Starting phenix.real_space_refine on Thu Jul 2 18:17:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vl9_32021/07_2026/7vl9_32021.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vl9_32021/07_2026/7vl9_32021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vl9_32021/07_2026/7vl9_32021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vl9_32021/07_2026/7vl9_32021.map" model { file = "/net/cci-nas-00/data/ceres_data/7vl9_32021/07_2026/7vl9_32021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vl9_32021/07_2026/7vl9_32021.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7vl9_32021/07_2026/7vl9_32021.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vl9_32021/07_2026/7vl9_32021.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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 68 5.16 5 C 6152 2.51 5 N 1616 2.21 5 O 1769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 9605 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 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: "L" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 496 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "R" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2493 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 10, 'TRANS': 291} Chain: "S" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.83, per 1000 atoms: 0.19 Number of scatterers: 9605 At special positions: 0 Unit cell: (110.313, 134.946, 126.378, 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 68 16.00 O 1769 8.00 N 1616 7.00 C 6152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS L 32 " - pdb=" SG CYS L 56 " distance=2.03 Simple disulfide: pdb=" SG CYS L 33 " - pdb=" SG CYS L 72 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 83 " distance=2.03 Simple disulfide: pdb=" SG CYS R 24 " - pdb=" SG CYS R 273 " distance=2.04 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 350.6 milliseconds 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2274 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 15 sheets defined 39.2% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.527A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.374A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.013A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.256A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.883A 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 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.520A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'L' and resid 42 through 44 No H-bonds generated for 'chain 'L' and resid 42 through 44' Processing helix chain 'L' and resid 77 through 87 removed outlier: 4.128A pdb=" N GLN L 81 " --> pdb=" O GLY L 77 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASP L 82 " --> pdb=" O PRO L 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 59 Proline residue: R 38 - end of helix removed outlier: 3.775A pdb=" N VAL R 46 " --> pdb=" O SER R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 97 removed outlier: 4.112A pdb=" N THR R 86 " --> pdb=" O LEU R 82 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU R 87 " --> pdb=" O PHE R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 139 through 143 Processing helix chain 'R' and resid 146 through 165 Processing helix chain 'R' and resid 165 through 172 removed outlier: 3.569A pdb=" N SER R 172 " --> pdb=" O GLY R 168 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 206 removed outlier: 3.647A pdb=" N LEU R 203 " --> pdb=" O GLN R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 228 removed outlier: 3.876A pdb=" N GLY R 221 " --> pdb=" O ILE R 217 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG R 228 " --> pdb=" O LYS R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 231 through 264 Proline residue: R 254 - end of helix Processing helix chain 'R' and resid 264 through 269 Processing helix chain 'R' and resid 274 through 302 removed outlier: 4.281A pdb=" N HIS R 278 " --> pdb=" O GLU R 274 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE R 289 " --> pdb=" O VAL R 285 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N CYS R 294 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N CYS R 295 " --> pdb=" O TYR R 291 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 305 through 318 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 8.710A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.684A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.584A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.019A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.583A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.091A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.662A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.696A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 46 through 51 Processing sheet with id=AB1, first strand: chain 'R' and resid 173 through 177 Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.027A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.027A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.624A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1383 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: 1.37 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1715 1.32 - 1.45: 2785 1.45 - 1.58: 5219 1.58 - 1.71: 2 1.71 - 1.84: 96 Bond restraints: 9817 Sorted by residual: bond pdb=" CA ILE S 100 " pdb=" C ILE S 100 " ideal model delta sigma weight residual 1.522 1.458 0.063 1.22e-02 6.72e+03 2.70e+01 bond pdb=" CA GLN S 82 " pdb=" C GLN S 82 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.20e-02 6.94e+03 2.44e+01 bond pdb=" CA LYS L 66 " pdb=" C LYS L 66 " ideal model delta sigma weight residual 1.524 1.464 0.060 1.32e-02 5.74e+03 2.08e+01 bond pdb=" CA LEU R 192 " pdb=" C LEU R 192 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.27e-02 6.20e+03 2.07e+01 bond pdb=" CA THR B 47 " pdb=" C THR B 47 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.33e-02 5.65e+03 1.51e+01 ... (remaining 9812 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 12817 2.27 - 4.54: 390 4.54 - 6.81: 59 6.81 - 9.09: 20 9.09 - 11.36: 4 Bond angle restraints: 13290 Sorted by residual: angle pdb=" N ASP B 205 " pdb=" CA ASP B 205 " pdb=" C ASP B 205 " ideal model delta sigma weight residual 112.88 103.30 9.58 1.29e+00 6.01e-01 5.52e+01 angle pdb=" N GLY L 68 " pdb=" CA GLY L 68 " pdb=" C GLY L 68 " ideal model delta sigma weight residual 115.21 124.60 -9.39 1.30e+00 5.92e-01 5.22e+01 angle pdb=" N LEU R 197 " pdb=" CA LEU R 197 " pdb=" C LEU R 197 " ideal model delta sigma weight residual 111.07 103.83 7.24 1.07e+00 8.73e-01 4.57e+01 angle pdb=" N LYS L 66 " pdb=" CA LYS L 66 " pdb=" C LYS L 66 " ideal model delta sigma weight residual 111.69 103.45 8.24 1.23e+00 6.61e-01 4.48e+01 angle pdb=" N ASP B 163 " pdb=" CA ASP B 163 " pdb=" C ASP B 163 " ideal model delta sigma weight residual 112.59 104.44 8.15 1.22e+00 6.72e-01 4.46e+01 ... (remaining 13285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5347 17.96 - 35.91: 398 35.91 - 53.87: 59 53.87 - 71.82: 18 71.82 - 89.78: 7 Dihedral angle restraints: 5829 sinusoidal: 2303 harmonic: 3526 Sorted by residual: dihedral pdb=" CB CYS S 159 " pdb=" SG CYS S 159 " pdb=" SG CYS S 229 " pdb=" CB CYS S 229 " ideal model delta sinusoidal sigma weight residual 93.00 3.86 89.14 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS R 106 " pdb=" SG CYS R 106 " pdb=" SG CYS R 183 " pdb=" CB CYS R 183 " ideal model delta sinusoidal sigma weight residual -86.00 -168.72 82.72 1 1.00e+01 1.00e-02 8.38e+01 dihedral pdb=" CB CYS L 32 " pdb=" SG CYS L 32 " pdb=" SG CYS L 56 " pdb=" CB CYS L 56 " ideal model delta sinusoidal sigma weight residual 93.00 147.84 -54.84 1 1.00e+01 1.00e-02 4.07e+01 ... (remaining 5826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1316 0.089 - 0.178: 159 0.178 - 0.267: 15 0.267 - 0.356: 5 0.356 - 0.445: 6 Chirality restraints: 1501 Sorted by residual: chirality pdb=" CA SER B 334 " pdb=" N SER B 334 " pdb=" C SER B 334 " pdb=" CB SER B 334 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" CA ASN S 77 " pdb=" N ASN S 77 " pdb=" C ASN S 77 " pdb=" CB ASN S 77 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CA THR B 164 " pdb=" N THR B 164 " pdb=" C THR B 164 " pdb=" CB THR B 164 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 1498 not shown) Planarity restraints: 1667 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR S 190 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.62e+00 pdb=" C TYR S 190 " 0.045 2.00e-02 2.50e+03 pdb=" O TYR S 190 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG S 191 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 63 " -0.015 2.00e-02 2.50e+03 1.38e-02 4.78e+00 pdb=" CG TRP B 63 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP B 63 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 63 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 63 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 63 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 63 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 63 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 63 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 63 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER S 106 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO S 107 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO S 107 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO S 107 " 0.030 5.00e-02 4.00e+02 ... (remaining 1664 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 495 2.72 - 3.27: 9495 3.27 - 3.81: 15710 3.81 - 4.36: 19997 4.36 - 4.90: 34316 Nonbonded interactions: 80013 Sorted by model distance: nonbonded pdb=" O PHE R 178 " pdb=" OG1 THR R 179 " model vdw 2.176 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 175 " model vdw 2.213 3.040 nonbonded pdb=" O MET S 192 " pdb=" OG SER S 193 " model vdw 2.216 3.040 nonbonded pdb=" O GLY B 224 " pdb=" NH1 ARG B 251 " model vdw 2.222 3.120 nonbonded pdb=" OE2 GLU L 51 " pdb=" NE2 GLN R 175 " model vdw 2.251 3.120 ... (remaining 80008 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: 0.770 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.380 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 : 0.007 0.063 9824 Z= 0.402 Angle : 0.961 11.358 13304 Z= 0.575 Chirality : 0.064 0.445 1501 Planarity : 0.005 0.054 1667 Dihedral : 12.958 89.775 3534 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.10 % Allowed : 1.43 % Favored : 98.48 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 2.78 % 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: 0.32 (0.24), residues: 1196 helix: 1.01 (0.25), residues: 414 sheet: 0.80 (0.30), residues: 279 loop : -0.76 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG B 68 TYR 0.034 0.003 TYR S 175 PHE 0.030 0.003 PHE S 212 TRP 0.036 0.003 TRP B 63 HIS 0.008 0.002 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00671 / 0.40 ( 9817) covalent geometry : angle 0.95545 / 0.57 (13290) SS BOND : bond 0.00496 / 0.28 ( 7) SS BOND : angle 3.40066 / 2.18 ( 14) hydrogen bonds : bond 0.14637 / 9.54 ( 491) hydrogen bonds : angle 6.18019 / 4.46 ( 1383) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.8022 (tptp) cc_final: 0.7581 (OUTLIER) REVERT: B 129 ARG cc_start: 0.7324 (ttt180) cc_final: 0.7023 (tpt90) REVERT: B 245 SER cc_start: 0.8329 (p) cc_final: 0.8105 (p) REVERT: S 80 PHE cc_start: 0.8260 (m-80) cc_final: 0.8013 (m-80) REVERT: S 83 MET cc_start: 0.8889 (mtm) cc_final: 0.8687 (mtp) outliers start: 1 outliers final: 1 residues processed: 176 average time/residue: 0.6186 time to fit residues: 116.1359 Evaluate side-chains 133 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN R 61 GLN R 75 ASN ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.197617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.142437 restraints weight = 9855.773| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.54 r_work: 0.3353 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 9824 Z= 0.162 Angle : 0.621 7.988 13304 Z= 0.334 Chirality : 0.044 0.167 1501 Planarity : 0.005 0.049 1667 Dihedral : 5.449 57.641 1321 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.29 % Allowed : 8.19 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.76 (0.24), residues: 1196 helix: 1.64 (0.25), residues: 423 sheet: 0.71 (0.30), residues: 282 loop : -0.59 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 307 TYR 0.021 0.002 TYR S 175 PHE 0.022 0.002 PHE R 32 TRP 0.021 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 9817) covalent geometry : angle 0.61716 / 0.33 (13290) SS BOND : bond 0.00397 / 0.23 ( 7) SS BOND : angle 2.18161 / 1.37 ( 14) hydrogen bonds : bond 0.04706 / 3.18 ( 491) hydrogen bonds : angle 4.89270 / 3.52 ( 1383) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8305 (m-40) cc_final: 0.7980 (m110) REVERT: B 23 LYS cc_start: 0.7729 (tptp) cc_final: 0.7077 (mmpt) REVERT: B 129 ARG cc_start: 0.7857 (ttt180) cc_final: 0.7442 (tpt90) REVERT: B 155 ASN cc_start: 0.8605 (t0) cc_final: 0.8309 (t0) REVERT: B 219 ARG cc_start: 0.8088 (mpt90) cc_final: 0.7777 (mmm160) REVERT: L 46 MET cc_start: 0.6661 (OUTLIER) cc_final: 0.5950 (ptt) REVERT: S 76 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7484 (mppt) outliers start: 24 outliers final: 11 residues processed: 148 average time/residue: 0.6203 time to fit residues: 97.9370 Evaluate side-chains 135 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 87 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 108 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 ASN B 175 GLN B 268 ASN S 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.197575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.141882 restraints weight = 9853.736| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.56 r_work: 0.3347 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9824 Z= 0.142 Angle : 0.559 7.398 13304 Z= 0.303 Chirality : 0.043 0.165 1501 Planarity : 0.005 0.054 1667 Dihedral : 5.218 56.703 1321 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.38 % Allowed : 10.38 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.00 (0.24), residues: 1196 helix: 2.03 (0.25), residues: 426 sheet: 0.69 (0.30), residues: 276 loop : -0.55 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 307 TYR 0.020 0.001 TYR S 190 PHE 0.021 0.002 PHE R 32 TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 9817) covalent geometry : angle 0.55783 / 0.30 (13290) SS BOND : bond 0.00354 / 0.19 ( 7) SS BOND : angle 1.40376 / 0.86 ( 14) hydrogen bonds : bond 0.04198 / 2.84 ( 491) hydrogen bonds : angle 4.59103 / 3.31 ( 1383) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8334 (m-40) cc_final: 0.8056 (m-40) REVERT: B 23 LYS cc_start: 0.7983 (tptp) cc_final: 0.7782 (tptp) REVERT: B 155 ASN cc_start: 0.8609 (t0) cc_final: 0.8321 (t0) REVERT: S 76 LYS cc_start: 0.7944 (mtpp) cc_final: 0.7420 (mtpt) REVERT: S 90 ASP cc_start: 0.8655 (m-30) cc_final: 0.8432 (m-30) outliers start: 25 outliers final: 13 residues processed: 145 average time/residue: 0.6178 time to fit residues: 95.6197 Evaluate side-chains 135 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 20 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 15 optimal weight: 0.0020 chunk 63 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 8 optimal weight: 0.0970 chunk 85 optimal weight: 0.8980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.199579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.144822 restraints weight = 10018.426| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.56 r_work: 0.3398 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9824 Z= 0.108 Angle : 0.500 6.452 13304 Z= 0.272 Chirality : 0.041 0.164 1501 Planarity : 0.004 0.060 1667 Dihedral : 4.965 57.131 1321 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.00 % Allowed : 12.10 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.24), residues: 1196 helix: 2.22 (0.25), residues: 427 sheet: 0.73 (0.30), residues: 270 loop : -0.53 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 307 TYR 0.018 0.001 TYR S 190 PHE 0.017 0.001 PHE R 45 TRP 0.018 0.001 TRP B 82 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 9817) covalent geometry : angle 0.49857 / 0.27 (13290) SS BOND : bond 0.00286 / 0.14 ( 7) SS BOND : angle 1.14461 / 0.69 ( 14) hydrogen bonds : bond 0.03610 / 2.44 ( 491) hydrogen bonds : angle 4.35130 / 3.12 ( 1383) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8220 (m-40) cc_final: 0.7988 (m-40) REVERT: A 32 ARG cc_start: 0.7815 (mtt-85) cc_final: 0.7489 (mmt90) REVERT: B 101 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8377 (mpp) REVERT: B 155 ASN cc_start: 0.8633 (t0) cc_final: 0.7969 (t0) REVERT: B 217 MET cc_start: 0.8439 (pmm) cc_final: 0.8096 (pp-130) REVERT: B 258 ASP cc_start: 0.8339 (t0) cc_final: 0.8134 (t70) REVERT: G 58 GLU cc_start: 0.7593 (pt0) cc_final: 0.7370 (pt0) REVERT: G 62 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.6644 (ptp-170) REVERT: L 46 MET cc_start: 0.6580 (OUTLIER) cc_final: 0.5713 (ptt) REVERT: R 166 MET cc_start: 0.6569 (mmt) cc_final: 0.6223 (mmp) REVERT: S 76 LYS cc_start: 0.7927 (mtpp) cc_final: 0.7410 (mtpt) REVERT: S 90 ASP cc_start: 0.8589 (m-30) cc_final: 0.8357 (m-30) outliers start: 21 outliers final: 7 residues processed: 138 average time/residue: 0.6043 time to fit residues: 88.9687 Evaluate side-chains 133 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 100 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 60 optimal weight: 30.0000 chunk 74 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 268 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.195252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.143339 restraints weight = 10126.362| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.65 r_work: 0.3335 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 9824 Z= 0.174 Angle : 0.574 8.826 13304 Z= 0.310 Chirality : 0.043 0.177 1501 Planarity : 0.004 0.060 1667 Dihedral : 5.130 54.384 1321 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.57 % Allowed : 12.48 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.24), residues: 1196 helix: 2.20 (0.25), residues: 428 sheet: 0.62 (0.30), residues: 275 loop : -0.49 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 307 TYR 0.024 0.002 TYR S 190 PHE 0.018 0.002 PHE R 45 TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 9817) covalent geometry : angle 0.57265 / 0.31 (13290) SS BOND : bond 0.00416 / 0.23 ( 7) SS BOND : angle 1.37113 / 0.85 ( 14) hydrogen bonds : bond 0.04266 / 2.91 ( 491) hydrogen bonds : angle 4.49520 / 3.24 ( 1383) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8401 (m-40) cc_final: 0.8075 (m-40) REVERT: A 32 ARG cc_start: 0.7977 (mtt-85) cc_final: 0.7678 (mmt90) REVERT: A 275 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8487 (tp30) REVERT: B 101 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8384 (mtm) REVERT: G 58 GLU cc_start: 0.7650 (pt0) cc_final: 0.7398 (pt0) REVERT: L 46 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.5767 (ptt) REVERT: S 76 LYS cc_start: 0.8119 (mtpp) cc_final: 0.7656 (mtpt) outliers start: 27 outliers final: 11 residues processed: 132 average time/residue: 0.5799 time to fit residues: 81.6109 Evaluate side-chains 129 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 54 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 ASN B 155 ASN ** R 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.190557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.138640 restraints weight = 10120.120| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.71 r_work: 0.3258 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.150 9824 Z= 0.374 Angle : 0.773 13.934 13304 Z= 0.412 Chirality : 0.052 0.241 1501 Planarity : 0.006 0.060 1667 Dihedral : 5.587 48.329 1321 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.52 % Allowed : 12.38 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.65 (0.24), residues: 1196 helix: 1.85 (0.24), residues: 419 sheet: 0.36 (0.29), residues: 291 loop : -0.77 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 307 TYR 0.026 0.003 TYR S 190 PHE 0.027 0.003 PHE S 110 TRP 0.019 0.003 TRP B 211 HIS 0.007 0.002 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00892 / 0.37 ( 9817) covalent geometry : angle 0.77078 / 0.41 (13290) SS BOND : bond 0.00652 / 0.34 ( 7) SS BOND : angle 1.82496 / 1.14 ( 14) hydrogen bonds : bond 0.05773 / 3.92 ( 491) hydrogen bonds : angle 4.87663 / 3.52 ( 1383) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8475 (m-40) cc_final: 0.8015 (m110) REVERT: A 32 ARG cc_start: 0.8220 (mtt-85) cc_final: 0.7823 (mmt90) REVERT: A 275 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8362 (tp30) REVERT: B 101 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8647 (mpp) REVERT: B 127 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8472 (mmtt) REVERT: B 217 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.8106 (pmt) REVERT: L 46 MET cc_start: 0.6774 (OUTLIER) cc_final: 0.5799 (ptt) REVERT: S 76 LYS cc_start: 0.8058 (mtpp) cc_final: 0.7522 (mtpt) outliers start: 37 outliers final: 15 residues processed: 136 average time/residue: 0.6048 time to fit residues: 87.6271 Evaluate side-chains 131 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 70 GLN R 25 GLN S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.195050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.143046 restraints weight = 9991.941| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.62 r_work: 0.3332 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 9824 Z= 0.155 Angle : 0.568 9.084 13304 Z= 0.304 Chirality : 0.043 0.170 1501 Planarity : 0.004 0.056 1667 Dihedral : 5.108 56.938 1321 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.76 % Allowed : 14.29 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.24), residues: 1196 helix: 2.21 (0.24), residues: 419 sheet: 0.51 (0.30), residues: 275 loop : -0.68 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 307 TYR 0.019 0.002 TYR S 190 PHE 0.019 0.002 PHE R 45 TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 9817) covalent geometry : angle 0.56716 / 0.30 (13290) SS BOND : bond 0.00377 / 0.21 ( 7) SS BOND : angle 1.27621 / 0.79 ( 14) hydrogen bonds : bond 0.04152 / 2.83 ( 491) hydrogen bonds : angle 4.51036 / 3.24 ( 1383) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8371 (m-40) cc_final: 0.8039 (m-40) REVERT: A 32 ARG cc_start: 0.8148 (mtt-85) cc_final: 0.7825 (mmt90) REVERT: A 275 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8396 (tp30) REVERT: B 101 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8372 (mtm) REVERT: B 217 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8149 (pmt) REVERT: G 58 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6993 (tt0) REVERT: L 46 MET cc_start: 0.6657 (OUTLIER) cc_final: 0.5728 (ptt) REVERT: R 311 TYR cc_start: 0.5911 (t80) cc_final: 0.5605 (t80) REVERT: S 76 LYS cc_start: 0.8032 (mtpp) cc_final: 0.7481 (mtpt) outliers start: 29 outliers final: 11 residues processed: 133 average time/residue: 0.6305 time to fit residues: 89.2131 Evaluate side-chains 129 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 101 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 62 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.196234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.144638 restraints weight = 10088.548| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.74 r_work: 0.3356 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9824 Z= 0.123 Angle : 0.526 7.523 13304 Z= 0.282 Chirality : 0.042 0.160 1501 Planarity : 0.004 0.061 1667 Dihedral : 4.865 54.341 1321 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.81 % Allowed : 15.52 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.08 (0.24), residues: 1196 helix: 2.31 (0.25), residues: 425 sheet: 0.51 (0.29), residues: 282 loop : -0.58 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 307 TYR 0.019 0.001 TYR S 190 PHE 0.020 0.001 PHE R 45 TRP 0.018 0.002 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 9817) covalent geometry : angle 0.52481 / 0.28 (13290) SS BOND : bond 0.00310 / 0.17 ( 7) SS BOND : angle 1.08553 / 0.67 ( 14) hydrogen bonds : bond 0.03758 / 2.56 ( 491) hydrogen bonds : angle 4.36759 / 3.14 ( 1383) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8314 (m-40) cc_final: 0.8016 (m-40) REVERT: A 32 ARG cc_start: 0.8147 (mtt-85) cc_final: 0.7833 (mmt90) REVERT: A 275 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8404 (tp30) REVERT: B 45 MET cc_start: 0.8616 (mtt) cc_final: 0.8391 (mmm) REVERT: B 101 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8367 (mtm) REVERT: B 217 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8169 (pmt) REVERT: G 58 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7033 (tt0) REVERT: L 46 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.5843 (ptt) REVERT: R 311 TYR cc_start: 0.5925 (t80) cc_final: 0.5609 (t80) REVERT: S 76 LYS cc_start: 0.8016 (mtpp) cc_final: 0.7474 (mtpt) outliers start: 19 outliers final: 9 residues processed: 124 average time/residue: 0.6035 time to fit residues: 79.6797 Evaluate side-chains 125 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 175 GLN B 259 GLN S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.194225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.142008 restraints weight = 10071.152| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.67 r_work: 0.3327 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 9824 Z= 0.173 Angle : 0.579 9.042 13304 Z= 0.309 Chirality : 0.043 0.178 1501 Planarity : 0.005 0.061 1667 Dihedral : 5.018 53.947 1321 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.38 % Allowed : 15.33 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.05 (0.24), residues: 1196 helix: 2.29 (0.25), residues: 424 sheet: 0.52 (0.29), residues: 283 loop : -0.60 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 307 TYR 0.024 0.002 TYR S 190 PHE 0.019 0.002 PHE R 45 TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 9817) covalent geometry : angle 0.57776 / 0.31 (13290) SS BOND : bond 0.00406 / 0.23 ( 7) SS BOND : angle 1.24636 / 0.77 ( 14) hydrogen bonds : bond 0.04212 / 2.87 ( 491) hydrogen bonds : angle 4.44581 / 3.20 ( 1383) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8363 (m-40) cc_final: 0.8039 (m-40) REVERT: A 32 ARG cc_start: 0.8156 (mtt-85) cc_final: 0.7826 (mmt90) REVERT: A 275 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8375 (tp30) REVERT: B 101 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8378 (mtm) REVERT: B 217 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8166 (pmt) REVERT: B 234 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.7726 (m-80) REVERT: G 58 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7098 (tt0) REVERT: L 46 MET cc_start: 0.6658 (OUTLIER) cc_final: 0.5681 (ptt) REVERT: R 311 TYR cc_start: 0.5877 (t80) cc_final: 0.5568 (t80) REVERT: S 76 LYS cc_start: 0.8038 (mtpp) cc_final: 0.7487 (mtpt) outliers start: 25 outliers final: 13 residues processed: 124 average time/residue: 0.5961 time to fit residues: 78.8879 Evaluate side-chains 130 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 100 optimal weight: 0.0370 chunk 86 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 0.0370 chunk 0 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 175 GLN B 259 GLN S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.197255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146394 restraints weight = 10089.770| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.66 r_work: 0.3377 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9824 Z= 0.111 Angle : 0.511 7.298 13304 Z= 0.273 Chirality : 0.041 0.151 1501 Planarity : 0.004 0.062 1667 Dihedral : 4.683 46.106 1321 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.71 % Allowed : 16.00 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.22 (0.25), residues: 1196 helix: 2.46 (0.25), residues: 424 sheet: 0.56 (0.29), residues: 282 loop : -0.50 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 307 TYR 0.016 0.001 TYR S 190 PHE 0.019 0.001 PHE R 45 TRP 0.019 0.001 TRP B 63 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 9817) covalent geometry : angle 0.50984 / 0.27 (13290) SS BOND : bond 0.00277 / 0.17 ( 7) SS BOND : angle 0.98315 / 0.59 ( 14) hydrogen bonds : bond 0.03535 / 2.40 ( 491) hydrogen bonds : angle 4.28017 / 3.07 ( 1383) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8277 (m-40) cc_final: 0.8009 (m-40) REVERT: A 32 ARG cc_start: 0.8138 (mtt-85) cc_final: 0.7813 (mmt90) REVERT: A 275 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8408 (tp30) REVERT: B 101 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8366 (mtm) REVERT: B 217 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8156 (pmt) REVERT: B 234 PHE cc_start: 0.9221 (OUTLIER) cc_final: 0.7664 (m-80) REVERT: G 58 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7132 (tt0) REVERT: L 46 MET cc_start: 0.6719 (OUTLIER) cc_final: 0.5873 (ptt) REVERT: R 311 TYR cc_start: 0.5929 (t80) cc_final: 0.5622 (t80) REVERT: S 76 LYS cc_start: 0.8031 (mtpp) cc_final: 0.7484 (mtpt) outliers start: 18 outliers final: 10 residues processed: 124 average time/residue: 0.6337 time to fit residues: 83.5989 Evaluate side-chains 126 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 13 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 91 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 175 GLN B 259 GLN S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.196619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.145082 restraints weight = 10081.579| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.62 r_work: 0.3369 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9824 Z= 0.122 Angle : 0.522 7.146 13304 Z= 0.279 Chirality : 0.041 0.163 1501 Planarity : 0.004 0.062 1667 Dihedral : 4.654 40.954 1321 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.81 % Allowed : 16.48 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.25 (0.25), residues: 1196 helix: 2.49 (0.25), residues: 425 sheet: 0.43 (0.29), residues: 289 loop : -0.42 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 307 TYR 0.021 0.001 TYR S 190 PHE 0.019 0.001 PHE R 45 TRP 0.018 0.002 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 9817) covalent geometry : angle 0.52107 / 0.28 (13290) SS BOND : bond 0.00296 / 0.18 ( 7) SS BOND : angle 0.98969 / 0.61 ( 14) hydrogen bonds : bond 0.03650 / 2.49 ( 491) hydrogen bonds : angle 4.26093 / 3.06 ( 1383) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4527.19 seconds wall clock time: 77 minutes 47.87 seconds (4667.87 seconds total)