residues: 282 loop : -0.76 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 249 TYR 0.019 0.001 TYR E 236 PHE 0.018 0.001 PHE R 259 TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 ( 9034) covalent geometry : angle 0.53321 / 0.28 (12231) SS BOND : bond 0.00366 / 0.15 ( 3) SS BOND : angle 0.50143 / 0.29 ( 6) hydrogen bonds : bond 0.04384 / 3.05 ( 401) hydrogen bonds : angle 4.62416 / 3.39 ( 1143) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: B 197 ARG cc_start: 0.7804 (mmt90) cc_final: 0.7588 (mpt180) REVERT: B 215 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7656 (mm-30) REVERT: B 219 ARG cc_start: 0.7379 (ttm-80) cc_final: 0.7104 (mtt-85) REVERT: E 173 THR cc_start: 0.7949 (OUTLIER) cc_final: 0.7669 (t) REVERT: E 235 GLU cc_start: 0.7731 (mt-10) cc_final: 0.6967 (mm-30) REVERT: E 236 TYR cc_start: 0.6226 (OUTLIER) cc_final: 0.5358 (t80) outliers start: 18 outliers final: 7 residues processed: 114 average time/residue: 0.5677 time to fit residues: 69.3081 Evaluate side-chains 101 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 236 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 ASN B 175 GLN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.151133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.103955 restraints weight = 10585.237| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.35 r_work: 0.3017 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9037 Z= 0.190 Angle : 0.601 7.563 12237 Z= 0.315 Chirality : 0.045 0.266 1395 Planarity : 0.004 0.055 1532 Dihedral : 5.669 55.110 1252 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.46 % Allowed : 17.17 % Favored : 79.37 % 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: 0.45 (0.25), residues: 1105 helix: 1.67 (0.29), residues: 362 sheet: 0.33 (0.30), residues: 283 loop : -0.81 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.028 0.002 TYR E 236 PHE 0.022 0.002 PHE R 169 TRP 0.016 0.002 TRP E 47 HIS 0.006 0.001 HIS E 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 ( 9034) covalent geometry : angle 0.60054 / 0.31 (12231) SS BOND : bond 0.00435 / 0.21 ( 3) SS BOND : angle 0.60194 / 0.36 ( 6) hydrogen bonds : bond 0.04908 / 3.39 ( 401) hydrogen bonds : angle 4.55105 / 3.36 ( 1143) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: R 271 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6936 (mp) REVERT: B 214 ARG cc_start: 0.7790 (mtt-85) cc_final: 0.7462 (mtm180) REVERT: B 215 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7689 (mm-30) REVERT: B 219 ARG cc_start: 0.7427 (ttm-80) cc_final: 0.7055 (mtt-85) REVERT: A 53 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.6544 (mtp) REVERT: E 203 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6973 (mtp180) REVERT: E 231 MET cc_start: 0.8723 (tpt) cc_final: 0.7256 (tpt) REVERT: E 235 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7096 (mm-30) REVERT: E 246 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6880 (mp) outliers start: 33 outliers final: 15 residues processed: 131 average time/residue: 0.5439 time to fit residues: 76.2991 Evaluate side-chains 123 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 0.0040 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 58 ASN R 250 ASN B 175 GLN A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.153974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.106482 restraints weight = 10510.184| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.36 r_work: 0.3045 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9037 Z= 0.124 Angle : 0.524 6.762 12237 Z= 0.275 Chirality : 0.042 0.209 1395 Planarity : 0.004 0.052 1532 Dihedral : 5.446 54.939 1252 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.93 % Allowed : 17.49 % Favored : 79.58 % 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: 0.51 (0.25), residues: 1105 helix: 1.77 (0.29), residues: 368 sheet: 0.41 (0.30), residues: 283 loop : -0.90 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 214 TYR 0.016 0.001 TYR E 236 PHE 0.016 0.001 PHE E 68 TRP 0.013 0.001 TRP R 77 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 9034) covalent geometry : angle 0.52453 / 0.27 (12231) SS BOND : bond 0.00359 / 0.17 ( 3) SS BOND : angle 0.46487 / 0.28 ( 6) hydrogen bonds : bond 0.03986 / 2.77 ( 401) hydrogen bonds : angle 4.30083 / 3.17 ( 1143) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: R 58 ASN cc_start: 0.6123 (m-40) cc_final: 0.5699 (m-40) REVERT: R 271 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.7002 (mp) REVERT: B 161 SER cc_start: 0.8876 (OUTLIER) cc_final: 0.8639 (t) REVERT: B 214 ARG cc_start: 0.7957 (mtt-85) cc_final: 0.7466 (mtm180) REVERT: B 215 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7715 (mm-30) REVERT: B 219 ARG cc_start: 0.7414 (ttm-80) cc_final: 0.7111 (mtt-85) REVERT: G 28 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.7003 (pp) REVERT: A 53 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.6373 (mtp) REVERT: E 62 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7236 (p0) REVERT: E 203 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.7072 (mtp180) REVERT: E 235 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7058 (mm-30) outliers start: 28 outliers final: 8 residues processed: 129 average time/residue: 0.5447 time to fit residues: 75.4256 Evaluate side-chains 119 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 216 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 53 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 250 ASN B 175 GLN A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.153854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.106338 restraints weight = 10546.196| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.37 r_work: 0.3051 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9037 Z= 0.119 Angle : 0.530 9.159 12237 Z= 0.272 Chirality : 0.042 0.201 1395 Planarity : 0.004 0.051 1532 Dihedral : 5.364 58.333 1252 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.56 % Allowed : 17.80 % Favored : 78.64 % 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: 0.55 (0.25), residues: 1105 helix: 1.84 (0.29), residues: 366 sheet: 0.42 (0.30), residues: 282 loop : -0.88 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.017 0.001 TYR E 236 PHE 0.026 0.001 PHE R 169 TRP 0.013 0.001 TRP R 77 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 9034) covalent geometry : angle 0.52963 / 0.27 (12231) SS BOND : bond 0.00319 / 0.15 ( 3) SS BOND : angle 0.50682 / 0.31 ( 6) hydrogen bonds : bond 0.03885 / 2.70 ( 401) hydrogen bonds : angle 4.21338 / 3.11 ( 1143) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: R 58 ASN cc_start: 0.6083 (m-40) cc_final: 0.5719 (m-40) REVERT: R 271 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.7036 (mp) REVERT: B 214 ARG cc_start: 0.7898 (mtt-85) cc_final: 0.7515 (mtm180) REVERT: B 215 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7658 (mm-30) REVERT: B 219 ARG cc_start: 0.7424 (ttm-80) cc_final: 0.7114 (mtt-85) REVERT: G 28 ILE cc_start: 0.7260 (OUTLIER) cc_final: 0.7024 (pp) REVERT: A 261 ASP cc_start: 0.8644 (p0) cc_final: 0.8398 (p0) REVERT: E 62 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7199 (p0) REVERT: E 203 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.7196 (mtp180) REVERT: E 235 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7084 (mm-30) outliers start: 34 outliers final: 13 residues processed: 133 average time/residue: 0.5474 time to fit residues: 78.0511 Evaluate side-chains 122 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 232 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 25 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 3 optimal weight: 0.0370 chunk 36 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 250 ASN B 175 GLN A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.154204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.107147 restraints weight = 10547.115| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.35 r_work: 0.3055 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9037 Z= 0.122 Angle : 0.536 9.691 12237 Z= 0.274 Chirality : 0.042 0.199 1395 Planarity : 0.004 0.050 1532 Dihedral : 5.276 57.830 1252 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.56 % Allowed : 18.22 % Favored : 78.22 % 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 are not related in a simple way. whole: 0.59 (0.25), residues: 1105 helix: 1.89 (0.29), residues: 366 sheet: 0.45 (0.30), residues: 282 loop : -0.87 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.019 0.001 TYR E 236 PHE 0.028 0.001 PHE R 169 TRP 0.013 0.001 TRP R 77 HIS 0.004 0.001 HIS E 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 9034) covalent geometry : angle 0.53579 / 0.27 (12231) SS BOND : bond 0.00333 / 0.16 ( 3) SS BOND : angle 0.57678 / 0.35 ( 6) hydrogen bonds : bond 0.03852 / 2.68 ( 401) hydrogen bonds : angle 4.18115 / 3.09 ( 1143) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: R 58 ASN cc_start: 0.5990 (m-40) cc_final: 0.5659 (m-40) REVERT: R 271 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.7050 (mp) REVERT: B 214 ARG cc_start: 0.7863 (mtt-85) cc_final: 0.7468 (mtm180) REVERT: B 215 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7722 (mm-30) REVERT: B 219 ARG cc_start: 0.7480 (ttm-80) cc_final: 0.7107 (mtt-85) REVERT: G 28 ILE cc_start: 0.7273 (OUTLIER) cc_final: 0.7038 (pp) REVERT: A 53 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.7249 (mmm) REVERT: A 261 ASP cc_start: 0.8646 (p0) cc_final: 0.8398 (p0) REVERT: E 62 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7234 (p0) REVERT: E 203 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7215 (mtp180) REVERT: E 235 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7051 (mm-30) outliers start: 34 outliers final: 19 residues processed: 132 average time/residue: 0.5270 time to fit residues: 74.7815 Evaluate side-chains 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 232 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 16 optimal weight: 30.0000 chunk 60 optimal weight: 0.0570 chunk 103 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 250 ASN B 88 ASN B 175 GLN A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.152549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.105757 restraints weight = 10611.217| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.32 r_work: 0.3017 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9037 Z= 0.152 Angle : 0.567 11.756 12237 Z= 0.288 Chirality : 0.044 0.217 1395 Planarity : 0.004 0.052 1532 Dihedral : 5.348 58.986 1252 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.04 % Allowed : 18.95 % Favored : 78.01 % 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: 0.56 (0.25), residues: 1105 helix: 1.88 (0.29), residues: 366 sheet: 0.39 (0.30), residues: 282 loop : -0.88 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.021 0.001 TYR E 236 PHE 0.014 0.001 PHE E 68 TRP 0.013 0.002 TRP R 77 HIS 0.007 0.001 HIS E 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 9034) covalent geometry : angle 0.56658 / 0.29 (12231) SS BOND : bond 0.00385 / 0.18 ( 3) SS BOND : angle 0.56199 / 0.35 ( 6) hydrogen bonds : bond 0.04155 / 2.87 ( 401) hydrogen bonds : angle 4.23589 / 3.14 ( 1143) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: R 58 ASN cc_start: 0.6016 (m-40) cc_final: 0.5621 (m-40) REVERT: R 271 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6976 (mp) REVERT: B 214 ARG cc_start: 0.7854 (mtt-85) cc_final: 0.7473 (mtm180) REVERT: B 215 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7659 (mm-30) REVERT: B 219 ARG cc_start: 0.7477 (ttm-80) cc_final: 0.7065 (mtt-85) REVERT: G 28 ILE cc_start: 0.7229 (OUTLIER) cc_final: 0.6993 (pp) REVERT: A 53 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7266 (mmm) REVERT: A 261 ASP cc_start: 0.8643 (p0) cc_final: 0.8400 (p0) REVERT: E 11 LEU cc_start: 0.8129 (tt) cc_final: 0.7546 (mp) REVERT: E 62 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7239 (p0) REVERT: E 203 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7198 (mtp180) REVERT: E 235 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7379 (mt-10) outliers start: 29 outliers final: 22 residues processed: 125 average time/residue: 0.5889 time to fit residues: 78.9355 Evaluate side-chains 133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 232 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 96 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 72 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 250 ASN B 175 GLN A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.152766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105410 restraints weight = 10532.224| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.36 r_work: 0.3038 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9037 Z= 0.133 Angle : 0.553 11.337 12237 Z= 0.281 Chirality : 0.043 0.214 1395 Planarity : 0.004 0.050 1532 Dihedral : 5.285 59.624 1252 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.14 % Allowed : 19.16 % Favored : 77.70 % 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: 0.61 (0.25), residues: 1105 helix: 1.91 (0.29), residues: 366 sheet: 0.44 (0.30), residues: 282 loop : -0.86 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.019 0.001 TYR E 236 PHE 0.028 0.001 PHE R 169 TRP 0.013 0.001 TRP R 77 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 9034) covalent geometry : angle 0.55327 / 0.28 (12231) SS BOND : bond 0.00352 / 0.17 ( 3) SS BOND : angle 0.54979 / 0.35 ( 6) hydrogen bonds : bond 0.03991 / 2.77 ( 401) hydrogen bonds : angle 4.20194 / 3.11 ( 1143) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.375 Fit side-chains REVERT: R 58 ASN cc_start: 0.6029 (m-40) cc_final: 0.5654 (m-40) REVERT: R 271 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.7056 (mp) REVERT: B 214 ARG cc_start: 0.7877 (mtt-85) cc_final: 0.7498 (mtm180) REVERT: B 215 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7645 (mm-30) REVERT: B 219 ARG cc_start: 0.7500 (ttm-80) cc_final: 0.7103 (mtt-85) REVERT: G 28 ILE cc_start: 0.7299 (OUTLIER) cc_final: 0.7075 (pp) REVERT: A 53 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.7280 (mmm) REVERT: E 62 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7195 (p0) REVERT: E 203 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7249 (mtp180) REVERT: E 235 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7051 (mm-30) outliers start: 30 outliers final: 19 residues processed: 127 average time/residue: 0.5196 time to fit residues: 70.5362 Evaluate side-chains 129 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 232 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 70 optimal weight: 1.9990 chunk 3 optimal weight: 0.0170 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 250 ASN B 175 GLN A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.154048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.106790 restraints weight = 10522.759| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.36 r_work: 0.3050 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9037 Z= 0.106 Angle : 0.528 11.927 12237 Z= 0.268 Chirality : 0.042 0.190 1395 Planarity : 0.004 0.051 1532 Dihedral : 5.062 59.181 1251 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.83 % Allowed : 19.69 % Favored : 77.49 % 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: 0.68 (0.25), residues: 1105 helix: 1.98 (0.29), residues: 365 sheet: 0.48 (0.30), residues: 282 loop : -0.82 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.018 0.001 TYR E 236 PHE 0.031 0.001 PHE R 169 TRP 0.013 0.001 TRP R 77 HIS 0.004 0.001 HIS E 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 9034) covalent geometry : angle 0.52804 / 0.27 (12231) SS BOND : bond 0.00291 / 0.14 ( 3) SS BOND : angle 0.80581 / 0.50 ( 6) hydrogen bonds : bond 0.03654 / 2.55 ( 401) hydrogen bonds : angle 4.13770 / 3.06 ( 1143) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.320 Fit side-chains REVERT: R 58 ASN cc_start: 0.5879 (m-40) cc_final: 0.5587 (m-40) REVERT: B 214 ARG cc_start: 0.7869 (mtt-85) cc_final: 0.7468 (mtm180) REVERT: B 215 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7704 (mm-30) REVERT: B 219 ARG cc_start: 0.7435 (ttm-80) cc_final: 0.7060 (mtt-85) REVERT: G 28 ILE cc_start: 0.7236 (OUTLIER) cc_final: 0.7002 (pp) REVERT: A 53 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.7041 (mmm) REVERT: E 62 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7183 (p0) REVERT: E 89 GLU cc_start: 0.7812 (pt0) cc_final: 0.7144 (pp20) REVERT: E 203 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.7244 (mtp180) REVERT: E 235 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7291 (mt-10) outliers start: 27 outliers final: 15 residues processed: 128 average time/residue: 0.5252 time to fit residues: 72.1711 Evaluate side-chains 127 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 232 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 66 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 39 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 250 ASN B 175 GLN A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.154279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107407 restraints weight = 10525.195| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.33 r_work: 0.3045 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9037 Z= 0.115 Angle : 0.539 13.822 12237 Z= 0.272 Chirality : 0.042 0.190 1395 Planarity : 0.004 0.052 1532 Dihedral : 5.012 58.355 1250 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.20 % Allowed : 20.10 % Favored : 77.70 % 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: 0.68 (0.25), residues: 1105 helix: 2.00 (0.29), residues: 365 sheet: 0.49 (0.30), residues: 282 loop : -0.84 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.018 0.001 TYR E 236 PHE 0.014 0.001 PHE R 190 TRP 0.013 0.001 TRP R 77 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 9034) covalent geometry : angle 0.53894 / 0.27 (12231) SS BOND : bond 0.00302 / 0.14 ( 3) SS BOND : angle 0.70897 / 0.45 ( 6) hydrogen bonds : bond 0.03713 / 2.58 ( 401) hydrogen bonds : angle 4.11539 / 3.05 ( 1143) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.276 Fit side-chains REVERT: R 58 ASN cc_start: 0.5890 (m-40) cc_final: 0.5594 (m-40) REVERT: B 214 ARG cc_start: 0.7853 (mtt-85) cc_final: 0.7425 (mtm180) REVERT: B 215 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7687 (mm-30) REVERT: B 219 ARG cc_start: 0.7427 (ttm-80) cc_final: 0.7050 (mtt-85) REVERT: G 28 ILE cc_start: 0.7231 (OUTLIER) cc_final: 0.6996 (pp) REVERT: A 53 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6960 (mmm) REVERT: E 62 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7280 (p0) REVERT: E 89 GLU cc_start: 0.7828 (pt0) cc_final: 0.7149 (pp20) REVERT: E 203 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7223 (mtp180) REVERT: E 235 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7266 (mt-10) outliers start: 21 outliers final: 17 residues processed: 123 average time/residue: 0.5457 time to fit residues: 71.9199 Evaluate side-chains 125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 232 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 87 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 250 ASN B 175 GLN B 239 ASN A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.155014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108155 restraints weight = 10387.834| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.32 r_work: 0.3075 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9037 Z= 0.099 Angle : 0.522 13.669 12237 Z= 0.263 Chirality : 0.041 0.175 1395 Planarity : 0.004 0.050 1532 Dihedral : 4.897 58.174 1250 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.99 % Allowed : 20.52 % Favored : 77.49 % 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 (0.25), residues: 1105 helix: 2.00 (0.29), residues: 366 sheet: 0.49 (0.30), residues: 284 loop : -0.80 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.016 0.001 TYR E 236 PHE 0.029 0.001 PHE R 169 TRP 0.013 0.001 TRP R 77 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 9034) covalent geometry : angle 0.52203 / 0.26 (12231) SS BOND : bond 0.00265 / 0.13 ( 3) SS BOND : angle 0.70708 / 0.44 ( 6) hydrogen bonds : bond 0.03488 / 2.44 ( 401) hydrogen bonds : angle 4.06618 / 3.01 ( 1143) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3309.12 seconds wall clock time: 57 minutes 16.38 seconds (3436.38 seconds total)