Starting phenix.real_space_refine on Tue Mar 3 22:20:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t6s_25726/03_2026/7t6s_25726.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6s_25726/03_2026/7t6s_25726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t6s_25726/03_2026/7t6s_25726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6s_25726/03_2026/7t6s_25726.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t6s_25726/03_2026/7t6s_25726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6s_25726/03_2026/7t6s_25726.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 63 5.16 5 Cl 1 4.86 5 C 5702 2.51 5 N 1504 2.21 5 O 1636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 8906 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1753 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "E" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1778 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2346 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'FUI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.99, per 1000 atoms: 0.22 Number of scatterers: 8906 At special positions: 0 Unit cell: (117.72, 115.56, 103.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 63 16.00 O 1636 8.00 N 1504 7.00 C 5702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 316.4 milliseconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 38.3% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 8 through 31 removed outlier: 3.544A pdb=" N ASP A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.506A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.637A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.633A 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 242 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.831A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.011A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 7 through 26 removed outlier: 3.532A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.944A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.730A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 23 through 26 Processing helix chain 'R' and resid 27 through 54 Processing helix chain 'R' and resid 58 through 77 removed outlier: 3.512A pdb=" N THR R 75 " --> pdb=" O ASP R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 87 removed outlier: 3.881A pdb=" N SER R 84 " --> pdb=" O PHE R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 129 removed outlier: 3.560A pdb=" N HIS R 102 " --> pdb=" O CYS R 98 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE R 103 " --> pdb=" O LYS R 99 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE R 114 " --> pdb=" O PHE R 110 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL R 127 " --> pdb=" O ARG R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 136 Processing helix chain 'R' and resid 138 through 147 removed outlier: 3.951A pdb=" N VAL R 147 " --> pdb=" O MET R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 156 Processing helix chain 'R' and resid 157 through 163 Processing helix chain 'R' and resid 180 through 185 Processing helix chain 'R' and resid 186 through 208 removed outlier: 3.637A pdb=" N ARG R 205 " --> pdb=" O ARG R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 231 removed outlier: 3.850A pdb=" N ILE R 228 " --> pdb=" O ILE R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 267 removed outlier: 3.935A pdb=" N PHE R 250 " --> pdb=" O VAL R 246 " (cutoff:3.500A) Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 267 through 273 Processing helix chain 'R' and resid 277 through 303 removed outlier: 4.242A pdb=" N ASP R 281 " --> pdb=" O TYR R 277 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASN R 285 " --> pdb=" O ASP R 281 " (cutoff:3.500A) Proline residue: R 286 - end of helix removed outlier: 3.583A pdb=" N ASN R 294 " --> pdb=" O LEU R 290 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER R 295 " --> pdb=" O ALA R 291 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS R 296 " --> pdb=" O PHE R 292 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 306 through 314 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.621A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.523A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.504A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.929A 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: 6.245A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.830A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.693A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.388A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.214A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.650A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.650A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.094A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN E 194 " --> pdb=" O TYR E 190 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 164 through 168 447 hydrogen bonds defined for protein. 1248 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: 1.43 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1430 1.30 - 1.43: 2465 1.43 - 1.56: 5111 1.56 - 1.68: 0 1.68 - 1.81: 93 Bond restraints: 9099 Sorted by residual: bond pdb=" C08 FUI R 401 " pdb=" N07 FUI R 401 " ideal model delta sigma weight residual 1.383 1.292 0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C PRO C 49 " pdb=" O PRO C 49 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.16e-02 7.43e+03 2.04e+01 bond pdb=" C PHE R 110 " pdb=" O PHE R 110 " ideal model delta sigma weight residual 1.236 1.177 0.058 1.31e-02 5.83e+03 1.98e+01 bond pdb=" C PRO B 94 " pdb=" O PRO B 94 " ideal model delta sigma weight residual 1.235 1.201 0.034 7.90e-03 1.60e+04 1.86e+01 bond pdb=" C18 FUI R 401 " pdb=" N19 FUI R 401 " ideal model delta sigma weight residual 1.371 1.453 -0.082 2.00e-02 2.50e+03 1.68e+01 ... (remaining 9094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 11459 2.24 - 4.49: 801 4.49 - 6.73: 53 6.73 - 8.97: 11 8.97 - 11.21: 5 Bond angle restraints: 12329 Sorted by residual: angle pdb=" N LEU R 81 " pdb=" CA LEU R 81 " pdb=" C LEU R 81 " ideal model delta sigma weight residual 113.97 105.43 8.54 1.28e+00 6.10e-01 4.46e+01 angle pdb=" N GLY R 209 " pdb=" CA GLY R 209 " pdb=" C GLY R 209 " ideal model delta sigma weight residual 113.37 121.86 -8.49 1.34e+00 5.57e-01 4.02e+01 angle pdb=" N VAL B 315 " pdb=" CA VAL B 315 " pdb=" C VAL B 315 " ideal model delta sigma weight residual 109.58 101.51 8.07 1.29e+00 6.01e-01 3.91e+01 angle pdb=" N PHE R 110 " pdb=" CA PHE R 110 " pdb=" C PHE R 110 " ideal model delta sigma weight residual 113.18 106.19 6.99 1.21e+00 6.83e-01 3.33e+01 angle pdb=" N THR R 265 " pdb=" CA THR R 265 " pdb=" C THR R 265 " ideal model delta sigma weight residual 113.41 106.69 6.72 1.22e+00 6.72e-01 3.03e+01 ... (remaining 12324 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 4880 17.57 - 35.14: 419 35.14 - 52.71: 60 52.71 - 70.28: 14 70.28 - 87.84: 10 Dihedral angle restraints: 5383 sinusoidal: 2109 harmonic: 3274 Sorted by residual: dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 170.64 -77.64 1 1.00e+01 1.00e-02 7.55e+01 dihedral pdb=" C ASN R 108 " pdb=" N ASN R 108 " pdb=" CA ASN R 108 " pdb=" CB ASN R 108 " ideal model delta harmonic sigma weight residual -122.60 -139.29 16.69 0 2.50e+00 1.60e-01 4.46e+01 dihedral pdb=" N ASN R 108 " pdb=" C ASN R 108 " pdb=" CA ASN R 108 " pdb=" CB ASN R 108 " ideal model delta harmonic sigma weight residual 122.80 136.20 -13.40 0 2.50e+00 1.60e-01 2.87e+01 ... (remaining 5380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1106 0.119 - 0.237: 271 0.237 - 0.356: 23 0.356 - 0.474: 2 0.474 - 0.593: 1 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CA ASN R 108 " pdb=" N ASN R 108 " pdb=" C ASN R 108 " pdb=" CB ASN R 108 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.79e+00 chirality pdb=" CA TRP R 254 " pdb=" N TRP R 254 " pdb=" C TRP R 254 " pdb=" CB TRP R 254 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" CA ARG E 191 " pdb=" N ARG E 191 " pdb=" C ARG E 191 " pdb=" CB ARG E 191 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 ... (remaining 1400 not shown) Planarity restraints: 1549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 54 " 0.017 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C LYS A 54 " -0.061 2.00e-02 2.50e+03 pdb=" O LYS A 54 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE A 55 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 191 " 0.016 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C ARG E 191 " -0.057 2.00e-02 2.50e+03 pdb=" O ARG E 191 " 0.021 2.00e-02 2.50e+03 pdb=" N MET E 192 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 99 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C LYS R 99 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS R 99 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU R 100 " 0.020 2.00e-02 2.50e+03 ... (remaining 1546 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1247 2.76 - 3.29: 8725 3.29 - 3.83: 14689 3.83 - 4.36: 19426 4.36 - 4.90: 32229 Nonbonded interactions: 76316 Sorted by model distance: nonbonded pdb=" OG SER E 161 " pdb=" O LYS E 163 " model vdw 2.223 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.257 3.040 nonbonded pdb=" NH1 ARG E 202 " pdb=" OD2 ASP E 223 " model vdw 2.281 3.120 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.285 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.293 3.040 ... (remaining 76311 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: 0.500 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.980 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.013 0.091 9101 Z= 0.906 Angle : 1.286 11.214 12333 Z= 0.916 Chirality : 0.096 0.593 1403 Planarity : 0.008 0.071 1549 Dihedral : 13.455 87.844 3267 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.57 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.24), residues: 1120 helix: -0.26 (0.25), residues: 392 sheet: 0.30 (0.31), residues: 268 loop : -0.87 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 219 TYR 0.014 0.003 TYR B 124 PHE 0.013 0.003 PHE R 80 TRP 0.013 0.003 TRP R 150 HIS 0.009 0.002 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.01303 ( 9099) covalent geometry : angle 1.28604 (12329) SS BOND : bond 0.00589 ( 2) SS BOND : angle 1.85959 ( 4) hydrogen bonds : bond 0.21995 ( 434) hydrogen bonds : angle 8.76030 ( 1248) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7245 (tt0) cc_final: 0.7004 (pt0) REVERT: B 271 CYS cc_start: 0.7631 (p) cc_final: 0.7298 (p) REVERT: R 103 ILE cc_start: 0.8741 (mt) cc_final: 0.8388 (mp) REVERT: R 314 ILE cc_start: 0.7705 (pt) cc_final: 0.7440 (mm) outliers start: 1 outliers final: 1 residues processed: 158 average time/residue: 0.4874 time to fit residues: 82.6852 Evaluate side-chains 126 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 268 ASN E 113 GLN E 183 GLN E 186 GLN R 102 HIS R 294 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.143733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.108657 restraints weight = 10270.469| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.86 r_work: 0.2905 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9101 Z= 0.147 Angle : 0.591 9.604 12333 Z= 0.311 Chirality : 0.043 0.149 1403 Planarity : 0.005 0.048 1549 Dihedral : 5.474 50.389 1250 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.65 % Allowed : 11.34 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.40 (0.24), residues: 1120 helix: 0.09 (0.25), residues: 405 sheet: 0.31 (0.31), residues: 273 loop : -0.84 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.011 0.001 TYR E 190 PHE 0.014 0.001 PHE A 196 TRP 0.014 0.001 TRP B 169 HIS 0.007 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9099) covalent geometry : angle 0.59115 (12329) SS BOND : bond 0.00152 ( 2) SS BOND : angle 1.01242 ( 4) hydrogen bonds : bond 0.04398 ( 434) hydrogen bonds : angle 5.49900 ( 1248) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 245 GLU cc_start: 0.8018 (tt0) cc_final: 0.7544 (pt0) REVERT: B 258 ASP cc_start: 0.8446 (t0) cc_final: 0.7979 (t0) REVERT: C 21 MET cc_start: 0.7686 (mmp) cc_final: 0.7418 (mmm) REVERT: E 166 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8002 (tt) REVERT: E 219 LEU cc_start: 0.7957 (tt) cc_final: 0.7713 (tt) REVERT: R 103 ILE cc_start: 0.8458 (mt) cc_final: 0.8061 (mp) REVERT: R 197 MET cc_start: 0.5569 (OUTLIER) cc_final: 0.4421 (tpt) outliers start: 16 outliers final: 5 residues processed: 151 average time/residue: 0.4524 time to fit residues: 73.6357 Evaluate side-chains 136 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN E 82 GLN E 113 GLN E 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.141361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.106337 restraints weight = 10232.036| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.84 r_work: 0.2966 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9101 Z= 0.196 Angle : 0.606 9.403 12333 Z= 0.315 Chirality : 0.044 0.152 1403 Planarity : 0.004 0.040 1549 Dihedral : 5.487 48.773 1248 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.47 % Allowed : 13.51 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.46 (0.24), residues: 1120 helix: 0.23 (0.26), residues: 410 sheet: 0.11 (0.31), residues: 275 loop : -0.96 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.014 0.002 TYR E 190 PHE 0.014 0.002 PHE A 196 TRP 0.014 0.002 TRP B 82 HIS 0.007 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 9099) covalent geometry : angle 0.60564 (12329) SS BOND : bond 0.00140 ( 2) SS BOND : angle 1.09904 ( 4) hydrogen bonds : bond 0.04265 ( 434) hydrogen bonds : angle 5.33658 ( 1248) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7931 (tt0) cc_final: 0.7570 (pt0) REVERT: A 306 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.6485 (mp10) REVERT: B 258 ASP cc_start: 0.8415 (t0) cc_final: 0.7946 (t0) REVERT: C 21 MET cc_start: 0.7743 (mmp) cc_final: 0.7496 (mmm) REVERT: E 166 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8033 (tt) REVERT: R 103 ILE cc_start: 0.8474 (mt) cc_final: 0.7995 (mp) REVERT: R 197 MET cc_start: 0.5487 (OUTLIER) cc_final: 0.4331 (tpt) outliers start: 24 outliers final: 8 residues processed: 139 average time/residue: 0.4972 time to fit residues: 74.0783 Evaluate side-chains 130 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 144 LYS Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 197 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.6980 chunk 3 optimal weight: 0.2980 chunk 1 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 220 GLN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.145061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.110793 restraints weight = 10332.479| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.86 r_work: 0.2934 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9101 Z= 0.118 Angle : 0.535 12.108 12333 Z= 0.277 Chirality : 0.042 0.163 1403 Planarity : 0.004 0.040 1549 Dihedral : 5.200 48.683 1248 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.68 % Allowed : 14.64 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.29 (0.25), residues: 1120 helix: 0.49 (0.26), residues: 411 sheet: 0.09 (0.31), residues: 273 loop : -0.93 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 219 TYR 0.011 0.001 TYR E 190 PHE 0.013 0.001 PHE A 189 TRP 0.011 0.001 TRP B 169 HIS 0.005 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9099) covalent geometry : angle 0.53535 (12329) SS BOND : bond 0.00142 ( 2) SS BOND : angle 0.73386 ( 4) hydrogen bonds : bond 0.03614 ( 434) hydrogen bonds : angle 4.96940 ( 1248) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7882 (tt0) cc_final: 0.7588 (pt0) REVERT: B 258 ASP cc_start: 0.8297 (t0) cc_final: 0.7813 (t0) REVERT: E 89 GLU cc_start: 0.7738 (pm20) cc_final: 0.6923 (pp20) REVERT: E 166 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7984 (tt) REVERT: E 223 ASP cc_start: 0.8039 (m-30) cc_final: 0.7725 (m-30) REVERT: R 98 CYS cc_start: 0.7770 (t) cc_final: 0.6958 (t) REVERT: R 191 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7039 (tt) REVERT: R 197 MET cc_start: 0.5489 (OUTLIER) cc_final: 0.4913 (tmt) REVERT: R 312 ARG cc_start: 0.7530 (mmm160) cc_final: 0.7316 (mmm160) outliers start: 26 outliers final: 6 residues processed: 144 average time/residue: 0.4960 time to fit residues: 76.6022 Evaluate side-chains 133 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 197 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 40 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.142859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.108190 restraints weight = 10283.283| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.86 r_work: 0.2944 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9101 Z= 0.150 Angle : 0.564 12.247 12333 Z= 0.289 Chirality : 0.043 0.165 1403 Planarity : 0.004 0.040 1549 Dihedral : 5.241 48.947 1248 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.20 % Allowed : 15.15 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.28 (0.25), residues: 1120 helix: 0.56 (0.26), residues: 411 sheet: -0.01 (0.31), residues: 278 loop : -0.92 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.012 0.001 TYR E 190 PHE 0.016 0.001 PHE R 163 TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9099) covalent geometry : angle 0.56372 (12329) SS BOND : bond 0.00124 ( 2) SS BOND : angle 0.91104 ( 4) hydrogen bonds : bond 0.03726 ( 434) hydrogen bonds : angle 4.97617 ( 1248) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7846 (tt0) cc_final: 0.7507 (pt0) REVERT: B 258 ASP cc_start: 0.8406 (t0) cc_final: 0.7923 (t0) REVERT: C 21 MET cc_start: 0.7653 (mmp) cc_final: 0.7391 (mmm) REVERT: E 89 GLU cc_start: 0.7708 (pm20) cc_final: 0.6971 (pp20) REVERT: E 166 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8024 (tt) REVERT: E 223 ASP cc_start: 0.8094 (m-30) cc_final: 0.7880 (m-30) REVERT: R 98 CYS cc_start: 0.8066 (t) cc_final: 0.7152 (t) REVERT: R 103 ILE cc_start: 0.8366 (mt) cc_final: 0.8004 (mt) REVERT: R 191 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7100 (tt) REVERT: R 197 MET cc_start: 0.5456 (OUTLIER) cc_final: 0.4903 (tmt) outliers start: 31 outliers final: 14 residues processed: 141 average time/residue: 0.5311 time to fit residues: 80.3484 Evaluate side-chains 137 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 197 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 0.0010 chunk 35 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.142836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.108686 restraints weight = 10246.560| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.81 r_work: 0.2942 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9101 Z= 0.154 Angle : 0.560 12.634 12333 Z= 0.288 Chirality : 0.043 0.169 1403 Planarity : 0.004 0.040 1549 Dihedral : 5.233 48.903 1248 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.78 % Allowed : 16.29 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.25), residues: 1120 helix: 0.62 (0.26), residues: 411 sheet: -0.09 (0.31), residues: 272 loop : -0.95 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.012 0.001 TYR E 190 PHE 0.017 0.001 PHE R 163 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9099) covalent geometry : angle 0.56014 (12329) SS BOND : bond 0.00118 ( 2) SS BOND : angle 0.84877 ( 4) hydrogen bonds : bond 0.03699 ( 434) hydrogen bonds : angle 4.94640 ( 1248) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7843 (tt0) cc_final: 0.7507 (pt0) REVERT: A 330 LYS cc_start: 0.7293 (mtmm) cc_final: 0.6265 (tptt) REVERT: B 258 ASP cc_start: 0.8438 (t0) cc_final: 0.7965 (t0) REVERT: C 21 MET cc_start: 0.7684 (mmp) cc_final: 0.7419 (mmm) REVERT: E 89 GLU cc_start: 0.7605 (pm20) cc_final: 0.6903 (pp20) REVERT: E 166 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8020 (tt) REVERT: R 103 ILE cc_start: 0.8383 (mt) cc_final: 0.8014 (mt) REVERT: R 191 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7127 (tt) REVERT: R 197 MET cc_start: 0.5468 (OUTLIER) cc_final: 0.4907 (tmt) REVERT: R 270 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: R 317 LEU cc_start: 0.5770 (OUTLIER) cc_final: 0.5526 (tt) outliers start: 27 outliers final: 19 residues processed: 142 average time/residue: 0.4901 time to fit residues: 74.5995 Evaluate side-chains 148 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 270 GLU Chi-restraints excluded: chain R residue 317 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 72 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 58 optimal weight: 0.0470 chunk 37 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 333 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.142976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.108296 restraints weight = 10291.393| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.85 r_work: 0.2932 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9101 Z= 0.153 Angle : 0.558 12.005 12333 Z= 0.287 Chirality : 0.043 0.162 1403 Planarity : 0.004 0.042 1549 Dihedral : 5.225 48.870 1248 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.30 % Allowed : 17.01 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.29 (0.25), residues: 1120 helix: 0.66 (0.26), residues: 411 sheet: -0.14 (0.31), residues: 274 loop : -0.93 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.011 0.001 TYR E 190 PHE 0.018 0.001 PHE R 163 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9099) covalent geometry : angle 0.55779 (12329) SS BOND : bond 0.00115 ( 2) SS BOND : angle 0.82101 ( 4) hydrogen bonds : bond 0.03668 ( 434) hydrogen bonds : angle 4.92474 ( 1248) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7864 (tt0) cc_final: 0.7602 (pt0) REVERT: B 258 ASP cc_start: 0.8425 (t0) cc_final: 0.7946 (t0) REVERT: B 338 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8958 (mm) REVERT: C 21 MET cc_start: 0.7694 (mmp) cc_final: 0.7457 (mmm) REVERT: E 89 GLU cc_start: 0.7629 (pm20) cc_final: 0.6901 (pp20) REVERT: E 166 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8017 (tt) REVERT: R 103 ILE cc_start: 0.8415 (mt) cc_final: 0.8026 (mt) REVERT: R 191 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7132 (tt) REVERT: R 197 MET cc_start: 0.5498 (OUTLIER) cc_final: 0.4940 (tmt) REVERT: R 317 LEU cc_start: 0.5765 (OUTLIER) cc_final: 0.5551 (tp) outliers start: 32 outliers final: 18 residues processed: 144 average time/residue: 0.5040 time to fit residues: 77.8031 Evaluate side-chains 145 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 317 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 0.3980 chunk 1 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.144787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.111108 restraints weight = 10289.215| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.80 r_work: 0.2971 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9101 Z= 0.120 Angle : 0.541 13.244 12333 Z= 0.275 Chirality : 0.042 0.170 1403 Planarity : 0.004 0.040 1549 Dihedral : 5.086 48.794 1248 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.37 % Allowed : 18.25 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.18 (0.25), residues: 1120 helix: 0.79 (0.26), residues: 410 sheet: -0.05 (0.31), residues: 273 loop : -0.94 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.010 0.001 TYR E 190 PHE 0.018 0.001 PHE R 163 TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9099) covalent geometry : angle 0.54056 (12329) SS BOND : bond 0.00143 ( 2) SS BOND : angle 0.65372 ( 4) hydrogen bonds : bond 0.03447 ( 434) hydrogen bonds : angle 4.75522 ( 1248) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7877 (tt0) cc_final: 0.7629 (pt0) REVERT: A 330 LYS cc_start: 0.7282 (mtmm) cc_final: 0.6343 (tptt) REVERT: B 258 ASP cc_start: 0.8338 (t0) cc_final: 0.7847 (t0) REVERT: C 21 MET cc_start: 0.7676 (mmp) cc_final: 0.7460 (mmm) REVERT: E 82 GLN cc_start: 0.8511 (tp-100) cc_final: 0.8280 (tp40) REVERT: E 89 GLU cc_start: 0.7598 (pm20) cc_final: 0.6894 (pp20) REVERT: E 166 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8012 (tt) REVERT: R 103 ILE cc_start: 0.8347 (mt) cc_final: 0.7979 (mt) REVERT: R 191 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7114 (tt) REVERT: R 197 MET cc_start: 0.5713 (OUTLIER) cc_final: 0.5143 (tmt) outliers start: 23 outliers final: 16 residues processed: 142 average time/residue: 0.5945 time to fit residues: 89.9766 Evaluate side-chains 140 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 72 optimal weight: 0.0370 chunk 27 optimal weight: 3.9990 chunk 76 optimal weight: 0.0060 overall best weight: 1.1678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN E 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.144134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.109375 restraints weight = 10234.892| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.83 r_work: 0.2986 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9101 Z= 0.140 Angle : 0.546 12.767 12333 Z= 0.281 Chirality : 0.042 0.167 1403 Planarity : 0.004 0.039 1549 Dihedral : 5.131 48.829 1248 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.37 % Allowed : 18.66 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.20 (0.25), residues: 1120 helix: 0.75 (0.26), residues: 411 sheet: -0.10 (0.31), residues: 274 loop : -0.91 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 208 TYR 0.011 0.001 TYR E 190 PHE 0.018 0.001 PHE R 163 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9099) covalent geometry : angle 0.54598 (12329) SS BOND : bond 0.00095 ( 2) SS BOND : angle 0.74994 ( 4) hydrogen bonds : bond 0.03569 ( 434) hydrogen bonds : angle 4.83782 ( 1248) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7938 (tt0) cc_final: 0.7720 (pt0) REVERT: A 330 LYS cc_start: 0.7337 (mtmm) cc_final: 0.6384 (tptt) REVERT: B 258 ASP cc_start: 0.8348 (t0) cc_final: 0.7922 (t0) REVERT: B 338 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8939 (mm) REVERT: C 15 LEU cc_start: 0.6005 (OUTLIER) cc_final: 0.5329 (mp) REVERT: C 21 MET cc_start: 0.7697 (mmp) cc_final: 0.7469 (mmm) REVERT: E 82 GLN cc_start: 0.8463 (tp-100) cc_final: 0.8112 (tp-100) REVERT: E 89 GLU cc_start: 0.7639 (pm20) cc_final: 0.6913 (pp20) REVERT: E 166 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8013 (tt) REVERT: R 99 LYS cc_start: 0.7964 (ttmm) cc_final: 0.7675 (tptt) REVERT: R 103 ILE cc_start: 0.8480 (mt) cc_final: 0.8141 (mt) REVERT: R 191 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7124 (tt) REVERT: R 197 MET cc_start: 0.5539 (OUTLIER) cc_final: 0.4984 (tmt) outliers start: 23 outliers final: 16 residues processed: 140 average time/residue: 0.5463 time to fit residues: 81.8625 Evaluate side-chains 145 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 8 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.142951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.107960 restraints weight = 10255.268| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.88 r_work: 0.2897 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9101 Z= 0.161 Angle : 0.576 12.543 12333 Z= 0.294 Chirality : 0.043 0.166 1403 Planarity : 0.004 0.039 1549 Dihedral : 5.235 48.787 1248 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.37 % Allowed : 19.48 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.29 (0.25), residues: 1120 helix: 0.69 (0.26), residues: 411 sheet: -0.18 (0.31), residues: 273 loop : -0.95 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.022 0.001 TYR A 296 PHE 0.019 0.002 PHE R 163 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 9099) covalent geometry : angle 0.57610 (12329) SS BOND : bond 0.00088 ( 2) SS BOND : angle 0.87180 ( 4) hydrogen bonds : bond 0.03673 ( 434) hydrogen bonds : angle 4.95626 ( 1248) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7934 (tt0) cc_final: 0.7622 (pt0) REVERT: A 306 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.6300 (mp10) REVERT: B 258 ASP cc_start: 0.8336 (t0) cc_final: 0.7861 (t0) REVERT: B 338 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.9005 (mm) REVERT: C 21 MET cc_start: 0.7535 (mmp) cc_final: 0.7284 (mmm) REVERT: E 89 GLU cc_start: 0.7615 (pm20) cc_final: 0.6870 (pp20) REVERT: E 166 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7990 (tt) REVERT: R 25 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7156 (mp) REVERT: R 99 LYS cc_start: 0.8103 (ttmm) cc_final: 0.7798 (tptt) REVERT: R 103 ILE cc_start: 0.8406 (mt) cc_final: 0.8071 (mt) REVERT: R 191 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7008 (tm) REVERT: R 197 MET cc_start: 0.5381 (OUTLIER) cc_final: 0.4788 (tmt) REVERT: R 312 ARG cc_start: 0.7146 (mmm160) cc_final: 0.6917 (tpt90) outliers start: 23 outliers final: 15 residues processed: 142 average time/residue: 0.5400 time to fit residues: 82.3120 Evaluate side-chains 145 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 14 optimal weight: 0.0040 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN E 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.145881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.111924 restraints weight = 10244.567| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.81 r_work: 0.2954 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9101 Z= 0.114 Angle : 0.543 12.954 12333 Z= 0.276 Chirality : 0.042 0.169 1403 Planarity : 0.004 0.040 1549 Dihedral : 5.022 48.580 1248 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.96 % Allowed : 20.10 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.17 (0.25), residues: 1120 helix: 0.83 (0.26), residues: 411 sheet: -0.10 (0.31), residues: 272 loop : -0.94 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.009 0.001 TYR E 190 PHE 0.018 0.001 PHE R 163 TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9099) covalent geometry : angle 0.54305 (12329) SS BOND : bond 0.00148 ( 2) SS BOND : angle 0.56164 ( 4) hydrogen bonds : bond 0.03397 ( 434) hydrogen bonds : angle 4.78197 ( 1248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3419.11 seconds wall clock time: 59 minutes 0.03 seconds (3540.03 seconds total)