Starting phenix.real_space_refine on Thu Jul 2 09:42:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cfm_30344/07_2026/7cfm_30344.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cfm_30344/07_2026/7cfm_30344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cfm_30344/07_2026/7cfm_30344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cfm_30344/07_2026/7cfm_30344.map" model { file = "/net/cci-nas-00/data/ceres_data/7cfm_30344/07_2026/7cfm_30344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cfm_30344/07_2026/7cfm_30344.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7cfm_30344/07_2026/7cfm_30344.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cfm_30344/07_2026/7cfm_30344.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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 46 5.16 5 C 5140 2.51 5 N 1419 2.21 5 O 1476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 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: 8081 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1897 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 229, 1886 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "C" Number of residues, atoms: 229, 1886 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 1910 Chain: "B" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2604 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 965 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2063 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 251} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 114 Unusual residues: {'CLR': 3, 'FWX': 1} Classifications: {'undetermined': 4, 'water': 1} Link IDs: {None: 4} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 380 " occ=0.50 ... (20 atoms not shown) pdb=" NH2CARG A 380 " occ=0.62 Time building chain proxies: 2.20, per 1000 atoms: 0.27 Number of scatterers: 8081 At special positions: 0 Unit cell: (79.092, 113.568, 122.694, 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 46 16.00 O 1476 8.00 N 1419 7.00 C 5140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 155 " 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: 0.58 Conformation dependent library (CDL) restraints added in 557.0 milliseconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 41.2% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.889A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.610A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 237' Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.922A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.128A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.889A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 2 through 26 removed outlier: 3.667A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 6 through 24 removed outlier: 4.097A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.510A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'R' and resid 21 through 42 removed outlier: 4.095A pdb=" N ASP R 42 " --> pdb=" O GLY R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 68 removed outlier: 3.519A pdb=" N CYS R 52 " --> pdb=" O PRO R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 116 removed outlier: 3.921A pdb=" N LEU R 87 " --> pdb=" O TRP R 83 " (cutoff:3.500A) Proline residue: R 92 - end of helix Processing helix chain 'R' and resid 123 through 145 removed outlier: 3.776A pdb=" N ALA R 127 " --> pdb=" O SER R 123 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY R 134 " --> pdb=" O LEU R 130 " (cutoff:3.500A) Proline residue: R 135 - end of helix Proline residue: R 142 - end of helix removed outlier: 3.749A pdb=" N GLY R 145 " --> pdb=" O LEU R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 161 Processing helix chain 'R' and resid 162 through 173 Processing helix chain 'R' and resid 173 through 207 removed outlier: 3.522A pdb=" N VAL R 178 " --> pdb=" O LEU R 174 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU R 202 " --> pdb=" O ASP R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 252 removed outlier: 3.730A pdb=" N ALA R 217 " --> pdb=" O ALA R 213 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY R 238 " --> pdb=" O GLY R 234 " (cutoff:3.500A) Proline residue: R 239 - end of helix removed outlier: 3.675A pdb=" N GLU R 252 " --> pdb=" O VAL R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 284 Proline residue: R 277 - end of helix removed outlier: 3.548A pdb=" N GLY R 283 " --> pdb=" O ALA R 279 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP R 284 " --> pdb=" O MET R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 285 through 289 removed outlier: 3.561A pdb=" N THR R 288 " --> pdb=" O GLN R 285 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA R 289 " --> pdb=" O ARG R 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 285 through 289' Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213 removed outlier: 9.779A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.580A 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: 4.082A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.223A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 4.103A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.529A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.419A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.700A 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: 4.698A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.509A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU N 81 " --> pdb=" O LEU N 20 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.660A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1117 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: 1.25 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2594 1.34 - 1.46: 1957 1.46 - 1.59: 3645 1.59 - 1.71: 0 1.71 - 1.84: 63 Bond restraints: 8259 Sorted by residual: bond pdb=" C04 FWX R 401 " pdb=" N03 FWX R 401 " ideal model delta sigma weight residual 1.343 1.423 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C12 FWX R 401 " pdb=" N09 FWX R 401 " ideal model delta sigma weight residual 1.351 1.425 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C04 FWX R 401 " pdb=" N26 FWX R 401 " ideal model delta sigma weight residual 1.329 1.402 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C LYS N 87 " pdb=" N PRO N 88 " ideal model delta sigma weight residual 1.337 1.365 -0.028 9.80e-03 1.04e+04 8.35e+00 bond pdb=" C06 FWX R 401 " pdb=" N05 FWX R 401 " ideal model delta sigma weight residual 1.319 1.368 -0.049 2.00e-02 2.50e+03 5.94e+00 ... (remaining 8254 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 10723 2.09 - 4.18: 421 4.18 - 6.27: 63 6.27 - 8.36: 19 8.36 - 10.45: 6 Bond angle restraints: 11232 Sorted by residual: angle pdb=" C LYS B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 122.46 128.54 -6.08 1.41e+00 5.03e-01 1.86e+01 angle pdb=" N LEU R 45 " pdb=" CA LEU R 45 " pdb=" C LEU R 45 " ideal model delta sigma weight residual 111.36 115.87 -4.51 1.09e+00 8.42e-01 1.71e+01 angle pdb=" N GLY A 47 " pdb=" CA GLY A 47 " pdb=" C GLY A 47 " ideal model delta sigma weight residual 113.18 104.68 8.50 2.37e+00 1.78e-01 1.29e+01 angle pdb=" C PRO R 259 " pdb=" N GLY R 260 " pdb=" CA GLY R 260 " ideal model delta sigma weight residual 121.41 128.28 -6.87 1.96e+00 2.60e-01 1.23e+01 angle pdb=" CB MET B 262 " pdb=" CG MET B 262 " pdb=" SD MET B 262 " ideal model delta sigma weight residual 112.70 123.11 -10.41 3.00e+00 1.11e-01 1.20e+01 ... (remaining 11227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 4646 17.38 - 34.77: 198 34.77 - 52.15: 38 52.15 - 69.53: 6 69.53 - 86.92: 11 Dihedral angle restraints: 4899 sinusoidal: 1928 harmonic: 2971 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -7.94 -78.06 1 1.00e+01 1.00e-02 7.61e+01 dihedral pdb=" CA LYS B 301 " pdb=" C LYS B 301 " pdb=" N ALA B 302 " pdb=" CA ALA B 302 " ideal model delta harmonic sigma weight residual 180.00 152.55 27.45 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual -86.00 -127.69 41.69 1 1.00e+01 1.00e-02 2.43e+01 ... (remaining 4896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1102 0.092 - 0.185: 148 0.185 - 0.277: 13 0.277 - 0.369: 1 0.369 - 0.462: 1 Chirality restraints: 1265 Sorted by residual: chirality pdb=" C20 CLR R 402 " pdb=" C17 CLR R 402 " pdb=" C21 CLR R 402 " pdb=" C22 CLR R 402 " both_signs ideal model delta sigma weight residual False 2.59 2.13 0.46 2.00e-01 2.50e+01 5.33e+00 chirality pdb=" C17 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C16 CLR R 402 " pdb=" C20 CLR R 402 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB THR N 28 " pdb=" CA THR N 28 " pdb=" OG1 THR N 28 " pdb=" CG2 THR N 28 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1262 not shown) Planarity restraints: 1428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.73e+00 pdb=" N PRO B 236 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 281 " -0.021 2.00e-02 2.50e+03 1.35e-02 4.58e+00 pdb=" CG TRP A 281 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 281 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 281 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 281 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 281 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 281 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 281 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 281 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO A 332 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.029 5.00e-02 4.00e+02 ... (remaining 1425 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 37 2.57 - 3.15: 5964 3.15 - 3.74: 12202 3.74 - 4.32: 16650 4.32 - 4.90: 28524 Nonbonded interactions: 63377 Sorted by model distance: nonbonded pdb=" O ASN A 54 " pdb=" CD LYS A 58 " model vdw 1.988 3.440 nonbonded pdb=" OH TYR R 167 " pdb=" OE2 GLU R 252 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.293 3.040 nonbonded pdb=" O ASP N 90 " pdb=" OH TYR N 94 " model vdw 2.308 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.322 3.040 ... (remaining 63372 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.020 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.240 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 8262 Z= 0.282 Angle : 0.990 10.451 11238 Z= 0.517 Chirality : 0.062 0.462 1265 Planarity : 0.007 0.060 1428 Dihedral : 11.257 86.917 2974 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.24 % Allowed : 4.17 % Favored : 95.60 % 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: -2.23 (0.22), residues: 1016 helix: -1.26 (0.20), residues: 393 sheet: -0.89 (0.32), residues: 228 loop : -1.89 (0.26), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 251 TYR 0.022 0.003 TYR A 339 PHE 0.020 0.003 PHE A 212 TRP 0.035 0.003 TRP A 281 HIS 0.011 0.003 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.28 ( 8259) covalent geometry : angle 0.98902 / 0.52 (11232) SS BOND : bond 0.00278 / 0.14 ( 3) SS BOND : angle 2.35845 / 1.22 ( 6) hydrogen bonds : bond 0.17923 / 11.42 ( 380) hydrogen bonds : angle 6.70072 / 4.66 ( 1117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 187 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.7492 (ptt) cc_final: 0.7046 (pp-130) REVERT: B 228 ASP cc_start: 0.7736 (p0) cc_final: 0.7300 (p0) REVERT: B 270 ILE cc_start: 0.8285 (pp) cc_final: 0.7912 (pp) REVERT: G 21 MET cc_start: 0.7609 (tpt) cc_final: 0.7066 (mmm) outliers start: 2 outliers final: 0 residues processed: 188 average time/residue: 0.5495 time to fit residues: 109.3167 Evaluate side-chains 105 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN A 294 GLN B 230 ASN N 39 GLN N 77 ASN R 102 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.158308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.114910 restraints weight = 18601.108| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.71 r_work: 0.3152 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8262 Z= 0.146 Angle : 0.632 8.164 11238 Z= 0.317 Chirality : 0.044 0.171 1265 Planarity : 0.005 0.047 1428 Dihedral : 7.045 87.385 1164 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.33 % Allowed : 11.55 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.24), residues: 1016 helix: 0.76 (0.24), residues: 392 sheet: -0.61 (0.33), residues: 230 loop : -1.46 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 228 TYR 0.021 0.001 TYR A 339 PHE 0.019 0.002 PHE N 108 TRP 0.016 0.002 TRP A 281 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 8259) covalent geometry : angle 0.63144 / 0.32 (11232) SS BOND : bond 0.00326 / 0.16 ( 3) SS BOND : angle 1.20328 / 0.66 ( 6) hydrogen bonds : bond 0.04949 / 3.24 ( 380) hydrogen bonds : angle 4.67166 / 3.26 ( 1117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.7277 (p0) REVERT: A 378 ASP cc_start: 0.7681 (m-30) cc_final: 0.7465 (m-30) REVERT: B 212 ASP cc_start: 0.8157 (t70) cc_final: 0.7759 (t70) REVERT: B 217 MET cc_start: 0.8134 (ptt) cc_final: 0.7427 (pmt) REVERT: B 270 ILE cc_start: 0.8251 (pp) cc_final: 0.7846 (pp) REVERT: G 21 MET cc_start: 0.7598 (tpt) cc_final: 0.7020 (mmm) REVERT: R 27 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7012 (mp) REVERT: R 116 ARG cc_start: 0.7537 (mtp180) cc_final: 0.7318 (mtp85) REVERT: R 141 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7870 (mt) outliers start: 28 outliers final: 8 residues processed: 143 average time/residue: 0.5108 time to fit residues: 77.8454 Evaluate side-chains 120 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 149 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN A 278 ASN A 292 ASN N 39 GLN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.160333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.116587 restraints weight = 18579.382| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.71 r_work: 0.3146 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8262 Z= 0.124 Angle : 0.569 8.663 11238 Z= 0.281 Chirality : 0.043 0.181 1265 Planarity : 0.004 0.062 1428 Dihedral : 6.778 86.777 1164 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.21 % Allowed : 13.81 % Favored : 82.98 % 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: 0.19 (0.26), residues: 1016 helix: 1.69 (0.26), residues: 398 sheet: -0.30 (0.35), residues: 228 loop : -1.23 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 79 TYR 0.020 0.001 TYR A 339 PHE 0.016 0.001 PHE N 108 TRP 0.013 0.001 TRP A 281 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 8259) covalent geometry : angle 0.56854 / 0.28 (11232) SS BOND : bond 0.00277 / 0.13 ( 3) SS BOND : angle 1.32491 / 0.76 ( 6) hydrogen bonds : bond 0.04150 / 2.76 ( 380) hydrogen bonds : angle 4.27751 / 2.98 ( 1117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8517 (mttp) REVERT: A 295 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7280 (p0) REVERT: A 378 ASP cc_start: 0.7639 (m-30) cc_final: 0.7429 (m-30) REVERT: A 392 GLU cc_start: 0.8274 (tp30) cc_final: 0.7912 (mm-30) REVERT: B 212 ASP cc_start: 0.8099 (t70) cc_final: 0.7543 (t70) REVERT: B 215 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7251 (mm-30) REVERT: B 217 MET cc_start: 0.8209 (ptt) cc_final: 0.7451 (pmt) REVERT: B 226 GLU cc_start: 0.8326 (pt0) cc_final: 0.7690 (pt0) REVERT: B 262 MET cc_start: 0.8539 (ttp) cc_final: 0.8293 (ptm) REVERT: B 270 ILE cc_start: 0.8264 (pp) cc_final: 0.7870 (pp) REVERT: B 280 LYS cc_start: 0.8674 (tttm) cc_final: 0.8368 (ttpt) REVERT: G 21 MET cc_start: 0.7648 (tpt) cc_final: 0.7102 (mmm) REVERT: N 5 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7198 (mm110) REVERT: R 27 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.7009 (mp) REVERT: R 116 ARG cc_start: 0.7432 (mtp180) cc_final: 0.7211 (mtt90) REVERT: R 141 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7893 (mt) REVERT: R 252 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8491 (mm-30) outliers start: 27 outliers final: 8 residues processed: 138 average time/residue: 0.4279 time to fit residues: 63.3725 Evaluate side-chains 124 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 149 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 31 optimal weight: 0.0670 chunk 95 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 63 optimal weight: 0.0270 chunk 14 optimal weight: 0.0770 chunk 71 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.8338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 ASN N 39 GLN N 77 ASN R 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.157376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.112431 restraints weight = 28321.271| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 4.91 r_work: 0.3079 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8262 Z= 0.118 Angle : 0.544 8.391 11238 Z= 0.269 Chirality : 0.043 0.185 1265 Planarity : 0.004 0.040 1428 Dihedral : 6.548 87.755 1164 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.45 % Allowed : 14.76 % Favored : 81.79 % 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 (0.26), residues: 1016 helix: 2.13 (0.26), residues: 398 sheet: -0.12 (0.36), residues: 216 loop : -1.08 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.020 0.001 TYR A 339 PHE 0.015 0.001 PHE N 108 TRP 0.014 0.001 TRP A 281 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 8259) covalent geometry : angle 0.54323 / 0.27 (11232) SS BOND : bond 0.00280 / 0.14 ( 3) SS BOND : angle 1.39419 / 0.82 ( 6) hydrogen bonds : bond 0.03853 / 2.58 ( 380) hydrogen bonds : angle 4.07303 / 2.84 ( 1117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8561 (mttp) REVERT: A 295 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7085 (p0) REVERT: A 392 GLU cc_start: 0.8380 (tp30) cc_final: 0.8092 (mm-30) REVERT: B 212 ASP cc_start: 0.8100 (t70) cc_final: 0.7455 (t70) REVERT: B 215 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7151 (mm-30) REVERT: B 217 MET cc_start: 0.8227 (ptt) cc_final: 0.7357 (pmt) REVERT: B 226 GLU cc_start: 0.8396 (pt0) cc_final: 0.7713 (pt0) REVERT: B 262 MET cc_start: 0.8603 (ttp) cc_final: 0.8310 (ptm) REVERT: B 270 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7901 (pp) REVERT: B 280 LYS cc_start: 0.8661 (tttm) cc_final: 0.8416 (ttpt) REVERT: G 21 MET cc_start: 0.7584 (tpt) cc_final: 0.7028 (mmm) REVERT: R 97 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7412 (mt) REVERT: R 116 ARG cc_start: 0.7416 (mtp180) cc_final: 0.7177 (mtt90) REVERT: R 154 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.7951 (m110) REVERT: R 252 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8444 (mm-30) outliers start: 29 outliers final: 11 residues processed: 135 average time/residue: 0.4197 time to fit residues: 60.7596 Evaluate side-chains 125 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 149 TRP Chi-restraints excluded: chain R residue 154 ASN Chi-restraints excluded: chain R residue 231 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 39 GLN N 77 ASN R 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.155988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.109749 restraints weight = 22298.479| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.62 r_work: 0.3084 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8262 Z= 0.135 Angle : 0.565 10.040 11238 Z= 0.276 Chirality : 0.043 0.191 1265 Planarity : 0.004 0.041 1428 Dihedral : 6.581 89.925 1164 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.10 % Allowed : 15.83 % Favored : 81.07 % 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: 0.79 (0.27), residues: 1016 helix: 2.24 (0.26), residues: 400 sheet: -0.02 (0.36), residues: 216 loop : -0.95 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 19 TYR 0.020 0.001 TYR A 339 PHE 0.018 0.001 PHE N 108 TRP 0.014 0.001 TRP A 281 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 8259) covalent geometry : angle 0.56492 / 0.28 (11232) SS BOND : bond 0.00297 / 0.14 ( 3) SS BOND : angle 1.09130 / 0.67 ( 6) hydrogen bonds : bond 0.03963 / 2.66 ( 380) hydrogen bonds : angle 4.03845 / 2.82 ( 1117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8607 (mttp) REVERT: A 392 GLU cc_start: 0.8372 (tp30) cc_final: 0.8067 (mm-30) REVERT: B 14 LEU cc_start: 0.7914 (mt) cc_final: 0.7468 (mp) REVERT: B 212 ASP cc_start: 0.8159 (t70) cc_final: 0.7594 (t70) REVERT: B 215 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7370 (mm-30) REVERT: B 217 MET cc_start: 0.8112 (ptt) cc_final: 0.7746 (pmm) REVERT: B 226 GLU cc_start: 0.8380 (pt0) cc_final: 0.7644 (pt0) REVERT: B 262 MET cc_start: 0.8668 (ttp) cc_final: 0.8351 (ptm) REVERT: B 270 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7895 (pp) REVERT: B 280 LYS cc_start: 0.8723 (tttm) cc_final: 0.8417 (ttpt) REVERT: G 21 MET cc_start: 0.7443 (tpt) cc_final: 0.6950 (mmm) REVERT: N 60 TYR cc_start: 0.9052 (m-80) cc_final: 0.8682 (m-80) REVERT: R 27 LEU cc_start: 0.7007 (mp) cc_final: 0.6730 (tt) REVERT: R 97 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7465 (mt) REVERT: R 116 ARG cc_start: 0.7398 (mtp180) cc_final: 0.7156 (mtt90) REVERT: R 146 TRP cc_start: 0.7125 (OUTLIER) cc_final: 0.6094 (m-10) REVERT: R 154 ASN cc_start: 0.8350 (OUTLIER) cc_final: 0.8055 (m-40) REVERT: R 252 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8450 (mm-30) outliers start: 26 outliers final: 15 residues processed: 128 average time/residue: 0.4240 time to fit residues: 58.2890 Evaluate side-chains 126 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 146 TRP Chi-restraints excluded: chain R residue 149 TRP Chi-restraints excluded: chain R residue 154 ASN Chi-restraints excluded: chain R residue 231 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 ASN B 220 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.156303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111291 restraints weight = 18291.141| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.32 r_work: 0.3124 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8262 Z= 0.120 Angle : 0.538 7.986 11238 Z= 0.266 Chirality : 0.043 0.191 1265 Planarity : 0.004 0.045 1428 Dihedral : 6.554 88.550 1164 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.21 % Allowed : 16.19 % Favored : 80.60 % 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: 0.95 (0.27), residues: 1016 helix: 2.37 (0.26), residues: 400 sheet: 0.10 (0.36), residues: 223 loop : -0.90 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 19 TYR 0.019 0.001 TYR A 339 PHE 0.015 0.001 PHE N 108 TRP 0.012 0.001 TRP A 281 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 8259) covalent geometry : angle 0.53713 / 0.27 (11232) SS BOND : bond 0.00238 / 0.11 ( 3) SS BOND : angle 1.10594 / 0.71 ( 6) hydrogen bonds : bond 0.03793 / 2.55 ( 380) hydrogen bonds : angle 3.98293 / 2.78 ( 1117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8651 (mttp) REVERT: A 392 GLU cc_start: 0.8345 (tp30) cc_final: 0.8033 (mm-30) REVERT: B 14 LEU cc_start: 0.7920 (mt) cc_final: 0.7475 (mp) REVERT: B 212 ASP cc_start: 0.8099 (t70) cc_final: 0.7556 (t70) REVERT: B 215 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7378 (mm-30) REVERT: B 217 MET cc_start: 0.8130 (ptt) cc_final: 0.7749 (pmm) REVERT: B 226 GLU cc_start: 0.8353 (pt0) cc_final: 0.7706 (pt0) REVERT: B 262 MET cc_start: 0.8679 (ttp) cc_final: 0.8329 (ptm) REVERT: B 270 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7917 (pp) REVERT: B 280 LYS cc_start: 0.8696 (tttm) cc_final: 0.8448 (ttpt) REVERT: G 21 MET cc_start: 0.7436 (tpt) cc_final: 0.6931 (mmm) REVERT: R 97 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7449 (mt) REVERT: R 116 ARG cc_start: 0.7417 (mtp180) cc_final: 0.7168 (mtt90) REVERT: R 146 TRP cc_start: 0.7092 (OUTLIER) cc_final: 0.6054 (m-10) REVERT: R 252 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8451 (mm-30) outliers start: 27 outliers final: 14 residues processed: 128 average time/residue: 0.4481 time to fit residues: 61.6528 Evaluate side-chains 126 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 146 TRP Chi-restraints excluded: chain R residue 149 TRP Chi-restraints excluded: chain R residue 231 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 85 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 ASN B 155 ASN B 220 GLN N 77 ASN R 154 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.153929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.109809 restraints weight = 22614.315| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 4.12 r_work: 0.3059 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8262 Z= 0.135 Angle : 0.543 7.619 11238 Z= 0.270 Chirality : 0.043 0.196 1265 Planarity : 0.004 0.042 1428 Dihedral : 6.557 86.514 1164 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.21 % Allowed : 16.19 % Favored : 80.60 % 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: 0.94 (0.27), residues: 1016 helix: 2.24 (0.26), residues: 413 sheet: 0.01 (0.35), residues: 222 loop : -0.79 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 19 TYR 0.019 0.001 TYR A 339 PHE 0.020 0.001 PHE N 108 TRP 0.014 0.001 TRP A 281 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 8259) covalent geometry : angle 0.54218 / 0.27 (11232) SS BOND : bond 0.00299 / 0.14 ( 3) SS BOND : angle 1.08311 / 0.69 ( 6) hydrogen bonds : bond 0.03914 / 2.63 ( 380) hydrogen bonds : angle 3.99282 / 2.80 ( 1117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8550 (mtmt) REVERT: A 392 GLU cc_start: 0.8430 (tp30) cc_final: 0.8099 (mm-30) REVERT: B 14 LEU cc_start: 0.7842 (mt) cc_final: 0.7392 (mp) REVERT: B 96 ARG cc_start: 0.7789 (ttt180) cc_final: 0.7466 (ttm170) REVERT: B 212 ASP cc_start: 0.8127 (t70) cc_final: 0.7576 (t70) REVERT: B 215 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7322 (mm-30) REVERT: B 217 MET cc_start: 0.8203 (ptt) cc_final: 0.7759 (pmm) REVERT: B 228 ASP cc_start: 0.8386 (p0) cc_final: 0.8030 (p0) REVERT: B 270 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7920 (pp) REVERT: B 280 LYS cc_start: 0.8656 (tttm) cc_final: 0.8384 (ttpt) REVERT: G 21 MET cc_start: 0.7435 (tpt) cc_final: 0.6928 (mmm) REVERT: N 5 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.7309 (mm-40) REVERT: N 52 SER cc_start: 0.8527 (t) cc_final: 0.8310 (p) REVERT: R 97 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7486 (mt) REVERT: R 116 ARG cc_start: 0.7455 (mtp180) cc_final: 0.7137 (mtt90) REVERT: R 146 TRP cc_start: 0.7282 (OUTLIER) cc_final: 0.6235 (m-10) REVERT: R 252 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8454 (mm-30) outliers start: 27 outliers final: 13 residues processed: 134 average time/residue: 0.4735 time to fit residues: 67.8626 Evaluate side-chains 129 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 146 TRP Chi-restraints excluded: chain R residue 149 TRP Chi-restraints excluded: chain R residue 231 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 48 optimal weight: 0.0870 chunk 47 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 ASN B 155 ASN B 220 GLN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.157028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.113271 restraints weight = 25110.623| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 4.76 r_work: 0.3091 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8262 Z= 0.107 Angle : 0.523 7.529 11238 Z= 0.261 Chirality : 0.042 0.191 1265 Planarity : 0.004 0.052 1428 Dihedral : 6.448 85.023 1164 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.50 % Allowed : 18.10 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.27), residues: 1016 helix: 2.43 (0.26), residues: 413 sheet: 0.09 (0.36), residues: 214 loop : -0.68 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 19 TYR 0.017 0.001 TYR A 339 PHE 0.011 0.001 PHE B 241 TRP 0.011 0.001 TRP A 281 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 8259) covalent geometry : angle 0.52320 / 0.26 (11232) SS BOND : bond 0.00202 / 0.10 ( 3) SS BOND : angle 0.83981 / 0.55 ( 6) hydrogen bonds : bond 0.03527 / 2.38 ( 380) hydrogen bonds : angle 3.88377 / 2.72 ( 1117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.303 Fit side-chains REVERT: A 211 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8573 (mtmt) REVERT: A 392 GLU cc_start: 0.8401 (tp30) cc_final: 0.8087 (mm-30) REVERT: B 14 LEU cc_start: 0.7813 (mt) cc_final: 0.7385 (mp) REVERT: B 96 ARG cc_start: 0.7786 (ttt180) cc_final: 0.7465 (ttm170) REVERT: B 212 ASP cc_start: 0.8108 (t70) cc_final: 0.7561 (t70) REVERT: B 217 MET cc_start: 0.8227 (ptt) cc_final: 0.7779 (pmm) REVERT: B 226 GLU cc_start: 0.8489 (pt0) cc_final: 0.8269 (pt0) REVERT: B 228 ASP cc_start: 0.8356 (p0) cc_final: 0.8033 (p0) REVERT: B 270 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7904 (pp) REVERT: G 21 MET cc_start: 0.7374 (tpt) cc_final: 0.6895 (mmm) REVERT: N 52 SER cc_start: 0.8470 (t) cc_final: 0.8268 (p) REVERT: N 60 TYR cc_start: 0.8958 (m-80) cc_final: 0.8630 (m-80) REVERT: R 97 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7516 (mt) REVERT: R 116 ARG cc_start: 0.7438 (mtp180) cc_final: 0.7082 (mtt90) REVERT: R 146 TRP cc_start: 0.7239 (OUTLIER) cc_final: 0.6218 (m-10) REVERT: R 252 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8495 (mm-30) outliers start: 21 outliers final: 13 residues processed: 126 average time/residue: 0.4695 time to fit residues: 63.2495 Evaluate side-chains 129 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 146 TRP Chi-restraints excluded: chain R residue 149 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 25 optimal weight: 0.0980 chunk 17 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 ASN B 155 ASN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.156691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111347 restraints weight = 19540.395| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.41 r_work: 0.3093 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8262 Z= 0.109 Angle : 0.520 7.444 11238 Z= 0.259 Chirality : 0.042 0.190 1265 Planarity : 0.004 0.051 1428 Dihedral : 6.379 83.686 1164 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.14 % Allowed : 19.17 % Favored : 78.69 % 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: 1.30 (0.27), residues: 1016 helix: 2.59 (0.26), residues: 407 sheet: 0.22 (0.35), residues: 224 loop : -0.64 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 19 TYR 0.017 0.001 TYR A 339 PHE 0.012 0.001 PHE N 108 TRP 0.012 0.001 TRP A 281 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 8259) covalent geometry : angle 0.51935 / 0.26 (11232) SS BOND : bond 0.00224 / 0.11 ( 3) SS BOND : angle 0.87030 / 0.54 ( 6) hydrogen bonds : bond 0.03483 / 2.35 ( 380) hydrogen bonds : angle 3.84610 / 2.69 ( 1117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.280 Fit side-chains REVERT: A 211 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8518 (mtmt) REVERT: A 392 GLU cc_start: 0.8356 (tp30) cc_final: 0.8034 (mm-30) REVERT: B 14 LEU cc_start: 0.7916 (mt) cc_final: 0.7486 (mp) REVERT: B 96 ARG cc_start: 0.7771 (ttt180) cc_final: 0.7481 (ttm170) REVERT: B 212 ASP cc_start: 0.8133 (t70) cc_final: 0.7654 (t70) REVERT: B 214 ARG cc_start: 0.7600 (mtm110) cc_final: 0.7365 (mtm110) REVERT: B 217 MET cc_start: 0.8205 (ptt) cc_final: 0.7771 (pmm) REVERT: B 228 ASP cc_start: 0.8329 (p0) cc_final: 0.8023 (p0) REVERT: B 270 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7905 (pp) REVERT: G 21 MET cc_start: 0.7384 (tpt) cc_final: 0.6906 (mmm) REVERT: N 60 TYR cc_start: 0.9006 (m-80) cc_final: 0.8676 (m-80) REVERT: R 79 ARG cc_start: 0.8273 (tpp80) cc_final: 0.7301 (tpm170) REVERT: R 116 ARG cc_start: 0.7416 (mtp180) cc_final: 0.7075 (mtt90) REVERT: R 146 TRP cc_start: 0.7245 (OUTLIER) cc_final: 0.6201 (m-10) outliers start: 18 outliers final: 14 residues processed: 124 average time/residue: 0.4217 time to fit residues: 56.0322 Evaluate side-chains 128 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 146 TRP Chi-restraints excluded: chain R residue 149 TRP Chi-restraints excluded: chain R residue 231 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 96 optimal weight: 0.0030 chunk 92 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 0.0970 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 ASN B 155 ASN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.158111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.114061 restraints weight = 21420.315| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.93 r_work: 0.3108 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8262 Z= 0.100 Angle : 0.511 7.320 11238 Z= 0.254 Chirality : 0.041 0.186 1265 Planarity : 0.004 0.053 1428 Dihedral : 6.294 82.698 1164 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.90 % Allowed : 19.64 % Favored : 78.45 % 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: 1.47 (0.27), residues: 1016 helix: 2.73 (0.26), residues: 404 sheet: 0.34 (0.36), residues: 222 loop : -0.53 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 19 TYR 0.016 0.001 TYR A 339 PHE 0.011 0.001 PHE B 241 TRP 0.010 0.001 TRP A 281 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 8259) covalent geometry : angle 0.51070 / 0.25 (11232) SS BOND : bond 0.00202 / 0.10 ( 3) SS BOND : angle 0.77307 / 0.46 ( 6) hydrogen bonds : bond 0.03280 / 2.21 ( 380) hydrogen bonds : angle 3.77755 / 2.64 ( 1117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8584 (mtmt) REVERT: A 392 GLU cc_start: 0.8365 (tp30) cc_final: 0.8035 (mm-30) REVERT: B 14 LEU cc_start: 0.7787 (mt) cc_final: 0.7369 (mp) REVERT: B 29 THR cc_start: 0.8397 (m) cc_final: 0.8040 (p) REVERT: B 96 ARG cc_start: 0.7762 (ttt180) cc_final: 0.7450 (ttm170) REVERT: B 212 ASP cc_start: 0.8093 (t70) cc_final: 0.7600 (t70) REVERT: B 217 MET cc_start: 0.8222 (ptt) cc_final: 0.7757 (pmm) REVERT: B 228 ASP cc_start: 0.8254 (p0) cc_final: 0.7930 (p0) REVERT: B 270 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7870 (pp) REVERT: G 21 MET cc_start: 0.7359 (tpt) cc_final: 0.6835 (mmm) REVERT: N 59 SER cc_start: 0.7778 (OUTLIER) cc_final: 0.7436 (t) REVERT: N 60 TYR cc_start: 0.9014 (m-80) cc_final: 0.8662 (m-80) REVERT: R 27 LEU cc_start: 0.6923 (mp) cc_final: 0.6670 (tt) REVERT: R 79 ARG cc_start: 0.8303 (tpp80) cc_final: 0.7336 (tpm170) REVERT: R 116 ARG cc_start: 0.7289 (mtp180) cc_final: 0.7019 (mtt90) outliers start: 16 outliers final: 11 residues processed: 125 average time/residue: 0.4644 time to fit residues: 62.1608 Evaluate side-chains 126 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 149 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 29 optimal weight: 0.4980 chunk 35 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 ASN B 155 ASN B 259 GLN N 39 GLN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.157181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.111756 restraints weight = 20524.526| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.49 r_work: 0.3136 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8262 Z= 0.103 Angle : 0.508 7.267 11238 Z= 0.253 Chirality : 0.041 0.186 1265 Planarity : 0.004 0.055 1428 Dihedral : 6.246 82.493 1164 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.02 % Allowed : 19.17 % Favored : 78.81 % 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: 1.50 (0.27), residues: 1016 helix: 2.78 (0.26), residues: 404 sheet: 0.32 (0.36), residues: 222 loop : -0.52 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 19 TYR 0.016 0.001 TYR A 339 PHE 0.011 0.001 PHE B 241 TRP 0.011 0.001 TRP A 281 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 8259) covalent geometry : angle 0.50745 / 0.25 (11232) SS BOND : bond 0.00213 / 0.10 ( 3) SS BOND : angle 0.79819 / 0.48 ( 6) hydrogen bonds : bond 0.03315 / 2.24 ( 380) hydrogen bonds : angle 3.77129 / 2.63 ( 1117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2720.91 seconds wall clock time: 47 minutes 0.60 seconds (2820.60 seconds total)