Starting phenix.real_space_refine on Thu Jul 2 14:24:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wig_32529/07_2026/7wig_32529.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wig_32529/07_2026/7wig_32529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wig_32529/07_2026/7wig_32529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wig_32529/07_2026/7wig_32529.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wig_32529/07_2026/7wig_32529.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wig_32529/07_2026/7wig_32529.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wig_32529/07_2026/7wig_32529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wig_32529/07_2026/7wig_32529.map" } resolution = 2.7 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= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 5697 2.51 5 N 1507 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 8931 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2234 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 1 Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1795 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'9FI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.66, per 1000 atoms: 0.19 Number of scatterers: 8931 At special positions: 0 Unit cell: (106.47, 126.75, 111.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 1660 8.00 N 1507 7.00 C 5697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 115 " - pdb=" SG CYS R 193 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 438.3 milliseconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 38.5% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'R' and resid 41 through 69 Processing helix chain 'R' and resid 77 through 96 Processing helix chain 'R' and resid 97 through 105 removed outlier: 3.961A pdb=" N MET R 101 " --> pdb=" O PRO R 97 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN R 102 " --> pdb=" O PHE R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 145 removed outlier: 3.891A pdb=" N PHE R 127 " --> pdb=" O GLY R 123 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE R 130 " --> pdb=" O GLN R 126 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE R 131 " --> pdb=" O PHE R 127 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS R 132 " --> pdb=" O THR R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 154 removed outlier: 4.103A pdb=" N LYS R 152 " --> pdb=" O ILE R 148 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TRP R 153 " --> pdb=" O LYS R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 174 removed outlier: 3.888A pdb=" N ILE R 174 " --> pdb=" O SER R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 180 Processing helix chain 'R' and resid 202 through 243 removed outlier: 5.273A pdb=" N VAL R 219 " --> pdb=" O LEU R 215 " (cutoff:3.500A) Proline residue: R 220 - end of helix Processing helix chain 'R' and resid 246 through 282 removed outlier: 3.759A pdb=" N SER R 250 " --> pdb=" O LYS R 246 " (cutoff:3.500A) Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 287 through 314 removed outlier: 3.752A pdb=" N SER R 305 " --> pdb=" O THR R 301 " (cutoff:3.500A) Proline residue: R 309 - end of helix Processing helix chain 'R' and resid 316 through 327 removed outlier: 3.841A pdb=" N SER R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN R 325 " --> pdb=" O LYS R 321 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL R 326 " --> pdb=" O SER R 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.550A pdb=" N GLU A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 removed outlier: 3.733A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.536A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.085A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.569A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.511A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.550A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.617A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.610A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.766A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.537A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 181 through 183 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.620A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.736A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.583A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.740A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.641A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.671A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.705A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.725A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.103A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.103A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.777A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1278 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: 1.14 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1444 1.30 - 1.43: 2413 1.43 - 1.56: 5163 1.56 - 1.69: 1 1.69 - 1.82: 98 Bond restraints: 9119 Sorted by residual: bond pdb=" C19 9FI R 401 " pdb=" N1 9FI R 401 " ideal model delta sigma weight residual 1.369 1.492 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C11 9FI R 401 " pdb=" N1 9FI R 401 " ideal model delta sigma weight residual 1.455 1.571 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C20 9FI R 401 " pdb=" N3 9FI R 401 " ideal model delta sigma weight residual 1.444 1.334 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C12 9FI R 401 " pdb=" N1 9FI R 401 " ideal model delta sigma weight residual 1.456 1.347 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C PHE R 127 " pdb=" O PHE R 127 " ideal model delta sigma weight residual 1.235 1.168 0.067 1.33e-02 5.65e+03 2.53e+01 ... (remaining 9114 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.87: 12308 4.87 - 9.75: 37 9.75 - 14.62: 3 14.62 - 19.50: 1 19.50 - 24.37: 1 Bond angle restraints: 12350 Sorted by residual: angle pdb=" C22 9FI R 401 " pdb=" C20 9FI R 401 " pdb=" N3 9FI R 401 " ideal model delta sigma weight residual 110.53 86.16 24.37 3.00e+00 1.11e-01 6.60e+01 angle pdb=" N ILE R 124 " pdb=" CA ILE R 124 " pdb=" C ILE R 124 " ideal model delta sigma weight residual 111.81 105.17 6.64 8.60e-01 1.35e+00 5.96e+01 angle pdb=" C6 9FI R 401 " pdb=" C12 9FI R 401 " pdb=" N1 9FI R 401 " ideal model delta sigma weight residual 111.52 127.12 -15.60 3.00e+00 1.11e-01 2.70e+01 angle pdb=" N ALA R 307 " pdb=" CA ALA R 307 " pdb=" C ALA R 307 " ideal model delta sigma weight residual 111.36 116.61 -5.25 1.09e+00 8.42e-01 2.32e+01 angle pdb=" C TYR R 302 " pdb=" N ALA R 303 " pdb=" CA ALA R 303 " ideal model delta sigma weight residual 120.28 126.19 -5.91 1.34e+00 5.57e-01 1.94e+01 ... (remaining 12345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 4870 16.36 - 32.72: 431 32.72 - 49.07: 86 49.07 - 65.43: 15 65.43 - 81.79: 7 Dihedral angle restraints: 5409 sinusoidal: 2112 harmonic: 3297 Sorted by residual: dihedral pdb=" CA LEU R 105 " pdb=" C LEU R 105 " pdb=" N VAL R 106 " pdb=" CA VAL R 106 " ideal model delta harmonic sigma weight residual -180.00 -161.70 -18.30 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA GLU B 130 " pdb=" C GLU B 130 " pdb=" N GLY B 131 " pdb=" CA GLY B 131 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA TYR S 190 " pdb=" C TYR S 190 " pdb=" N ARG S 191 " pdb=" CA ARG S 191 " ideal model delta harmonic sigma weight residual 180.00 163.54 16.46 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 5406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1231 0.069 - 0.138: 158 0.138 - 0.207: 6 0.207 - 0.275: 7 0.275 - 0.344: 2 Chirality restraints: 1404 Sorted by residual: chirality pdb=" CA ASN R 125 " pdb=" N ASN R 125 " pdb=" C ASN R 125 " pdb=" CB ASN R 125 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CA THR R 128 " pdb=" N THR R 128 " pdb=" C THR R 128 " pdb=" CB THR R 128 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB ILE R 174 " pdb=" CA ILE R 174 " pdb=" CG1 ILE R 174 " pdb=" CG2 ILE R 174 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1401 not shown) Planarity restraints: 1550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 9FI R 401 " -0.007 2.00e-02 2.50e+03 5.42e-01 8.07e+03 pdb=" C10 9FI R 401 " 0.025 2.00e-02 2.50e+03 pdb=" C14 9FI R 401 " -0.004 2.00e-02 2.50e+03 pdb=" C16 9FI R 401 " 0.010 2.00e-02 2.50e+03 pdb=" C17 9FI R 401 " -0.010 2.00e-02 2.50e+03 pdb=" C18 9FI R 401 " 0.002 2.00e-02 2.50e+03 pdb=" C21 9FI R 401 " -0.003 2.00e-02 2.50e+03 pdb=" C23 9FI R 401 " 0.008 2.00e-02 2.50e+03 pdb=" C25 9FI R 401 " -0.015 2.00e-02 2.50e+03 pdb=" C5 9FI R 401 " -1.274 2.00e-02 2.50e+03 pdb=" C6 9FI R 401 " 1.266 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 9FI R 401 " -0.004 2.00e-02 2.50e+03 2.87e-02 1.44e+01 pdb=" C12 9FI R 401 " -0.028 2.00e-02 2.50e+03 pdb=" C19 9FI R 401 " 0.017 2.00e-02 2.50e+03 pdb=" C20 9FI R 401 " -0.050 2.00e-02 2.50e+03 pdb=" N1 9FI R 401 " 0.002 2.00e-02 2.50e+03 pdb=" N3 9FI R 401 " 0.040 2.00e-02 2.50e+03 pdb=" O1 9FI R 401 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 127 " 0.035 2.00e-02 2.50e+03 2.61e-02 1.19e+01 pdb=" CG PHE R 127 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE R 127 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE R 127 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 127 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE R 127 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE R 127 " 0.029 2.00e-02 2.50e+03 ... (remaining 1547 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 527 2.73 - 3.27: 8601 3.27 - 3.82: 14610 3.82 - 4.36: 17149 4.36 - 4.90: 30796 Nonbonded interactions: 71683 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.192 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 175 " model vdw 2.244 3.040 nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 2.252 3.040 nonbonded pdb=" O HIS R 146 " pdb=" OG SER R 150 " model vdw 2.302 3.040 nonbonded pdb=" NH1 ARG B 48 " pdb=" O ARG G 62 " model vdw 2.307 3.120 ... (remaining 71678 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.600 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:5.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 9122 Z= 0.354 Angle : 0.746 24.373 12356 Z= 0.383 Chirality : 0.048 0.344 1404 Planarity : 0.014 0.542 1550 Dihedral : 13.129 81.791 3274 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.26), residues: 1123 helix: 1.86 (0.27), residues: 398 sheet: 0.93 (0.32), residues: 282 loop : -0.39 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 251 TYR 0.016 0.001 TYR R 211 PHE 0.051 0.001 PHE R 127 TRP 0.012 0.001 TRP R 108 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.35 ( 9119) covalent geometry : angle 0.74647 / 0.38 (12350) SS BOND : bond 0.00294 / 0.14 ( 3) SS BOND : angle 0.79614 / 0.42 ( 6) hydrogen bonds : bond 0.18215 / 12.56 ( 442) hydrogen bonds : angle 6.46646 / 4.65 ( 1278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7294 (mp0) cc_final: 0.6651 (mp0) REVERT: B 135 VAL cc_start: 0.8506 (t) cc_final: 0.8177 (p) REVERT: B 217 MET cc_start: 0.6505 (ppp) cc_final: 0.6131 (ppp) outliers start: 0 outliers final: 1 residues processed: 187 average time/residue: 0.4698 time to fit residues: 93.7392 Evaluate side-chains 176 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0010 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 125 ASN A 188 HIS A 195 HIS B 176 GLN B 220 GLN B 239 ASN B 259 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.138384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.118439 restraints weight = 12435.915| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.90 r_work: 0.3424 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9122 Z= 0.132 Angle : 0.912 57.124 12356 Z= 0.378 Chirality : 0.043 0.249 1404 Planarity : 0.004 0.041 1550 Dihedral : 5.396 62.880 1246 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.02 % Allowed : 9.31 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.26), residues: 1123 helix: 2.08 (0.27), residues: 401 sheet: 1.02 (0.31), residues: 276 loop : -0.32 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.028 0.001 TYR S 190 PHE 0.022 0.001 PHE R 92 TRP 0.014 0.001 TRP B 297 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 9119) covalent geometry : angle 0.91162 / 0.38 (12350) SS BOND : bond 0.00616 / 0.30 ( 3) SS BOND : angle 0.95570 / 0.43 ( 6) hydrogen bonds : bond 0.04475 / 2.97 ( 442) hydrogen bonds : angle 4.68253 / 3.40 ( 1278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 181 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: R 119 MET cc_start: 0.6871 (mmm) cc_final: 0.6661 (mpp) REVERT: A 20 ASP cc_start: 0.7979 (m-30) cc_final: 0.7775 (m-30) REVERT: A 28 GLU cc_start: 0.7787 (mp0) cc_final: 0.6922 (mp0) REVERT: A 255 ASN cc_start: 0.8503 (m-40) cc_final: 0.8268 (m-40) REVERT: B 135 VAL cc_start: 0.8614 (t) cc_final: 0.8286 (p) REVERT: S 140 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8104 (mtp) outliers start: 10 outliers final: 3 residues processed: 183 average time/residue: 0.4778 time to fit residues: 93.5850 Evaluate side-chains 181 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 177 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 140 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.135406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.115371 restraints weight = 12112.218| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.87 r_work: 0.3390 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9122 Z= 0.197 Angle : 0.931 56.855 12356 Z= 0.392 Chirality : 0.045 0.243 1404 Planarity : 0.004 0.040 1550 Dihedral : 5.515 66.150 1244 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.05 % Allowed : 11.46 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.26), residues: 1123 helix: 2.13 (0.26), residues: 401 sheet: 0.94 (0.31), residues: 277 loop : -0.42 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.030 0.002 TYR S 190 PHE 0.022 0.002 PHE R 92 TRP 0.018 0.002 TRP R 108 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 ( 9119) covalent geometry : angle 0.93095 / 0.39 (12350) SS BOND : bond 0.00845 / 0.42 ( 3) SS BOND : angle 1.51700 / 0.68 ( 6) hydrogen bonds : bond 0.04832 / 3.20 ( 442) hydrogen bonds : angle 4.54611 / 3.32 ( 1278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.326 Fit side-chains REVERT: A 8 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7615 (mt-10) REVERT: A 20 ASP cc_start: 0.7958 (m-30) cc_final: 0.7728 (m-30) REVERT: A 53 MET cc_start: 0.5441 (mmm) cc_final: 0.5216 (mmp) REVERT: A 255 ASN cc_start: 0.8562 (m-40) cc_final: 0.8336 (m-40) REVERT: A 330 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7640 (mmmm) REVERT: B 135 VAL cc_start: 0.8753 (t) cc_final: 0.8458 (p) REVERT: B 217 MET cc_start: 0.7869 (ppp) cc_final: 0.7384 (ppp) REVERT: B 219 ARG cc_start: 0.7675 (mpt180) cc_final: 0.7172 (mpt180) REVERT: S 140 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8137 (mtp) outliers start: 20 outliers final: 8 residues processed: 186 average time/residue: 0.5145 time to fit residues: 102.1427 Evaluate side-chains 187 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 90 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 132 ASN B 220 GLN B 259 GLN B 340 ASN S 142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.136743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.116903 restraints weight = 12423.737| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.89 r_work: 0.3404 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9122 Z= 0.130 Angle : 0.893 56.924 12356 Z= 0.366 Chirality : 0.043 0.210 1404 Planarity : 0.003 0.039 1550 Dihedral : 5.385 67.547 1244 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.66 % Allowed : 11.98 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.26), residues: 1123 helix: 2.34 (0.26), residues: 401 sheet: 0.96 (0.31), residues: 278 loop : -0.31 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.024 0.001 TYR S 190 PHE 0.012 0.001 PHE R 92 TRP 0.013 0.001 TRP R 108 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 9119) covalent geometry : angle 0.89259 / 0.37 (12350) SS BOND : bond 0.00636 / 0.31 ( 3) SS BOND : angle 1.20002 / 0.54 ( 6) hydrogen bonds : bond 0.04037 / 2.67 ( 442) hydrogen bonds : angle 4.38764 / 3.20 ( 1278) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.312 Fit side-chains REVERT: A 20 ASP cc_start: 0.7951 (m-30) cc_final: 0.7725 (m-30) REVERT: A 53 MET cc_start: 0.5458 (mmm) cc_final: 0.5202 (mmp) REVERT: B 135 VAL cc_start: 0.8697 (t) cc_final: 0.8409 (p) REVERT: B 212 ASP cc_start: 0.7757 (p0) cc_final: 0.7514 (p0) REVERT: B 217 MET cc_start: 0.7866 (ppp) cc_final: 0.7283 (ppp) REVERT: B 219 ARG cc_start: 0.7682 (tpt170) cc_final: 0.7136 (mpt180) REVERT: S 140 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8161 (mtp) REVERT: S 141 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8285 (p) outliers start: 26 outliers final: 11 residues processed: 184 average time/residue: 0.5337 time to fit residues: 104.7843 Evaluate side-chains 190 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 77 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 69 optimal weight: 0.0980 chunk 108 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 132 ASN B 220 GLN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.135706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.115783 restraints weight = 12356.701| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.89 r_work: 0.3391 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9122 Z= 0.170 Angle : 0.912 57.219 12356 Z= 0.378 Chirality : 0.044 0.225 1404 Planarity : 0.004 0.041 1550 Dihedral : 5.455 68.365 1244 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.97 % Allowed : 13.00 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.26), residues: 1123 helix: 2.34 (0.26), residues: 401 sheet: 1.04 (0.31), residues: 276 loop : -0.39 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 219 TYR 0.025 0.001 TYR S 190 PHE 0.013 0.001 PHE R 92 TRP 0.016 0.001 TRP R 108 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 9119) covalent geometry : angle 0.91124 / 0.38 (12350) SS BOND : bond 0.00775 / 0.38 ( 3) SS BOND : angle 1.43170 / 0.64 ( 6) hydrogen bonds : bond 0.04333 / 2.87 ( 442) hydrogen bonds : angle 4.39444 / 3.21 ( 1278) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.343 Fit side-chains REVERT: R 53 VAL cc_start: 0.5717 (OUTLIER) cc_final: 0.5452 (t) REVERT: A 20 ASP cc_start: 0.7940 (m-30) cc_final: 0.7714 (m-30) REVERT: A 255 ASN cc_start: 0.8394 (m-40) cc_final: 0.8169 (m-40) REVERT: A 275 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7378 (mm-30) REVERT: B 135 VAL cc_start: 0.8701 (t) cc_final: 0.8432 (p) REVERT: B 212 ASP cc_start: 0.7639 (p0) cc_final: 0.7331 (p0) REVERT: B 217 MET cc_start: 0.7846 (ppp) cc_final: 0.7252 (ppp) REVERT: B 219 ARG cc_start: 0.7678 (tpt170) cc_final: 0.7140 (mpt180) REVERT: S 140 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8170 (mtp) REVERT: S 141 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8311 (p) outliers start: 29 outliers final: 13 residues processed: 183 average time/residue: 0.5171 time to fit residues: 101.0960 Evaluate side-chains 188 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 54 optimal weight: 0.0980 chunk 2 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN B 75 GLN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.137362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.117485 restraints weight = 12241.541| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.89 r_work: 0.3413 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9122 Z= 0.117 Angle : 0.884 57.207 12356 Z= 0.361 Chirality : 0.042 0.198 1404 Planarity : 0.003 0.040 1550 Dihedral : 5.278 67.451 1244 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.56 % Allowed : 14.02 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.26), residues: 1123 helix: 2.47 (0.27), residues: 402 sheet: 1.05 (0.31), residues: 277 loop : -0.34 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 251 TYR 0.021 0.001 TYR S 190 PHE 0.008 0.001 PHE B 151 TRP 0.012 0.001 TRP R 108 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 9119) covalent geometry : angle 0.88342 / 0.36 (12350) SS BOND : bond 0.00525 / 0.26 ( 3) SS BOND : angle 1.13923 / 0.52 ( 6) hydrogen bonds : bond 0.03690 / 2.44 ( 442) hydrogen bonds : angle 4.26324 / 3.12 ( 1278) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.310 Fit side-chains REVERT: R 53 VAL cc_start: 0.5695 (OUTLIER) cc_final: 0.5432 (t) REVERT: A 20 ASP cc_start: 0.7944 (m-30) cc_final: 0.7712 (m-30) REVERT: A 255 ASN cc_start: 0.8312 (m-40) cc_final: 0.8110 (m-40) REVERT: A 275 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7391 (mm-30) REVERT: A 314 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8333 (mttm) REVERT: B 135 VAL cc_start: 0.8581 (t) cc_final: 0.8315 (p) REVERT: B 212 ASP cc_start: 0.7601 (p0) cc_final: 0.7263 (p0) REVERT: B 219 ARG cc_start: 0.7677 (tpt170) cc_final: 0.7122 (mpt180) REVERT: S 140 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7915 (mtp) REVERT: S 141 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.8277 (p) outliers start: 25 outliers final: 9 residues processed: 189 average time/residue: 0.5086 time to fit residues: 102.8072 Evaluate side-chains 190 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 60 optimal weight: 0.0060 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 101 optimal weight: 30.0000 chunk 94 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 62 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.139232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118679 restraints weight = 12266.074| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.94 r_work: 0.3430 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9122 Z= 0.115 Angle : 0.885 57.366 12356 Z= 0.360 Chirality : 0.042 0.196 1404 Planarity : 0.003 0.040 1550 Dihedral : 5.207 66.539 1244 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.25 % Allowed : 14.12 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.26), residues: 1123 helix: 2.51 (0.27), residues: 403 sheet: 1.00 (0.31), residues: 282 loop : -0.31 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 251 TYR 0.021 0.001 TYR S 190 PHE 0.008 0.001 PHE B 234 TRP 0.011 0.001 TRP R 108 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 9119) covalent geometry : angle 0.88481 / 0.36 (12350) SS BOND : bond 0.00532 / 0.26 ( 3) SS BOND : angle 1.09422 / 0.49 ( 6) hydrogen bonds : bond 0.03614 / 2.40 ( 442) hydrogen bonds : angle 4.23152 / 3.09 ( 1278) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.358 Fit side-chains REVERT: R 53 VAL cc_start: 0.5711 (OUTLIER) cc_final: 0.5448 (t) REVERT: A 20 ASP cc_start: 0.7924 (m-30) cc_final: 0.7702 (m-30) REVERT: A 255 ASN cc_start: 0.8348 (m-40) cc_final: 0.8123 (m-40) REVERT: A 275 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7375 (mm-30) REVERT: A 314 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8328 (mttm) REVERT: B 135 VAL cc_start: 0.8574 (t) cc_final: 0.8298 (p) REVERT: B 212 ASP cc_start: 0.7647 (p0) cc_final: 0.7300 (p0) REVERT: B 219 ARG cc_start: 0.7695 (tpt170) cc_final: 0.7240 (mpt180) REVERT: S 140 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7897 (mtp) REVERT: S 141 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8261 (p) outliers start: 22 outliers final: 10 residues processed: 185 average time/residue: 0.5195 time to fit residues: 102.6827 Evaluate side-chains 194 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.138316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.117897 restraints weight = 12135.064| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.93 r_work: 0.3419 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9122 Z= 0.142 Angle : 0.904 57.563 12356 Z= 0.372 Chirality : 0.043 0.212 1404 Planarity : 0.003 0.041 1550 Dihedral : 5.239 66.586 1244 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.35 % Allowed : 14.64 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.26), residues: 1123 helix: 2.43 (0.27), residues: 403 sheet: 1.03 (0.31), residues: 279 loop : -0.36 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 251 TYR 0.022 0.001 TYR S 190 PHE 0.010 0.001 PHE B 234 TRP 0.014 0.001 TRP R 108 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 9119) covalent geometry : angle 0.90398 / 0.37 (12350) SS BOND : bond 0.00639 / 0.31 ( 3) SS BOND : angle 1.23123 / 0.56 ( 6) hydrogen bonds : bond 0.03925 / 2.60 ( 442) hydrogen bonds : angle 4.35226 / 3.19 ( 1278) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: R 53 VAL cc_start: 0.5705 (OUTLIER) cc_final: 0.5445 (t) REVERT: A 20 ASP cc_start: 0.7938 (m-30) cc_final: 0.7711 (m-30) REVERT: A 255 ASN cc_start: 0.8404 (m-40) cc_final: 0.8145 (m-40) REVERT: A 275 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7378 (mm-30) REVERT: A 314 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8338 (mttm) REVERT: B 135 VAL cc_start: 0.8589 (t) cc_final: 0.8340 (p) REVERT: B 219 ARG cc_start: 0.7726 (tpt170) cc_final: 0.7186 (mpt180) REVERT: B 254 ASP cc_start: 0.7977 (t70) cc_final: 0.7629 (p0) REVERT: S 140 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.7881 (mtp) REVERT: S 141 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8290 (p) outliers start: 23 outliers final: 10 residues processed: 186 average time/residue: 0.4940 time to fit residues: 98.2302 Evaluate side-chains 191 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 14 optimal weight: 0.0070 chunk 15 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.138916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.118489 restraints weight = 12114.456| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.93 r_work: 0.3428 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9122 Z= 0.127 Angle : 0.901 57.507 12356 Z= 0.368 Chirality : 0.043 0.203 1404 Planarity : 0.003 0.041 1550 Dihedral : 5.213 66.087 1244 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.74 % Allowed : 15.35 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.26), residues: 1123 helix: 2.45 (0.26), residues: 403 sheet: 1.03 (0.31), residues: 281 loop : -0.35 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 251 TYR 0.020 0.001 TYR S 190 PHE 0.010 0.001 PHE B 234 TRP 0.014 0.001 TRP R 269 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 9119) covalent geometry : angle 0.90119 / 0.37 (12350) SS BOND : bond 0.00570 / 0.28 ( 3) SS BOND : angle 1.15154 / 0.52 ( 6) hydrogen bonds : bond 0.03837 / 2.56 ( 442) hydrogen bonds : angle 4.33694 / 3.17 ( 1278) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: R 53 VAL cc_start: 0.5711 (OUTLIER) cc_final: 0.5422 (t) REVERT: A 20 ASP cc_start: 0.7931 (m-30) cc_final: 0.7701 (m-30) REVERT: A 255 ASN cc_start: 0.8356 (m-40) cc_final: 0.8110 (m-40) REVERT: A 275 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7392 (mm-30) REVERT: A 314 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8321 (mttm) REVERT: B 135 VAL cc_start: 0.8575 (t) cc_final: 0.8334 (p) REVERT: B 219 ARG cc_start: 0.7707 (tpt170) cc_final: 0.7178 (mpt180) REVERT: B 254 ASP cc_start: 0.7959 (t70) cc_final: 0.7624 (p0) REVERT: S 140 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7868 (mtp) REVERT: S 141 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.8264 (p) outliers start: 17 outliers final: 11 residues processed: 189 average time/residue: 0.4546 time to fit residues: 92.0538 Evaluate side-chains 195 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 0.0670 chunk 28 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.139461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.119042 restraints weight = 12161.252| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.93 r_work: 0.3436 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9122 Z= 0.117 Angle : 0.900 57.567 12356 Z= 0.367 Chirality : 0.042 0.197 1404 Planarity : 0.003 0.040 1550 Dihedral : 5.154 63.904 1244 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.84 % Allowed : 15.15 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.26), residues: 1123 helix: 2.39 (0.27), residues: 404 sheet: 1.05 (0.31), residues: 281 loop : -0.30 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 251 TYR 0.019 0.001 TYR S 190 PHE 0.010 0.001 PHE R 92 TRP 0.011 0.001 TRP R 108 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 9119) covalent geometry : angle 0.89986 / 0.37 (12350) SS BOND : bond 0.00502 / 0.25 ( 3) SS BOND : angle 1.05274 / 0.47 ( 6) hydrogen bonds : bond 0.03665 / 2.44 ( 442) hydrogen bonds : angle 4.31236 / 3.16 ( 1278) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: R 53 VAL cc_start: 0.5566 (OUTLIER) cc_final: 0.5283 (t) REVERT: R 178 MET cc_start: 0.5319 (mmm) cc_final: 0.5071 (mmm) REVERT: A 20 ASP cc_start: 0.7916 (m-30) cc_final: 0.7671 (m-30) REVERT: A 25 GLU cc_start: 0.8043 (tt0) cc_final: 0.7735 (tt0) REVERT: A 255 ASN cc_start: 0.8312 (m-40) cc_final: 0.8081 (m-40) REVERT: A 275 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7389 (mm-30) REVERT: A 314 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8266 (mttm) REVERT: B 135 VAL cc_start: 0.8543 (t) cc_final: 0.8322 (p) REVERT: B 219 ARG cc_start: 0.7704 (tpt170) cc_final: 0.7169 (mpt180) REVERT: B 254 ASP cc_start: 0.7923 (t70) cc_final: 0.7693 (p0) REVERT: S 140 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7901 (mtp) REVERT: S 141 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8258 (p) outliers start: 18 outliers final: 8 residues processed: 189 average time/residue: 0.4715 time to fit residues: 95.5489 Evaluate side-chains 190 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 85 optimal weight: 0.0050 chunk 110 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.139655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.119295 restraints weight = 12036.875| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.92 r_work: 0.3440 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9122 Z= 0.112 Angle : 0.897 57.630 12356 Z= 0.364 Chirality : 0.042 0.250 1404 Planarity : 0.003 0.040 1550 Dihedral : 5.080 61.069 1244 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.54 % Allowed : 15.76 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.26), residues: 1123 helix: 2.46 (0.27), residues: 404 sheet: 1.06 (0.31), residues: 281 loop : -0.28 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 251 TYR 0.019 0.001 TYR S 190 PHE 0.009 0.001 PHE R 92 TRP 0.011 0.001 TRP R 108 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 9119) covalent geometry : angle 0.89681 / 0.36 (12350) SS BOND : bond 0.00489 / 0.24 ( 3) SS BOND : angle 1.00528 / 0.45 ( 6) hydrogen bonds : bond 0.03503 / 2.32 ( 442) hydrogen bonds : angle 4.24272 / 3.12 ( 1278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3321.68 seconds wall clock time: 57 minutes 15.30 seconds (3435.30 seconds total)