Starting phenix.real_space_refine on Wed Mar 4 00:49:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vl9_32021/03_2026/7vl9_32021.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vl9_32021/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7vl9_32021/03_2026/7vl9_32021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vl9_32021/03_2026/7vl9_32021.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vl9_32021/03_2026/7vl9_32021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vl9_32021/03_2026/7vl9_32021.map" } 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-5986/lib/python3.9/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: 2.18, per 1000 atoms: 0.23 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: 0.71 Conformation dependent library (CDL) restraints added in 297.4 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: 0.33 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: 1.47 Time building geometry restraints manager: 0.97 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: 5389 17.96 - 35.91: 403 35.91 - 53.87: 67 53.87 - 71.82: 19 71.82 - 89.78: 7 Dihedral angle restraints: 5885 sinusoidal: 2359 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 5882 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.750 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 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 : 13.152 89.775 3590 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 covalent geometry : bond 0.00671 ( 9817) covalent geometry : angle 0.95545 (13290) SS BOND : bond 0.00496 ( 7) SS BOND : angle 3.40066 ( 14) hydrogen bonds : bond 0.14637 ( 491) hydrogen bonds : angle 6.18019 ( 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 : 0.386 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: 0.6240 time to fit residues: 116.8109 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 : 0.369 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.197631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.142089 restraints weight = 9859.480| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.54 r_work: 0.3354 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1456 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 : 0.620 8.019 13304 Z= 0.334 Chirality : 0.044 0.167 1501 Planarity : 0.005 0.049 1667 Dihedral : 6.589 59.393 1377 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.29 % Allowed : 8.10 % Favored : 89.62 % 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 0.020 0.002 TYR S 175 PHE 0.021 0.002 PHE R 32 TRP 0.021 0.002 TRP B 82 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9817) covalent geometry : angle 0.61617 (13290) SS BOND : bond 0.00408 ( 7) SS BOND : angle 2.16594 ( 14) hydrogen bonds : bond 0.04696 ( 491) hydrogen bonds : angle 4.89216 ( 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 : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8315 (m-40) cc_final: 0.7991 (m110) REVERT: B 23 LYS cc_start: 0.7730 (tptp) cc_final: 0.7079 (mmpt) REVERT: B 129 ARG cc_start: 0.7879 (ttt180) cc_final: 0.7441 (tpt90) REVERT: B 155 ASN cc_start: 0.8607 (t0) cc_final: 0.8309 (t0) REVERT: B 219 ARG cc_start: 0.8087 (mpt90) cc_final: 0.7771 (mmm160) REVERT: S 76 LYS cc_start: 0.8038 (mtpp) cc_final: 0.7474 (mppt) outliers start: 24 outliers final: 12 residues processed: 148 average time/residue: 0.6280 time to fit residues: 98.8766 Evaluate side-chains 136 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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: 0.9980 chunk 43 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 108 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 268 ASN S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.197888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.142372 restraints weight = 9853.708| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.56 r_work: 0.3351 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9824 Z= 0.138 Angle : 0.553 7.289 13304 Z= 0.300 Chirality : 0.042 0.165 1501 Planarity : 0.004 0.054 1667 Dihedral : 6.002 56.490 1377 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.38 % Allowed : 10.29 % Favored : 87.33 % 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: 2.04 (0.25), residues: 426 sheet: 0.66 (0.29), residues: 278 loop : -0.54 (0.27), residues: 492 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 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9817) covalent geometry : angle 0.55114 (13290) SS BOND : bond 0.00341 ( 7) SS BOND : angle 1.36758 ( 14) hydrogen bonds : bond 0.04166 ( 491) hydrogen bonds : angle 4.58169 ( 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 161 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8317 (m-40) cc_final: 0.8044 (m-40) REVERT: B 155 ASN cc_start: 0.8604 (t0) cc_final: 0.8319 (t0) REVERT: L 46 MET cc_start: 0.6709 (OUTLIER) cc_final: 0.5778 (ptt) REVERT: S 76 LYS cc_start: 0.7969 (mtpp) cc_final: 0.7414 (mtpt) REVERT: S 90 ASP cc_start: 0.8653 (m-30) cc_final: 0.8430 (m-30) outliers start: 25 outliers final: 11 residues processed: 147 average time/residue: 0.6308 time to fit residues: 98.7497 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 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: 8.9990 chunk 63 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 64 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.194283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.142168 restraints weight = 10157.339| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.64 r_work: 0.3332 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1982 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= 0.180 Angle : 0.585 9.055 13304 Z= 0.317 Chirality : 0.044 0.177 1501 Planarity : 0.005 0.058 1667 Dihedral : 5.905 48.767 1377 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.57 % Allowed : 11.62 % Favored : 85.81 % 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: 1.04 (0.24), residues: 1196 helix: 2.16 (0.25), residues: 421 sheet: 0.61 (0.30), residues: 275 loop : -0.53 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 307 TYR 0.023 0.002 TYR S 190 PHE 0.017 0.002 PHE A 196 TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 9817) covalent geometry : angle 0.58324 (13290) SS BOND : bond 0.00381 ( 7) SS BOND : angle 1.39519 ( 14) hydrogen bonds : bond 0.04411 ( 491) hydrogen bonds : angle 4.58460 ( 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 150 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8378 (m-40) cc_final: 0.8071 (m-40) REVERT: B 44 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7817 (mp10) REVERT: B 101 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8377 (mtm) REVERT: B 217 MET cc_start: 0.8516 (pmm) cc_final: 0.8190 (pp-130) REVERT: G 58 GLU cc_start: 0.7735 (pt0) cc_final: 0.7466 (pt0) REVERT: L 46 MET cc_start: 0.6720 (OUTLIER) cc_final: 0.5837 (ptt) REVERT: S 76 LYS cc_start: 0.8014 (mtpp) cc_final: 0.7511 (mtpt) outliers start: 27 outliers final: 13 residues processed: 138 average time/residue: 0.6209 time to fit residues: 91.1274 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 : 0.373 ------------------------------------------------------------------------------- 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 44 GLN Chi-restraints excluded: chain B residue 96 ARG 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 100 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 60 optimal weight: 50.0000 chunk 74 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 268 ASN S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.195035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.143714 restraints weight = 10174.180| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.62 r_work: 0.3347 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 9824 Z= 0.154 Angle : 0.548 8.074 13304 Z= 0.298 Chirality : 0.042 0.169 1501 Planarity : 0.004 0.060 1667 Dihedral : 5.619 49.268 1377 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.86 % Allowed : 12.00 % Favored : 85.14 % 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: 1.06 (0.24), residues: 1196 helix: 2.21 (0.25), residues: 426 sheet: 0.54 (0.30), residues: 275 loop : -0.52 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 307 TYR 0.021 0.002 TYR S 190 PHE 0.017 0.002 PHE R 45 TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9817) covalent geometry : angle 0.54701 (13290) SS BOND : bond 0.00387 ( 7) SS BOND : angle 1.31018 ( 14) hydrogen bonds : bond 0.04097 ( 491) hydrogen bonds : angle 4.46369 ( 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 151 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8391 (m-40) cc_final: 0.8073 (m-40) REVERT: A 275 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8495 (tp30) REVERT: B 101 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8384 (mtm) REVERT: G 58 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7027 (tt0) REVERT: L 46 MET cc_start: 0.6712 (OUTLIER) cc_final: 0.5846 (ptt) REVERT: R 311 TYR cc_start: 0.5827 (t80) cc_final: 0.5614 (t80) REVERT: S 76 LYS cc_start: 0.8016 (mtpp) cc_final: 0.7515 (mtpt) REVERT: S 90 ASP cc_start: 0.8628 (m-30) cc_final: 0.8401 (m-30) outliers start: 30 outliers final: 11 residues processed: 136 average time/residue: 0.6592 time to fit residues: 95.1130 Evaluate side-chains 132 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 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 96 ARG 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 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 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: 5.9990 chunk 93 optimal weight: 7.9990 chunk 95 optimal weight: 0.0970 chunk 5 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 0.0870 chunk 14 optimal weight: 4.9990 chunk 88 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.9358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 70 GLN R 25 GLN R 181 HIS S 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.195782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.144342 restraints weight = 10160.373| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.62 r_work: 0.3356 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9824 Z= 0.135 Angle : 0.530 7.756 13304 Z= 0.287 Chirality : 0.042 0.164 1501 Planarity : 0.004 0.060 1667 Dihedral : 5.549 52.065 1377 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.48 % Allowed : 12.57 % 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: 1.16 (0.24), residues: 1196 helix: 2.36 (0.25), residues: 424 sheet: 0.55 (0.30), residues: 277 loop : -0.49 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 307 TYR 0.021 0.001 TYR S 190 PHE 0.018 0.001 PHE R 45 TRP 0.017 0.002 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9817) covalent geometry : angle 0.52865 (13290) SS BOND : bond 0.00356 ( 7) SS BOND : angle 1.22685 ( 14) hydrogen bonds : bond 0.03870 ( 491) hydrogen bonds : angle 4.38179 ( 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 146 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8356 (m-40) cc_final: 0.8051 (m-40) REVERT: A 275 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8437 (tp30) REVERT: B 101 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8380 (mtm) REVERT: B 217 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8172 (pmt) REVERT: G 58 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7046 (tt0) REVERT: G 62 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6779 (ptp-170) REVERT: L 46 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.5780 (ptt) REVERT: R 311 TYR cc_start: 0.5836 (t80) cc_final: 0.5615 (t80) REVERT: S 76 LYS cc_start: 0.8002 (mtpp) cc_final: 0.7489 (mtpt) outliers start: 26 outliers final: 10 residues processed: 134 average time/residue: 0.6524 time to fit residues: 92.9257 Evaluate side-chains 134 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 197 ARG 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 G residue 62 ARG 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 204 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN L 70 GLN R 25 GLN S 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.193559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.141226 restraints weight = 10030.950| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.62 r_work: 0.3321 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 9824 Z= 0.201 Angle : 0.599 10.211 13304 Z= 0.322 Chirality : 0.044 0.183 1501 Planarity : 0.005 0.057 1667 Dihedral : 6.024 59.565 1377 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.57 % Allowed : 13.14 % Favored : 84.29 % 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: 1.12 (0.24), residues: 1196 helix: 2.35 (0.25), residues: 419 sheet: 0.58 (0.30), residues: 279 loop : -0.55 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 307 TYR 0.026 0.002 TYR S 190 PHE 0.020 0.002 PHE R 45 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 9817) covalent geometry : angle 0.59719 (13290) SS BOND : bond 0.00477 ( 7) SS BOND : angle 1.38001 ( 14) hydrogen bonds : bond 0.04507 ( 491) hydrogen bonds : angle 4.52979 ( 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 143 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8429 (m-40) cc_final: 0.8053 (m-40) REVERT: A 275 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8415 (tp30) REVERT: B 101 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8554 (mpp) REVERT: B 217 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8151 (pmt) REVERT: G 58 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6961 (tt0) REVERT: L 46 MET cc_start: 0.6706 (OUTLIER) cc_final: 0.5763 (ptt) REVERT: R 250 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7792 (mp) REVERT: R 311 TYR cc_start: 0.5745 (t80) cc_final: 0.5442 (t80) REVERT: S 76 LYS cc_start: 0.8021 (mtpp) cc_final: 0.7493 (mtpt) outliers start: 27 outliers final: 12 residues processed: 129 average time/residue: 0.7321 time to fit residues: 99.9455 Evaluate side-chains 131 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 197 ARG 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 250 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 101 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 15 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN L 70 GLN R 25 GLN S 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.196311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.144480 restraints weight = 10088.772| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.68 r_work: 0.3364 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9824 Z= 0.127 Angle : 0.519 7.495 13304 Z= 0.280 Chirality : 0.041 0.159 1501 Planarity : 0.004 0.059 1667 Dihedral : 5.547 56.385 1377 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.10 % Allowed : 14.00 % Favored : 83.90 % 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: 1.21 (0.24), residues: 1196 helix: 2.42 (0.25), residues: 425 sheet: 0.60 (0.29), residues: 283 loop : -0.52 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 307 TYR 0.018 0.001 TYR S 190 PHE 0.019 0.001 PHE R 45 TRP 0.017 0.002 TRP B 82 HIS 0.003 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9817) covalent geometry : angle 0.51825 (13290) SS BOND : bond 0.00331 ( 7) SS BOND : angle 1.09154 ( 14) hydrogen bonds : bond 0.03749 ( 491) hydrogen bonds : angle 4.33671 ( 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 146 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8327 (m-40) cc_final: 0.8036 (m-40) REVERT: A 275 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8417 (tp30) REVERT: B 101 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8355 (mtm) REVERT: B 217 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8145 (pmt) REVERT: B 234 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.7646 (m-80) REVERT: B 258 ASP cc_start: 0.8608 (t0) cc_final: 0.8383 (t0) REVERT: G 58 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7020 (tt0) REVERT: L 46 MET cc_start: 0.6646 (OUTLIER) cc_final: 0.5790 (ptt) REVERT: R 311 TYR cc_start: 0.5939 (t80) cc_final: 0.5650 (t80) REVERT: S 76 LYS cc_start: 0.7987 (mtpp) cc_final: 0.7469 (mtpt) outliers start: 22 outliers final: 10 residues processed: 135 average time/residue: 0.6927 time to fit residues: 99.1523 Evaluate side-chains 134 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.194907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142586 restraints weight = 10116.317| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.64 r_work: 0.3346 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9824 Z= 0.156 Angle : 0.552 9.161 13304 Z= 0.297 Chirality : 0.042 0.171 1501 Planarity : 0.004 0.059 1667 Dihedral : 5.508 53.206 1377 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.48 % Allowed : 14.48 % Favored : 83.05 % 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: 1.23 (0.24), residues: 1196 helix: 2.42 (0.25), residues: 425 sheet: 0.62 (0.29), residues: 284 loop : -0.51 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 307 TYR 0.023 0.001 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 B 183 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 9817) covalent geometry : angle 0.55105 (13290) SS BOND : bond 0.00371 ( 7) SS BOND : angle 1.18652 ( 14) hydrogen bonds : bond 0.04022 ( 491) hydrogen bonds : angle 4.40000 ( 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 140 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8336 (m-40) cc_final: 0.8010 (m-40) REVERT: A 32 ARG cc_start: 0.8035 (mtt-85) cc_final: 0.7779 (mmt90) REVERT: A 275 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8396 (tp30) REVERT: B 101 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8365 (mtm) REVERT: B 217 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8123 (pmt) REVERT: B 234 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.7711 (m-80) REVERT: B 258 ASP cc_start: 0.8604 (t0) cc_final: 0.8384 (t0) REVERT: G 58 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7106 (tt0) REVERT: L 46 MET cc_start: 0.6599 (OUTLIER) cc_final: 0.5696 (ptt) REVERT: R 311 TYR cc_start: 0.5931 (t80) cc_final: 0.5616 (t80) REVERT: S 76 LYS cc_start: 0.8110 (mtpp) cc_final: 0.7617 (mtpt) outliers start: 26 outliers final: 13 residues processed: 128 average time/residue: 0.7035 time to fit residues: 95.5303 Evaluate side-chains 133 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 96 ARG 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: 0.6980 chunk 86 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.196391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.144186 restraints weight = 10092.662| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.62 r_work: 0.3372 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9824 Z= 0.123 Angle : 0.515 7.877 13304 Z= 0.278 Chirality : 0.041 0.163 1501 Planarity : 0.004 0.060 1667 Dihedral : 5.265 49.826 1377 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.19 % Allowed : 14.67 % Favored : 83.14 % 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: 1.29 (0.25), residues: 1196 helix: 2.50 (0.25), residues: 425 sheet: 0.62 (0.30), residues: 283 loop : -0.48 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 307 TYR 0.018 0.001 TYR S 190 PHE 0.019 0.001 PHE R 45 TRP 0.017 0.002 TRP B 63 HIS 0.003 0.001 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9817) covalent geometry : angle 0.51424 (13290) SS BOND : bond 0.00312 ( 7) SS BOND : angle 1.05994 ( 14) hydrogen bonds : bond 0.03662 ( 491) hydrogen bonds : angle 4.30725 ( 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 141 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8288 (m-40) cc_final: 0.8006 (m-40) REVERT: A 32 ARG cc_start: 0.7915 (mtt-85) cc_final: 0.7651 (mmt90) REVERT: A 275 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8396 (tp30) REVERT: B 101 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8345 (mtm) REVERT: B 155 ASN cc_start: 0.8696 (t0) cc_final: 0.8265 (t0) REVERT: B 217 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8120 (pmt) REVERT: B 234 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.7710 (m-80) REVERT: B 258 ASP cc_start: 0.8594 (t0) cc_final: 0.8369 (t0) REVERT: G 58 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7120 (tt0) REVERT: L 46 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.5868 (ptt) REVERT: R 311 TYR cc_start: 0.5879 (t80) cc_final: 0.5592 (t80) REVERT: S 76 LYS cc_start: 0.8019 (mtpp) cc_final: 0.7480 (mtpt) outliers start: 23 outliers final: 15 residues processed: 129 average time/residue: 0.7073 time to fit residues: 96.8461 Evaluate side-chains 138 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 96 ARG 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 21 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.195748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.145085 restraints weight = 10093.804| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.77 r_work: 0.3341 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9824 Z= 0.136 Angle : 0.531 8.148 13304 Z= 0.286 Chirality : 0.042 0.168 1501 Planarity : 0.004 0.061 1667 Dihedral : 5.227 47.212 1377 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.19 % Allowed : 14.95 % Favored : 82.86 % 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: 1.29 (0.24), residues: 1196 helix: 2.50 (0.25), residues: 425 sheet: 0.65 (0.29), residues: 281 loop : -0.49 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 307 TYR 0.022 0.001 TYR S 190 PHE 0.020 0.001 PHE R 45 TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9817) covalent geometry : angle 0.53061 (13290) SS BOND : bond 0.00323 ( 7) SS BOND : angle 1.07680 ( 14) hydrogen bonds : bond 0.03809 ( 491) hydrogen bonds : angle 4.31463 ( 1383) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4849.79 seconds wall clock time: 83 minutes 5.13 seconds (4985.13 seconds total)