Starting phenix.real_space_refine on Thu Jul 2 12:45:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ihb_35442/07_2026/8ihb_35442.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihb_35442/07_2026/8ihb_35442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ihb_35442/07_2026/8ihb_35442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihb_35442/07_2026/8ihb_35442.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihb_35442/07_2026/8ihb_35442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihb_35442/07_2026/8ihb_35442.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ihb_35442/07_2026/8ihb_35442.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ihb_35442/07_2026/8ihb_35442.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.044 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: 5 Type Number sf(0) Gaussians S 62 5.16 5 Cl 1 4.86 5 C 5568 2.51 5 N 1480 2.21 5 O 1597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8708 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2385 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 281} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1706 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "S" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1709 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2491 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 4, 'GLN:plan1': 5, 'ARG:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 85 Chain: "C" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 386 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "R" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'NAG': 1, 'OKL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.89, per 1000 atoms: 0.22 Number of scatterers: 8708 At special positions: 0 Unit cell: (86.32, 116.2, 135.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 62 16.00 O 1597 8.00 N 1480 7.00 C 5568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.04 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " 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 Links applied NAG-ASN " NAG R 601 " - " ASN R 17 " Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 401.1 milliseconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 15 sheets defined 37.7% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'R' and resid 23 through 28 removed outlier: 4.340A pdb=" N VAL R 27 " --> pdb=" O ASP R 23 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS R 28 " --> pdb=" O ASP R 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 23 through 28' Processing helix chain 'R' and resid 29 through 55 Processing helix chain 'R' and resid 60 through 78 Processing helix chain 'R' and resid 79 through 88 Processing helix chain 'R' and resid 97 through 130 removed outlier: 3.537A pdb=" N LEU R 104 " --> pdb=" O CYS R 100 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN R 110 " --> pdb=" O MET R 106 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL R 121 " --> pdb=" O PHE R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 139 removed outlier: 3.648A pdb=" N ILE R 139 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 158 Processing helix chain 'R' and resid 160 through 165 removed outlier: 3.635A pdb=" N LYS R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 196 Processing helix chain 'R' and resid 197 through 218 removed outlier: 3.560A pdb=" N ILE R 203 " --> pdb=" O LEU R 199 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 261 removed outlier: 3.527A pdb=" N THR R 231 " --> pdb=" O LYS R 227 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 269 through 281 removed outlier: 3.595A pdb=" N LEU R 274 " --> pdb=" O ARG R 270 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE R 277 " --> pdb=" O ASP R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 295 removed outlier: 3.714A pdb=" N MET R 288 " --> pdb=" O TYR R 284 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing helix chain 'A' and resid 7 through 31 removed outlier: 3.580A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.577A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.354A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.153A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.713A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.566A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.863A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 220 through 224 removed outlier: 4.189A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.682A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 removed outlier: 4.037A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'C' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'R' and resid 11 through 13 removed outlier: 4.089A pdb=" N ILE R 182 " --> pdb=" O CYS R 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 170 through 171 Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.638A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 18 through 23 Processing sheet with id=AA5, first strand: chain 'S' and resid 58 through 60 removed outlier: 4.248A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 45 through 46 Processing sheet with id=AA7, first strand: chain 'S' and resid 156 through 160 Processing sheet with id=AA8, first strand: chain 'S' and resid 194 through 195 removed outlier: 5.473A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.508A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.903A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.828A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.629A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.514A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.424A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.472A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1146 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: 1.36 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1902 1.33 - 1.46: 2600 1.46 - 1.58: 4313 1.58 - 1.71: 1 1.71 - 1.84: 88 Bond restraints: 8904 Sorted by residual: bond pdb=" C SER B 331 " pdb=" O SER B 331 " ideal model delta sigma weight residual 1.233 1.201 0.032 1.17e-02 7.31e+03 7.55e+00 bond pdb=" CA SER B 316 " pdb=" C SER B 316 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.37e-02 5.33e+03 7.18e+00 bond pdb=" C15 OKL R 602 " pdb=" N16 OKL R 602 " ideal model delta sigma weight residual 1.335 1.383 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" C SER B 316 " pdb=" O SER B 316 " ideal model delta sigma weight residual 1.236 1.207 0.029 1.29e-02 6.01e+03 4.97e+00 bond pdb=" CA SER B 316 " pdb=" CB SER B 316 " ideal model delta sigma weight residual 1.529 1.494 0.036 1.63e-02 3.76e+03 4.76e+00 ... (remaining 8899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 11792 1.39 - 2.78: 224 2.78 - 4.17: 42 4.17 - 5.56: 22 5.56 - 6.95: 4 Bond angle restraints: 12084 Sorted by residual: angle pdb=" N SER B 316 " pdb=" CA SER B 316 " pdb=" C SER B 316 " ideal model delta sigma weight residual 112.23 117.57 -5.34 1.26e+00 6.30e-01 1.80e+01 angle pdb=" N SER B 316 " pdb=" CA SER B 316 " pdb=" CB SER B 316 " ideal model delta sigma weight residual 110.30 105.45 4.85 1.54e+00 4.22e-01 9.92e+00 angle pdb=" N SER B 331 " pdb=" CA SER B 331 " pdb=" C SER B 331 " ideal model delta sigma weight residual 108.60 113.17 -4.57 1.46e+00 4.69e-01 9.80e+00 angle pdb=" C ASP R 97 " pdb=" N ILE R 98 " pdb=" CA ILE R 98 " ideal model delta sigma weight residual 120.33 122.57 -2.24 8.00e-01 1.56e+00 7.81e+00 angle pdb=" CA TYR S 235 " pdb=" CB TYR S 235 " pdb=" CG TYR S 235 " ideal model delta sigma weight residual 113.90 109.47 4.43 1.80e+00 3.09e-01 6.06e+00 ... (remaining 12079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.42: 4712 23.42 - 46.85: 430 46.85 - 70.27: 56 70.27 - 93.69: 7 93.69 - 117.11: 1 Dihedral angle restraints: 5206 sinusoidal: 1930 harmonic: 3276 Sorted by residual: dihedral pdb=" CA PHE R 117 " pdb=" C PHE R 117 " pdb=" N LEU R 118 " pdb=" CA LEU R 118 " ideal model delta harmonic sigma weight residual 180.00 155.45 24.55 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CB CYS R 100 " pdb=" SG CYS R 100 " pdb=" SG CYS R 177 " pdb=" CB CYS R 177 " ideal model delta sinusoidal sigma weight residual -86.00 -127.37 41.37 1 1.00e+01 1.00e-02 2.40e+01 dihedral pdb=" CA GLU S 234 " pdb=" C GLU S 234 " pdb=" N TYR S 235 " pdb=" CA TYR S 235 " ideal model delta harmonic sigma weight residual -180.00 -155.77 -24.23 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 5203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 800 0.029 - 0.058: 370 0.058 - 0.087: 119 0.087 - 0.116: 69 0.116 - 0.145: 19 Chirality restraints: 1377 Sorted by residual: chirality pdb=" CA ASP S 90 " pdb=" N ASP S 90 " pdb=" C ASP S 90 " pdb=" CB ASP S 90 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA GLU S 42 " pdb=" N GLU S 42 " pdb=" C GLU S 42 " pdb=" CB GLU S 42 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 1374 not shown) Planarity restraints: 1525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C05 OKL R 602 " -0.012 2.00e-02 2.50e+03 4.05e-02 5.34e+01 pdb=" C07 OKL R 602 " -0.020 2.00e-02 2.50e+03 pdb=" C10 OKL R 602 " 0.006 2.00e-02 2.50e+03 pdb=" C12 OKL R 602 " 0.040 2.00e-02 2.50e+03 pdb=" C13 OKL R 602 " 0.052 2.00e-02 2.50e+03 pdb=" C15 OKL R 602 " 0.019 2.00e-02 2.50e+03 pdb=" N06 OKL R 602 " 0.018 2.00e-02 2.50e+03 pdb=" N09 OKL R 602 " -0.020 2.00e-02 2.50e+03 pdb=" N14 OKL R 602 " 0.052 2.00e-02 2.50e+03 pdb=" N16 OKL R 602 " 0.023 2.00e-02 2.50e+03 pdb=" O08 OKL R 602 " -0.040 2.00e-02 2.50e+03 pdb=" O11 OKL R 602 " -0.016 2.00e-02 2.50e+03 pdb="CL17 OKL R 602 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 235 " 0.029 2.00e-02 2.50e+03 1.74e-02 6.04e+00 pdb=" CG TYR S 235 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR S 235 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR S 235 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR S 235 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR S 235 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR S 235 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR S 235 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO R 31 " 0.035 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO R 32 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO R 32 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 32 " 0.031 5.00e-02 4.00e+02 ... (remaining 1522 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 799 2.74 - 3.28: 8284 3.28 - 3.82: 14358 3.82 - 4.36: 17565 4.36 - 4.90: 31056 Nonbonded interactions: 72062 Sorted by model distance: nonbonded pdb=" NZ LYS A 209 " pdb=" OD2 ASP B 228 " model vdw 2.202 3.120 nonbonded pdb=" O ASP S 223 " pdb=" OH TYR S 227 " model vdw 2.230 3.040 nonbonded pdb=" OD1 ASP B 170 " pdb=" OG1 THR B 173 " model vdw 2.233 3.040 nonbonded pdb=" NH2 ARG B 256 " pdb=" OD2 ASP C 36 " model vdw 2.238 3.120 nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.240 3.120 ... (remaining 72057 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.840 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8908 Z= 0.172 Angle : 0.540 6.950 12093 Z= 0.287 Chirality : 0.042 0.145 1377 Planarity : 0.004 0.054 1524 Dihedral : 17.087 117.112 3079 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.44 % Allowed : 28.24 % Favored : 71.32 % 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: -0.70 (0.24), residues: 1115 helix: -0.01 (0.26), residues: 358 sheet: 0.17 (0.32), residues: 263 loop : -1.08 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.039 0.001 TYR S 235 PHE 0.016 0.001 PHE A 334 TRP 0.010 0.001 TRP S 47 HIS 0.002 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 8904) covalent geometry : angle 0.53642 / 0.29 (12084) SS BOND : bond 0.00694 / 0.36 ( 3) SS BOND : angle 1.48510 / 0.84 ( 6) hydrogen bonds : bond 0.26251 / 17.19 ( 413) hydrogen bonds : angle 8.29448 / 5.77 ( 1146) link_NAG-ASN : bond 0.00024 / 0.01 ( 1) link_NAG-ASN : angle 3.55407 / 2.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7931 (mtmm) cc_final: 0.7619 (ptpt) REVERT: R 63 ARG cc_start: 0.8370 (mtp85) cc_final: 0.8169 (mmt90) REVERT: R 170 GLN cc_start: 0.6941 (tm-30) cc_final: 0.6666 (tm130) REVERT: A 263 SER cc_start: 0.8696 (m) cc_final: 0.8295 (p) REVERT: S 83 MET cc_start: 0.9136 (mtm) cc_final: 0.8857 (mtp) REVERT: B 197 ARG cc_start: 0.7465 (mmm160) cc_final: 0.7256 (mmt-90) outliers start: 4 outliers final: 3 residues processed: 144 average time/residue: 0.5279 time to fit residues: 81.3403 Evaluate side-chains 137 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 134 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 39 GLN S 179 GLN S 183 GLN B 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.163281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.124615 restraints weight = 10218.272| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.03 r_work: 0.3186 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 8908 Z= 0.263 Angle : 0.648 7.983 12093 Z= 0.348 Chirality : 0.046 0.218 1377 Planarity : 0.005 0.049 1524 Dihedral : 6.550 113.191 1220 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.73 % Allowed : 26.04 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.11 (0.25), residues: 1115 helix: 1.06 (0.26), residues: 362 sheet: 0.21 (0.31), residues: 272 loop : -1.09 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 218 TYR 0.035 0.002 TYR S 235 PHE 0.016 0.002 PHE S 29 TRP 0.013 0.002 TRP B 63 HIS 0.006 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.26 ( 8904) covalent geometry : angle 0.64514 / 0.35 (12084) SS BOND : bond 0.00622 / 0.32 ( 3) SS BOND : angle 1.34529 / 0.88 ( 6) hydrogen bonds : bond 0.06451 / 4.32 ( 413) hydrogen bonds : angle 5.25788 / 3.68 ( 1146) link_NAG-ASN : bond 0.00345 / 0.18 ( 1) link_NAG-ASN : angle 3.80652 / 2.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 126 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7875 (mtmm) cc_final: 0.7571 (ptpt) REVERT: R 227 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7305 (ptpt) REVERT: R 298 SER cc_start: 0.8963 (m) cc_final: 0.8756 (t) REVERT: A 243 MET cc_start: 0.8488 (tpp) cc_final: 0.8221 (tpp) REVERT: A 276 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: A 313 ARG cc_start: 0.6139 (OUTLIER) cc_final: 0.5522 (pmm-80) REVERT: S 42 GLU cc_start: 0.7145 (pp20) cc_final: 0.6845 (pp20) REVERT: S 43 LYS cc_start: 0.9066 (mmmt) cc_final: 0.8620 (mmmt) REVERT: S 77 ASN cc_start: 0.8224 (m-40) cc_final: 0.8014 (m-40) REVERT: S 83 MET cc_start: 0.9314 (mtm) cc_final: 0.9002 (mtp) REVERT: S 223 ASP cc_start: 0.7970 (m-30) cc_final: 0.7764 (m-30) REVERT: B 195 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7606 (p0) REVERT: B 197 ARG cc_start: 0.8075 (mmm160) cc_final: 0.7844 (mmt-90) REVERT: B 219 ARG cc_start: 0.8471 (mmt90) cc_final: 0.8237 (mmt180) REVERT: B 293 ASN cc_start: 0.8551 (m-40) cc_final: 0.8224 (m-40) REVERT: B 336 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8990 (mp) outliers start: 43 outliers final: 15 residues processed: 158 average time/residue: 0.5138 time to fit residues: 86.7815 Evaluate side-chains 140 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 70 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 170 GLN ** S 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.167765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.128297 restraints weight = 9992.299| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.00 r_work: 0.3267 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8908 Z= 0.120 Angle : 0.530 6.196 12093 Z= 0.282 Chirality : 0.042 0.194 1377 Planarity : 0.004 0.046 1524 Dihedral : 5.857 105.690 1216 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.07 % Allowed : 27.36 % Favored : 68.57 % 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: 0.25 (0.25), residues: 1115 helix: 1.67 (0.27), residues: 364 sheet: 0.08 (0.30), residues: 292 loop : -0.98 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 63 TYR 0.026 0.001 TYR S 235 PHE 0.016 0.001 PHE A 334 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 8904) covalent geometry : angle 0.52470 / 0.28 (12084) SS BOND : bond 0.00610 / 0.32 ( 3) SS BOND : angle 1.26593 / 0.73 ( 6) hydrogen bonds : bond 0.04479 / 3.02 ( 413) hydrogen bonds : angle 4.58296 / 3.22 ( 1146) link_NAG-ASN : bond 0.00365 / 0.19 ( 1) link_NAG-ASN : angle 4.27360 / 2.34 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7619 (mtmm) cc_final: 0.7317 (ptpt) REVERT: R 112 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8559 (mt0) REVERT: R 227 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7330 (ptpt) REVERT: R 298 SER cc_start: 0.8999 (m) cc_final: 0.8784 (t) REVERT: A 9 ASP cc_start: 0.8430 (m-30) cc_final: 0.8158 (m-30) REVERT: A 21 ARG cc_start: 0.8268 (ptm-80) cc_final: 0.7960 (ptp90) REVERT: A 276 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: A 313 ARG cc_start: 0.6080 (OUTLIER) cc_final: 0.5497 (pmm-80) REVERT: S 43 LYS cc_start: 0.9068 (mmmt) cc_final: 0.8831 (mmmt) REVERT: S 235 TYR cc_start: 0.7442 (OUTLIER) cc_final: 0.6752 (t80) REVERT: B 52 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8340 (mtt90) REVERT: B 195 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7647 (p0) REVERT: B 197 ARG cc_start: 0.8032 (mmm160) cc_final: 0.7779 (mmt-90) REVERT: B 293 ASN cc_start: 0.8312 (m-40) cc_final: 0.7990 (m-40) outliers start: 37 outliers final: 15 residues processed: 162 average time/residue: 0.4032 time to fit residues: 70.1696 Evaluate side-chains 146 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 170 GLN S 183 GLN B 32 GLN B 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.163905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.125079 restraints weight = 10202.621| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.00 r_work: 0.3198 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 8908 Z= 0.239 Angle : 0.626 8.041 12093 Z= 0.330 Chirality : 0.046 0.229 1377 Planarity : 0.004 0.049 1524 Dihedral : 5.940 96.146 1216 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 6.15 % Allowed : 26.48 % Favored : 67.36 % 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: 0.08 (0.25), residues: 1115 helix: 1.59 (0.27), residues: 363 sheet: 0.07 (0.30), residues: 280 loop : -1.17 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.027 0.002 TYR S 235 PHE 0.017 0.002 PHE S 29 TRP 0.012 0.002 TRP B 63 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.24 ( 8904) covalent geometry : angle 0.62334 / 0.33 (12084) SS BOND : bond 0.00584 / 0.31 ( 3) SS BOND : angle 1.46345 / 0.93 ( 6) hydrogen bonds : bond 0.05243 / 3.48 ( 413) hydrogen bonds : angle 4.66984 / 3.30 ( 1146) link_NAG-ASN : bond 0.00175 / 0.09 ( 1) link_NAG-ASN : angle 3.49193 / 2.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 121 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7692 (mtmm) cc_final: 0.7407 (ptpt) REVERT: R 227 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7316 (ptpt) REVERT: A 257 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.7943 (ptmt) REVERT: A 276 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: A 313 ARG cc_start: 0.6231 (OUTLIER) cc_final: 0.5621 (pmm-80) REVERT: S 235 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.7049 (t80) REVERT: B 52 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8352 (mtt90) REVERT: B 195 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7607 (p0) REVERT: B 197 ARG cc_start: 0.8043 (mmm160) cc_final: 0.7803 (mmt-90) REVERT: B 336 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9012 (mp) outliers start: 56 outliers final: 27 residues processed: 158 average time/residue: 0.4561 time to fit residues: 77.4544 Evaluate side-chains 148 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 23 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 chunk 103 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 chunk 78 optimal weight: 0.8980 chunk 39 optimal weight: 0.0170 chunk 96 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.6422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 77 ASN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.168115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.129773 restraints weight = 10101.733| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.03 r_work: 0.3260 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8908 Z= 0.113 Angle : 0.532 7.174 12093 Z= 0.281 Chirality : 0.042 0.185 1377 Planarity : 0.004 0.044 1524 Dihedral : 5.509 93.181 1216 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.07 % Allowed : 28.57 % Favored : 67.36 % 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: 0.37 (0.25), residues: 1115 helix: 2.00 (0.27), residues: 363 sheet: 0.05 (0.29), residues: 295 loop : -1.05 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 15 TYR 0.025 0.001 TYR S 235 PHE 0.016 0.001 PHE A 334 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 8904) covalent geometry : angle 0.52790 / 0.28 (12084) SS BOND : bond 0.00756 / 0.40 ( 3) SS BOND : angle 1.58730 / 0.91 ( 6) hydrogen bonds : bond 0.04030 / 2.73 ( 413) hydrogen bonds : angle 4.35882 / 3.08 ( 1146) link_NAG-ASN : bond 0.00226 / 0.12 ( 1) link_NAG-ASN : angle 3.87720 / 2.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7551 (mtmm) cc_final: 0.7182 (ptpt) REVERT: R 101 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7521 (mtt-85) REVERT: R 112 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8521 (mt0) REVERT: R 298 SER cc_start: 0.8993 (m) cc_final: 0.8783 (t) REVERT: A 21 ARG cc_start: 0.8347 (ptm-80) cc_final: 0.7925 (ptp90) REVERT: A 276 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: A 313 ARG cc_start: 0.6170 (OUTLIER) cc_final: 0.5490 (pmm-80) REVERT: S 235 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6870 (t80) REVERT: B 52 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8407 (mtt90) REVERT: B 195 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7694 (p0) REVERT: B 197 ARG cc_start: 0.7979 (mmm160) cc_final: 0.7730 (mmt-90) REVERT: B 293 ASN cc_start: 0.8323 (m-40) cc_final: 0.8017 (m-40) outliers start: 37 outliers final: 18 residues processed: 157 average time/residue: 0.5246 time to fit residues: 88.1247 Evaluate side-chains 146 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 38 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 81 optimal weight: 0.0870 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 170 GLN S 183 GLN B 32 GLN B 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.166432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127912 restraints weight = 10122.518| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.98 r_work: 0.3239 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8908 Z= 0.155 Angle : 0.563 7.238 12093 Z= 0.296 Chirality : 0.043 0.196 1377 Planarity : 0.004 0.050 1524 Dihedral : 5.528 91.691 1216 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 5.05 % Allowed : 27.80 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.25), residues: 1115 helix: 2.02 (0.27), residues: 363 sheet: -0.02 (0.29), residues: 297 loop : -1.02 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.023 0.001 TYR S 235 PHE 0.016 0.001 PHE A 334 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 8904) covalent geometry : angle 0.55898 / 0.30 (12084) SS BOND : bond 0.00585 / 0.31 ( 3) SS BOND : angle 1.41910 / 0.84 ( 6) hydrogen bonds : bond 0.04349 / 2.92 ( 413) hydrogen bonds : angle 4.38300 / 3.10 ( 1146) link_NAG-ASN : bond 0.00174 / 0.09 ( 1) link_NAG-ASN : angle 3.65064 / 2.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 124 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7536 (mtmm) cc_final: 0.7166 (ptpt) REVERT: R 101 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7465 (mtt-85) REVERT: R 106 MET cc_start: 0.8706 (tpp) cc_final: 0.8282 (mmp) REVERT: R 112 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8543 (mt0) REVERT: R 298 SER cc_start: 0.9003 (m) cc_final: 0.8794 (t) REVERT: A 21 ARG cc_start: 0.8343 (ptm-80) cc_final: 0.7956 (ptp90) REVERT: A 207 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6887 (tt0) REVERT: A 257 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.7891 (ptmt) REVERT: A 276 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: A 313 ARG cc_start: 0.6252 (OUTLIER) cc_final: 0.5571 (pmm-80) REVERT: S 223 ASP cc_start: 0.7970 (m-30) cc_final: 0.7698 (m-30) REVERT: S 235 TYR cc_start: 0.7475 (OUTLIER) cc_final: 0.7049 (t80) REVERT: B 52 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8424 (mtt90) REVERT: B 195 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7666 (p0) REVERT: B 197 ARG cc_start: 0.8009 (mmm160) cc_final: 0.7770 (mmt-90) outliers start: 46 outliers final: 28 residues processed: 155 average time/residue: 0.5232 time to fit residues: 86.6835 Evaluate side-chains 155 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 38 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 170 GLN A 188 HIS B 32 GLN B 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.160117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.118168 restraints weight = 10297.627| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.99 r_work: 0.3199 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 8908 Z= 0.326 Angle : 0.701 9.335 12093 Z= 0.368 Chirality : 0.049 0.267 1377 Planarity : 0.005 0.044 1524 Dihedral : 6.094 93.456 1216 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 6.37 % Allowed : 26.81 % Favored : 66.81 % 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: -0.03 (0.25), residues: 1115 helix: 1.56 (0.27), residues: 362 sheet: -0.08 (0.29), residues: 285 loop : -1.24 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 314 TYR 0.032 0.002 TYR S 235 PHE 0.020 0.002 PHE S 29 TRP 0.013 0.002 TRP B 63 HIS 0.006 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00790 / 0.33 ( 8904) covalent geometry : angle 0.69846 / 0.37 (12084) SS BOND : bond 0.00685 / 0.36 ( 3) SS BOND : angle 1.71741 / 1.15 ( 6) hydrogen bonds : bond 0.05570 / 3.69 ( 413) hydrogen bonds : angle 4.67868 / 3.31 ( 1146) link_NAG-ASN : bond 0.00129 / 0.07 ( 1) link_NAG-ASN : angle 3.30063 / 1.90 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 124 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7620 (mtmm) cc_final: 0.7321 (ptpt) REVERT: R 106 MET cc_start: 0.8704 (tpp) cc_final: 0.7413 (mpp) REVERT: R 112 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8577 (mt0) REVERT: R 298 SER cc_start: 0.9027 (m) cc_final: 0.8815 (t) REVERT: A 207 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6920 (tt0) REVERT: A 257 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.7942 (ptmt) REVERT: A 276 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: A 312 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8340 (mptt) REVERT: A 313 ARG cc_start: 0.6170 (OUTLIER) cc_final: 0.5672 (pmm-80) REVERT: S 87 ARG cc_start: 0.7652 (mtm180) cc_final: 0.7301 (mtt180) REVERT: S 235 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.7136 (t80) REVERT: B 52 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8390 (mtt90) REVERT: B 153 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7961 (m-30) REVERT: B 195 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7582 (p0) REVERT: B 197 ARG cc_start: 0.8056 (mmm160) cc_final: 0.7824 (mmt-90) REVERT: B 303 ASP cc_start: 0.7217 (m-30) cc_final: 0.6959 (p0) outliers start: 58 outliers final: 29 residues processed: 169 average time/residue: 0.5122 time to fit residues: 92.7973 Evaluate side-chains 158 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 38 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 170 GLN S 77 ASN S 183 GLN B 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.167458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.127959 restraints weight = 10010.126| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.99 r_work: 0.3262 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8908 Z= 0.124 Angle : 0.564 9.631 12093 Z= 0.294 Chirality : 0.043 0.193 1377 Planarity : 0.004 0.044 1524 Dihedral : 5.535 88.776 1216 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.29 % Allowed : 28.79 % Favored : 66.92 % 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: 0.30 (0.25), residues: 1115 helix: 1.94 (0.27), residues: 363 sheet: 0.02 (0.29), residues: 291 loop : -1.09 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 98 TYR 0.025 0.001 TYR S 235 PHE 0.017 0.001 PHE A 334 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 8904) covalent geometry : angle 0.55997 / 0.29 (12084) SS BOND : bond 0.00788 / 0.41 ( 3) SS BOND : angle 2.02258 / 1.13 ( 6) hydrogen bonds : bond 0.04054 / 2.74 ( 413) hydrogen bonds : angle 4.34617 / 3.06 ( 1146) link_NAG-ASN : bond 0.00152 / 0.08 ( 1) link_NAG-ASN : angle 3.59299 / 2.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7539 (mtmm) cc_final: 0.7171 (ptpt) REVERT: R 101 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7404 (mtt-85) REVERT: R 112 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8547 (mt0) REVERT: R 298 SER cc_start: 0.9019 (m) cc_final: 0.8817 (t) REVERT: A 21 ARG cc_start: 0.8290 (ptm-80) cc_final: 0.7896 (ptp90) REVERT: A 207 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6746 (tt0) REVERT: A 257 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.7890 (ptmt) REVERT: A 276 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: A 313 ARG cc_start: 0.6108 (OUTLIER) cc_final: 0.5502 (pmm-80) REVERT: S 160 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7890 (mtm110) REVERT: S 223 ASP cc_start: 0.7964 (m-30) cc_final: 0.7646 (m-30) REVERT: S 235 TYR cc_start: 0.7335 (OUTLIER) cc_final: 0.6895 (t80) REVERT: S 244 LYS cc_start: 0.8533 (tttt) cc_final: 0.8109 (tttp) REVERT: B 52 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8352 (mtt90) REVERT: B 197 ARG cc_start: 0.7961 (mmm160) cc_final: 0.7746 (mmt-90) outliers start: 39 outliers final: 22 residues processed: 159 average time/residue: 0.5649 time to fit residues: 95.6944 Evaluate side-chains 155 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 36 optimal weight: 0.0370 chunk 15 optimal weight: 0.1980 chunk 99 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.0464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 170 GLN B 32 GLN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.166877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.127019 restraints weight = 10064.194| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.02 r_work: 0.3250 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8908 Z= 0.141 Angle : 0.577 10.087 12093 Z= 0.298 Chirality : 0.043 0.197 1377 Planarity : 0.004 0.047 1524 Dihedral : 5.477 88.480 1216 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.41 % Allowed : 30.11 % Favored : 66.48 % 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: 0.35 (0.25), residues: 1115 helix: 1.99 (0.27), residues: 363 sheet: -0.01 (0.29), residues: 296 loop : -1.03 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.023 0.001 TYR S 235 PHE 0.017 0.001 PHE A 334 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 8904) covalent geometry : angle 0.57288 / 0.30 (12084) SS BOND : bond 0.00750 / 0.39 ( 3) SS BOND : angle 1.89344 / 1.07 ( 6) hydrogen bonds : bond 0.04134 / 2.77 ( 413) hydrogen bonds : angle 4.33022 / 3.05 ( 1146) link_NAG-ASN : bond 0.00023 / 0.01 ( 1) link_NAG-ASN : angle 3.52051 / 2.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7501 (mtmm) cc_final: 0.7093 (ptpt) REVERT: R 101 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7405 (mtt-85) REVERT: R 106 MET cc_start: 0.8693 (tpp) cc_final: 0.8379 (mmp) REVERT: R 112 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8564 (mt0) REVERT: A 207 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6853 (tt0) REVERT: A 276 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: A 313 ARG cc_start: 0.6101 (OUTLIER) cc_final: 0.5553 (pmm-80) REVERT: S 160 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7900 (mtm110) REVERT: S 223 ASP cc_start: 0.8039 (m-30) cc_final: 0.7747 (m-30) REVERT: S 235 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.6987 (t80) REVERT: B 52 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8374 (mtt90) outliers start: 31 outliers final: 20 residues processed: 143 average time/residue: 0.5694 time to fit residues: 86.6562 Evaluate side-chains 148 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 93 optimal weight: 0.1980 chunk 103 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 72 optimal weight: 50.0000 chunk 37 optimal weight: 0.0770 chunk 54 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 170 GLN S 183 GLN B 32 GLN B 88 ASN B 237 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.169474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131206 restraints weight = 10088.274| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.99 r_work: 0.3295 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8908 Z= 0.108 Angle : 0.556 11.228 12093 Z= 0.285 Chirality : 0.042 0.169 1377 Planarity : 0.004 0.046 1524 Dihedral : 5.225 86.176 1216 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.97 % Allowed : 30.55 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.25), residues: 1115 helix: 2.18 (0.27), residues: 363 sheet: 0.12 (0.30), residues: 285 loop : -1.00 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 98 TYR 0.021 0.001 TYR S 235 PHE 0.019 0.001 PHE A 334 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 8904) covalent geometry : angle 0.55198 / 0.28 (12084) SS BOND : bond 0.00651 / 0.34 ( 3) SS BOND : angle 1.66698 / 0.99 ( 6) hydrogen bonds : bond 0.03644 / 2.46 ( 413) hydrogen bonds : angle 4.20233 / 2.96 ( 1146) link_NAG-ASN : bond 0.00126 / 0.07 ( 1) link_NAG-ASN : angle 3.41051 / 1.96 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7455 (mtmm) cc_final: 0.7086 (ptpt) REVERT: R 101 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7411 (mtt-85) REVERT: R 106 MET cc_start: 0.8658 (tpp) cc_final: 0.8335 (mmp) REVERT: R 112 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8548 (mt0) REVERT: A 21 ARG cc_start: 0.8265 (ptm-80) cc_final: 0.7891 (ptp90) REVERT: A 207 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6817 (tt0) REVERT: A 257 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.7972 (ptmt) REVERT: A 276 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: A 313 ARG cc_start: 0.6165 (OUTLIER) cc_final: 0.5565 (pmm-80) REVERT: S 145 SER cc_start: 0.7615 (m) cc_final: 0.7370 (t) REVERT: S 160 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7910 (mtm110) REVERT: S 213 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7869 (p) REVERT: S 235 TYR cc_start: 0.7161 (OUTLIER) cc_final: 0.6892 (t80) REVERT: B 52 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8366 (mtt90) outliers start: 27 outliers final: 13 residues processed: 152 average time/residue: 0.5694 time to fit residues: 92.3452 Evaluate side-chains 148 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 2.9990 chunk 82 optimal weight: 0.0060 chunk 94 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 0.0470 chunk 92 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 overall best weight: 0.5094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 170 GLN B 32 GLN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.170047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.131039 restraints weight = 9955.079| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.06 r_work: 0.3296 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8908 Z= 0.106 Angle : 0.558 12.798 12093 Z= 0.283 Chirality : 0.041 0.161 1377 Planarity : 0.004 0.048 1524 Dihedral : 5.099 84.791 1216 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.53 % Allowed : 31.32 % Favored : 66.15 % 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: 0.60 (0.26), residues: 1115 helix: 2.30 (0.28), residues: 363 sheet: 0.12 (0.30), residues: 285 loop : -0.97 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 98 TYR 0.020 0.001 TYR S 235 PHE 0.021 0.001 PHE A 334 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 8904) covalent geometry : angle 0.55384 / 0.28 (12084) SS BOND : bond 0.00637 / 0.33 ( 3) SS BOND : angle 1.57638 / 0.92 ( 6) hydrogen bonds : bond 0.03558 / 2.41 ( 413) hydrogen bonds : angle 4.15696 / 2.92 ( 1146) link_NAG-ASN : bond 0.00099 / 0.05 ( 1) link_NAG-ASN : angle 3.56150 / 2.03 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3290.36 seconds wall clock time: 56 minutes 48.47 seconds (3408.47 seconds total)