Starting phenix.real_space_refine on Wed Mar 4 00:12:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xa3_33086/03_2026/7xa3_33086.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xa3_33086/03_2026/7xa3_33086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xa3_33086/03_2026/7xa3_33086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xa3_33086/03_2026/7xa3_33086.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xa3_33086/03_2026/7xa3_33086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xa3_33086/03_2026/7xa3_33086.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.027 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 70 5.16 5 C 6116 2.51 5 N 1628 2.21 5 O 1777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 9591 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2377 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 10, 'TRANS': 284} Chain: "L" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 551 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "A" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1841 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 226} Chain breaks: 1 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Time building chain proxies: 1.86, per 1000 atoms: 0.19 Number of scatterers: 9591 At special positions: 0 Unit cell: (110.526, 140.946, 129.792, 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 70 16.00 O 1777 8.00 N 1628 7.00 C 6116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 32 " - pdb=" SG CYS R 277 " distance=2.02 Simple disulfide: pdb=" SG CYS R 113 " - pdb=" SG CYS R 190 " distance=2.03 Simple disulfide: pdb=" SG CYS L 11 " - pdb=" SG CYS L 36 " distance=2.03 Simple disulfide: pdb=" SG CYS L 12 " - pdb=" SG CYS L 52 " distance=2.03 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: 0.66 Conformation dependent library (CDL) restraints added in 333.2 milliseconds 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2282 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 15 sheets defined 39.0% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'R' and resid 34 through 70 removed outlier: 3.993A pdb=" N LYS R 38 " --> pdb=" O LYS R 34 " (cutoff:3.500A) Proline residue: R 46 - end of helix Processing helix chain 'R' and resid 75 through 94 removed outlier: 4.645A pdb=" N THR R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 102 Processing helix chain 'R' and resid 109 through 144 removed outlier: 3.592A pdb=" N GLY R 118 " --> pdb=" O LYS R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 152 removed outlier: 3.660A pdb=" N LYS R 150 " --> pdb=" O VAL R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 178 Proline residue: R 174 - end of helix removed outlier: 3.638A pdb=" N PHE R 178 " --> pdb=" O PRO R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 211 removed outlier: 3.564A pdb=" N THR R 203 " --> pdb=" O ASN R 199 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE R 204 " --> pdb=" O ASN R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 232 removed outlier: 3.711A pdb=" N GLY R 224 " --> pdb=" O ILE R 220 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG R 231 " --> pdb=" O LYS R 227 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N CYS R 232 " --> pdb=" O THR R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 234 through 269 Proline residue: R 258 - end of helix Processing helix chain 'R' and resid 276 through 306 removed outlier: 3.960A pdb=" N SER R 281 " --> pdb=" O CYS R 277 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN R 282 " --> pdb=" O GLU R 278 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS R 298 " --> pdb=" O GLY R 294 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS R 299 " --> pdb=" O MET R 295 " (cutoff:3.500A) Proline residue: R 302 - end of helix Processing helix chain 'R' and resid 309 through 323 Processing helix chain 'L' and resid 57 through 69 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.881A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 56 removed outlier: 4.123A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.783A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.927A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 327 through 352 removed outlier: 4.290A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 31 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.657A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.636A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.549A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.650A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 179 through 184 Processing sheet with id=AA2, first strand: chain 'L' and resid 25 through 31 Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.641A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 56 removed outlier: 5.511A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 63 through 68 removed outlier: 6.902A pdb=" N ALA B 78 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N MET B 66 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL B 76 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N TRP B 68 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU B 74 " --> pdb=" O TRP B 68 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 105 through 110 removed outlier: 7.024A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.642A pdb=" N THR B 183 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.642A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.516A pdb=" N ALA B 236 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.768A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASN B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 2 through 5 Processing sheet with id=AB3, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.193A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 147 removed outlier: 3.862A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR E 190 " --> pdb=" O ASN E 194 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN E 194 " --> pdb=" O TYR E 190 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 146 through 147 removed outlier: 3.862A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 500 hydrogen bonds defined for protein. 1416 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: 1.53 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3040 1.34 - 1.46: 2065 1.46 - 1.58: 4589 1.58 - 1.70: 1 1.70 - 1.82: 98 Bond restraints: 9793 Sorted by residual: bond pdb=" C ALA R 30 " pdb=" N PRO R 31 " ideal model delta sigma weight residual 1.334 1.405 -0.071 2.34e-02 1.83e+03 9.31e+00 bond pdb=" C VAL R 173 " pdb=" N PRO R 174 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.28e-02 6.10e+03 5.55e+00 bond pdb=" C PRO R 46 " pdb=" N PRO R 47 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.36e-02 5.41e+03 4.18e+00 bond pdb=" C THR R 257 " pdb=" N PRO R 258 " ideal model delta sigma weight residual 1.335 1.360 -0.024 1.36e-02 5.41e+03 3.21e+00 bond pdb=" CA ASP B 210 " pdb=" C ASP B 210 " ideal model delta sigma weight residual 1.518 1.586 -0.069 4.01e-02 6.22e+02 2.92e+00 ... (remaining 9788 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 12858 2.14 - 4.29: 339 4.29 - 6.43: 42 6.43 - 8.58: 12 8.58 - 10.72: 4 Bond angle restraints: 13255 Sorted by residual: angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 132.26 -10.72 1.91e+00 2.74e-01 3.15e+01 angle pdb=" N ALA R 30 " pdb=" CA ALA R 30 " pdb=" C ALA R 30 " ideal model delta sigma weight residual 109.81 119.48 -9.67 2.21e+00 2.05e-01 1.92e+01 angle pdb=" N PRO R 46 " pdb=" CA PRO R 46 " pdb=" C PRO R 46 " ideal model delta sigma weight residual 110.70 115.36 -4.66 1.22e+00 6.72e-01 1.46e+01 angle pdb=" CA PRO R 46 " pdb=" C PRO R 46 " pdb=" N PRO R 47 " ideal model delta sigma weight residual 117.93 122.31 -4.38 1.20e+00 6.94e-01 1.33e+01 angle pdb=" N LEU R 45 " pdb=" CA LEU R 45 " pdb=" C LEU R 45 " ideal model delta sigma weight residual 109.81 117.73 -7.92 2.21e+00 2.05e-01 1.28e+01 ... (remaining 13250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 5633 15.46 - 30.92: 165 30.92 - 46.38: 28 46.38 - 61.84: 0 61.84 - 77.30: 1 Dihedral angle restraints: 5827 sinusoidal: 2290 harmonic: 3537 Sorted by residual: dihedral pdb=" CB CYS L 11 " pdb=" SG CYS L 11 " pdb=" SG CYS L 36 " pdb=" CB CYS L 36 " ideal model delta sinusoidal sigma weight residual -86.00 -163.30 77.30 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CB CYS L 12 " pdb=" SG CYS L 12 " pdb=" SG CYS L 52 " pdb=" CB CYS L 52 " ideal model delta sinusoidal sigma weight residual 93.00 128.18 -35.18 1 1.00e+01 1.00e-02 1.75e+01 dihedral pdb=" CA GLN E 142 " pdb=" C GLN E 142 " pdb=" N ALA E 143 " pdb=" CA ALA E 143 " ideal model delta harmonic sigma weight residual -180.00 -160.39 -19.61 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 5824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1034 0.048 - 0.095: 354 0.095 - 0.143: 86 0.143 - 0.190: 24 0.190 - 0.238: 5 Chirality restraints: 1503 Sorted by residual: chirality pdb=" CB VAL L 47 " pdb=" CA VAL L 47 " pdb=" CG1 VAL L 47 " pdb=" CG2 VAL L 47 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA LEU R 95 " pdb=" N LEU R 95 " pdb=" C LEU R 95 " pdb=" CB LEU R 95 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA PRO R 31 " pdb=" N PRO R 31 " pdb=" C PRO R 31 " pdb=" CB PRO R 31 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1500 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 303 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.38e+00 pdb=" C ILE R 303 " -0.050 2.00e-02 2.50e+03 pdb=" O ILE R 303 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE R 304 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 110 " -0.018 2.00e-02 2.50e+03 1.60e-02 6.43e+00 pdb=" CG TRP E 110 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP E 110 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP E 110 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 110 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 110 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 110 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 110 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 110 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 110 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 240 " 0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO B 241 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 241 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 241 " 0.032 5.00e-02 4.00e+02 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1664 2.78 - 3.31: 8568 3.31 - 3.84: 15270 3.84 - 4.37: 17497 4.37 - 4.90: 31486 Nonbonded interactions: 74485 Sorted by model distance: nonbonded pdb=" O GLY R 175 " pdb=" OG1 THR R 179 " model vdw 2.250 3.040 nonbonded pdb=" OG SER B 336 " pdb=" OD1 ASP B 338 " model vdw 2.291 3.040 nonbonded pdb=" OG SER B 166 " pdb=" OD1 ASP B 168 " model vdw 2.301 3.040 nonbonded pdb=" OG SER E 6 " pdb=" OG SER E 20 " model vdw 2.321 3.040 nonbonded pdb=" O GLY E 111 " pdb=" OG SER E 184 " model vdw 2.340 3.040 ... (remaining 74480 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.180 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 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 : 0.005 0.071 9798 Z= 0.228 Angle : 0.854 10.720 13265 Z= 0.488 Chirality : 0.052 0.238 1503 Planarity : 0.006 0.057 1674 Dihedral : 7.874 45.992 3530 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.22), residues: 1204 helix: 1.43 (0.21), residues: 428 sheet: 0.96 (0.29), residues: 286 loop : -0.86 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 319 TYR 0.031 0.003 TYR E 93 PHE 0.032 0.003 PHE A 354 TRP 0.043 0.004 TRP E 110 HIS 0.009 0.002 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 9793) covalent geometry : angle 0.84952 (13255) SS BOND : bond 0.00377 ( 5) SS BOND : angle 3.43405 ( 10) hydrogen bonds : bond 0.12841 ( 496) hydrogen bonds : angle 5.93791 ( 1416) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 66 ILE cc_start: 0.8334 (mt) cc_final: 0.8010 (tp) REVERT: R 156 PHE cc_start: 0.6682 (t80) cc_final: 0.6360 (t80) REVERT: R 254 LEU cc_start: 0.8008 (mt) cc_final: 0.7750 (mt) REVERT: R 312 PHE cc_start: 0.7578 (t80) cc_final: 0.7148 (t80) REVERT: A 197 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7880 (mtpp) REVERT: A 342 VAL cc_start: 0.8600 (t) cc_final: 0.8329 (t) REVERT: A 349 LYS cc_start: 0.7770 (ttmm) cc_final: 0.7532 (ttmm) REVERT: B 27 ARG cc_start: 0.6342 (mtt180) cc_final: 0.6125 (mtt180) REVERT: B 180 GLN cc_start: 0.7069 (mm-40) cc_final: 0.6840 (mm-40) REVERT: B 270 SER cc_start: 0.7508 (t) cc_final: 0.7270 (m) REVERT: B 272 ASP cc_start: 0.7329 (m-30) cc_final: 0.7093 (m-30) REVERT: E 58 TYR cc_start: 0.8004 (m-80) cc_final: 0.7788 (m-80) REVERT: E 102 TYR cc_start: 0.8204 (t80) cc_final: 0.7833 (t80) REVERT: E 158 SER cc_start: 0.8185 (t) cc_final: 0.7956 (m) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.4826 time to fit residues: 147.0690 Evaluate side-chains 233 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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: 0.6980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.0570 chunk 113 optimal weight: 0.0770 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 104 ASN R 110 ASN R 121 HIS R 260 ASN R 285 GLN R 288 GLN A 204 GLN A 269 ASN B 96 HIS ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN B 271 HIS B 273 ASN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.149982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.127828 restraints weight = 14150.585| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.06 r_work: 0.3543 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9798 Z= 0.125 Angle : 0.553 7.315 13265 Z= 0.295 Chirality : 0.042 0.283 1503 Planarity : 0.004 0.042 1674 Dihedral : 4.210 18.213 1316 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.76 % Allowed : 10.74 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.40 (0.23), residues: 1204 helix: 2.43 (0.24), residues: 431 sheet: 1.26 (0.29), residues: 284 loop : -0.69 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 231 TYR 0.019 0.001 TYR R 124 PHE 0.023 0.001 PHE R 53 TRP 0.027 0.002 TRP B 344 HIS 0.003 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9793) covalent geometry : angle 0.55276 (13255) SS BOND : bond 0.00297 ( 5) SS BOND : angle 1.01794 ( 10) hydrogen bonds : bond 0.04598 ( 496) hydrogen bonds : angle 4.71465 ( 1416) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 243 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 66 ILE cc_start: 0.8313 (mt) cc_final: 0.8024 (tp) REVERT: R 79 ILE cc_start: 0.8053 (mt) cc_final: 0.7773 (mt) REVERT: R 205 MET cc_start: 0.7990 (tpp) cc_final: 0.7698 (tpp) REVERT: R 254 LEU cc_start: 0.8249 (mt) cc_final: 0.7952 (mt) REVERT: R 312 PHE cc_start: 0.7548 (t80) cc_final: 0.7058 (t80) REVERT: A 197 LYS cc_start: 0.8791 (mtpt) cc_final: 0.8488 (mtpp) REVERT: A 245 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7246 (mm-30) REVERT: A 276 GLU cc_start: 0.6709 (tp30) cc_final: 0.6457 (tp30) REVERT: A 332 VAL cc_start: 0.8454 (t) cc_final: 0.8237 (m) REVERT: A 349 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7749 (ttmm) REVERT: B 24 ARG cc_start: 0.6584 (ttp80) cc_final: 0.6317 (ttp80) REVERT: B 27 ARG cc_start: 0.7159 (mtt180) cc_final: 0.6944 (mtt180) REVERT: B 180 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7477 (mm-40) REVERT: B 193 MET cc_start: 0.8257 (mmm) cc_final: 0.7621 (mmm) REVERT: B 270 SER cc_start: 0.7783 (t) cc_final: 0.7511 (m) REVERT: B 272 ASP cc_start: 0.8031 (m-30) cc_final: 0.7752 (m-30) REVERT: B 281 VAL cc_start: 0.8486 (t) cc_final: 0.8142 (p) REVERT: B 308 ASP cc_start: 0.8053 (m-30) cc_final: 0.7758 (m-30) REVERT: B 319 ARG cc_start: 0.8277 (ttt90) cc_final: 0.7931 (ttm170) REVERT: B 345 ASN cc_start: 0.7871 (OUTLIER) cc_final: 0.7655 (m-40) REVERT: E 20 SER cc_start: 0.8291 (p) cc_final: 0.8077 (m) REVERT: E 158 SER cc_start: 0.8636 (t) cc_final: 0.8396 (m) outliers start: 29 outliers final: 12 residues processed: 253 average time/residue: 0.4987 time to fit residues: 135.3644 Evaluate side-chains 249 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 236 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 179 THR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 117 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 85 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 239 HIS R 285 GLN R 288 GLN A 346 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.147655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.125440 restraints weight = 14113.792| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.06 r_work: 0.3496 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9798 Z= 0.151 Angle : 0.558 9.407 13265 Z= 0.297 Chirality : 0.043 0.354 1503 Planarity : 0.004 0.040 1674 Dihedral : 4.238 19.498 1316 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.33 % Allowed : 12.17 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.23), residues: 1204 helix: 2.60 (0.24), residues: 427 sheet: 1.19 (0.29), residues: 288 loop : -0.59 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 231 TYR 0.017 0.002 TYR R 120 PHE 0.022 0.002 PHE R 156 TRP 0.019 0.002 TRP B 174 HIS 0.005 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9793) covalent geometry : angle 0.55744 (13255) SS BOND : bond 0.00319 ( 5) SS BOND : angle 1.10578 ( 10) hydrogen bonds : bond 0.04550 ( 496) hydrogen bonds : angle 4.64445 ( 1416) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 238 time to evaluate : 0.337 Fit side-chains REVERT: R 61 MET cc_start: 0.7213 (tpp) cc_final: 0.6969 (tpp) REVERT: R 90 LEU cc_start: 0.8025 (mt) cc_final: 0.7720 (tm) REVERT: R 205 MET cc_start: 0.8028 (tpp) cc_final: 0.7497 (tpp) REVERT: R 254 LEU cc_start: 0.8337 (mt) cc_final: 0.7989 (mt) REVERT: R 312 PHE cc_start: 0.7519 (t80) cc_final: 0.6972 (t80) REVERT: A 10 LYS cc_start: 0.8293 (mmtp) cc_final: 0.8083 (mmtm) REVERT: A 197 LYS cc_start: 0.8781 (mtpt) cc_final: 0.8485 (mtpp) REVERT: A 245 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7231 (mm-30) REVERT: A 276 GLU cc_start: 0.6827 (tp30) cc_final: 0.6617 (tp30) REVERT: A 332 VAL cc_start: 0.8499 (t) cc_final: 0.8212 (m) REVERT: A 349 LYS cc_start: 0.7944 (ttmm) cc_final: 0.7726 (ttmm) REVERT: B 24 ARG cc_start: 0.6584 (ttp80) cc_final: 0.6321 (ttp80) REVERT: B 27 ARG cc_start: 0.7098 (mtt180) cc_final: 0.6695 (mtt180) REVERT: B 180 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7766 (mm-40) REVERT: B 202 ARG cc_start: 0.7919 (mtp-110) cc_final: 0.7681 (mmm160) REVERT: B 217 ASP cc_start: 0.7729 (t0) cc_final: 0.7342 (p0) REVERT: B 263 ASP cc_start: 0.7085 (t70) cc_final: 0.6686 (t70) REVERT: B 270 SER cc_start: 0.7897 (t) cc_final: 0.7570 (m) REVERT: B 272 ASP cc_start: 0.8026 (m-30) cc_final: 0.7768 (m-30) REVERT: B 281 VAL cc_start: 0.8538 (t) cc_final: 0.8202 (p) REVERT: B 343 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8394 (mm) REVERT: E 158 SER cc_start: 0.8722 (t) cc_final: 0.8459 (m) outliers start: 35 outliers final: 18 residues processed: 250 average time/residue: 0.4887 time to fit residues: 131.3493 Evaluate side-chains 257 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 238 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 179 THR Chi-restraints excluded: chain R residue 281 SER Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 79 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 62 optimal weight: 0.0970 chunk 3 optimal weight: 10.0000 chunk 98 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 ASN A 255 ASN A 346 ASN B 264 GLN B 345 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.144184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.122092 restraints weight = 14171.617| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.06 r_work: 0.3464 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9798 Z= 0.184 Angle : 0.573 9.499 13265 Z= 0.305 Chirality : 0.044 0.365 1503 Planarity : 0.004 0.042 1674 Dihedral : 4.383 20.622 1316 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.99 % Allowed : 13.40 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.40 (0.23), residues: 1204 helix: 2.51 (0.25), residues: 424 sheet: 1.07 (0.28), residues: 290 loop : -0.60 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 142 TYR 0.021 0.002 TYR E 173 PHE 0.024 0.002 PHE R 156 TRP 0.018 0.002 TRP B 174 HIS 0.006 0.002 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 9793) covalent geometry : angle 0.57215 (13255) SS BOND : bond 0.00407 ( 5) SS BOND : angle 1.16502 ( 10) hydrogen bonds : bond 0.04792 ( 496) hydrogen bonds : angle 4.77026 ( 1416) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 0.363 Fit side-chains REVERT: R 61 MET cc_start: 0.7312 (tpp) cc_final: 0.7062 (tpp) REVERT: R 90 LEU cc_start: 0.8065 (mt) cc_final: 0.7760 (tm) REVERT: R 205 MET cc_start: 0.8133 (tpp) cc_final: 0.7624 (tpp) REVERT: R 249 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7507 (mmm) REVERT: R 254 LEU cc_start: 0.8362 (mt) cc_final: 0.8024 (mt) REVERT: R 300 ILE cc_start: 0.7406 (mm) cc_final: 0.6991 (pp) REVERT: R 312 PHE cc_start: 0.7402 (t80) cc_final: 0.7012 (t80) REVERT: A 197 LYS cc_start: 0.8795 (mtpt) cc_final: 0.8492 (mtpp) REVERT: A 245 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7306 (mm-30) REVERT: A 251 ASP cc_start: 0.8184 (t0) cc_final: 0.7949 (t0) REVERT: A 276 GLU cc_start: 0.6967 (tp30) cc_final: 0.6728 (tp30) REVERT: A 309 ASP cc_start: 0.7577 (t0) cc_final: 0.7375 (t70) REVERT: A 332 VAL cc_start: 0.8573 (t) cc_final: 0.8250 (m) REVERT: A 349 LYS cc_start: 0.7997 (ttmm) cc_final: 0.7785 (ttmm) REVERT: B 27 ARG cc_start: 0.7194 (mtt180) cc_final: 0.6856 (mtt180) REVERT: B 142 ARG cc_start: 0.8262 (tpp80) cc_final: 0.8004 (tpp-160) REVERT: B 193 MET cc_start: 0.8243 (mmm) cc_final: 0.7706 (mmm) REVERT: B 202 ARG cc_start: 0.7963 (mtp-110) cc_final: 0.7660 (mmm160) REVERT: B 263 ASP cc_start: 0.7225 (t70) cc_final: 0.6880 (t70) REVERT: B 281 VAL cc_start: 0.8561 (t) cc_final: 0.8238 (p) REVERT: B 343 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8374 (mm) REVERT: E 37 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8348 (ptt180) outliers start: 42 outliers final: 18 residues processed: 252 average time/residue: 0.5275 time to fit residues: 142.8705 Evaluate side-chains 245 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 179 THR Chi-restraints excluded: chain R residue 249 MET Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 109 optimal weight: 0.0970 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 60 optimal weight: 0.0570 chunk 50 optimal weight: 0.2980 chunk 51 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 104 ASN A 255 ASN A 346 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.146059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.123951 restraints weight = 14059.543| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.05 r_work: 0.3492 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9798 Z= 0.111 Angle : 0.513 9.866 13265 Z= 0.272 Chirality : 0.042 0.332 1503 Planarity : 0.003 0.041 1674 Dihedral : 4.112 20.355 1316 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.23 % Allowed : 16.16 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.50 (0.24), residues: 1204 helix: 2.70 (0.25), residues: 424 sheet: 0.92 (0.28), residues: 298 loop : -0.54 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 231 TYR 0.011 0.001 TYR B 150 PHE 0.026 0.001 PHE R 156 TRP 0.018 0.001 TRP B 216 HIS 0.002 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9793) covalent geometry : angle 0.51255 (13255) SS BOND : bond 0.00267 ( 5) SS BOND : angle 0.86925 ( 10) hydrogen bonds : bond 0.04022 ( 496) hydrogen bonds : angle 4.56051 ( 1416) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 90 LEU cc_start: 0.8036 (mt) cc_final: 0.7735 (tm) REVERT: R 205 MET cc_start: 0.8110 (tpp) cc_final: 0.7632 (tpp) REVERT: R 254 LEU cc_start: 0.8348 (mt) cc_final: 0.8011 (mt) REVERT: R 312 PHE cc_start: 0.7517 (t80) cc_final: 0.6996 (t80) REVERT: A 197 LYS cc_start: 0.8777 (mtpt) cc_final: 0.8475 (mtpp) REVERT: A 245 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7275 (mm-30) REVERT: A 270 LYS cc_start: 0.8214 (mttt) cc_final: 0.7925 (mttm) REVERT: A 276 GLU cc_start: 0.7034 (tp30) cc_final: 0.6803 (tp30) REVERT: A 309 ASP cc_start: 0.7546 (t0) cc_final: 0.7335 (t70) REVERT: A 332 VAL cc_start: 0.8428 (t) cc_final: 0.8111 (m) REVERT: A 345 LYS cc_start: 0.8302 (mtpt) cc_final: 0.8033 (mtmm) REVERT: A 349 LYS cc_start: 0.8070 (ttmm) cc_final: 0.7858 (ttmm) REVERT: B 27 ARG cc_start: 0.7085 (mtt180) cc_final: 0.6764 (mtt180) REVERT: B 50 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.8053 (mtm) REVERT: B 217 ASP cc_start: 0.7728 (t0) cc_final: 0.7391 (p0) REVERT: B 263 ASP cc_start: 0.7244 (t70) cc_final: 0.6882 (t70) REVERT: B 281 VAL cc_start: 0.8557 (t) cc_final: 0.8253 (p) REVERT: B 343 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8356 (mm) REVERT: E 37 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8201 (ptt180) outliers start: 34 outliers final: 17 residues processed: 235 average time/residue: 0.4912 time to fit residues: 124.2527 Evaluate side-chains 243 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 179 THR Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 158 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.143098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.121141 restraints weight = 14090.588| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.06 r_work: 0.3451 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9798 Z= 0.188 Angle : 0.580 11.721 13265 Z= 0.305 Chirality : 0.044 0.314 1503 Planarity : 0.004 0.043 1674 Dihedral : 4.327 20.230 1316 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.71 % Allowed : 16.83 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.37 (0.24), residues: 1204 helix: 2.44 (0.25), residues: 425 sheet: 0.88 (0.28), residues: 300 loop : -0.47 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 231 TYR 0.022 0.002 TYR R 120 PHE 0.028 0.002 PHE R 53 TRP 0.014 0.002 TRP B 87 HIS 0.005 0.002 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 9793) covalent geometry : angle 0.57894 (13255) SS BOND : bond 0.00456 ( 5) SS BOND : angle 1.15404 ( 10) hydrogen bonds : bond 0.04720 ( 496) hydrogen bonds : angle 4.75486 ( 1416) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: R 205 MET cc_start: 0.8178 (tpp) cc_final: 0.7835 (tpp) REVERT: R 249 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7472 (mpp) REVERT: R 254 LEU cc_start: 0.8365 (mt) cc_final: 0.8044 (mt) REVERT: A 197 LYS cc_start: 0.8781 (mtpt) cc_final: 0.8506 (mtpp) REVERT: A 225 VAL cc_start: 0.8787 (OUTLIER) cc_final: 0.8396 (m) REVERT: A 245 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7293 (mm-30) REVERT: A 270 LYS cc_start: 0.8248 (mttt) cc_final: 0.7959 (mttm) REVERT: A 276 GLU cc_start: 0.7117 (tp30) cc_final: 0.6908 (tp30) REVERT: A 332 VAL cc_start: 0.8518 (t) cc_final: 0.8175 (m) REVERT: A 345 LYS cc_start: 0.8326 (mtpt) cc_final: 0.8046 (mtmm) REVERT: A 349 LYS cc_start: 0.8095 (ttmm) cc_final: 0.7885 (ttmm) REVERT: B 27 ARG cc_start: 0.7217 (mtt180) cc_final: 0.6861 (mtt180) REVERT: B 64 TYR cc_start: 0.8528 (m-80) cc_final: 0.8326 (m-80) REVERT: B 239 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.7840 (m-80) REVERT: B 256 ARG cc_start: 0.8450 (mtt90) cc_final: 0.8191 (mtt-85) REVERT: B 263 ASP cc_start: 0.7285 (t70) cc_final: 0.6923 (t70) REVERT: B 281 VAL cc_start: 0.8585 (t) cc_final: 0.8279 (p) REVERT: B 343 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8366 (mm) REVERT: E 37 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8353 (ptt180) REVERT: E 230 MET cc_start: 0.8166 (tmm) cc_final: 0.7896 (ttm) outliers start: 39 outliers final: 18 residues processed: 243 average time/residue: 0.4921 time to fit residues: 129.2192 Evaluate side-chains 240 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 179 THR Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 249 MET Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 17 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 ASN A 346 ASN B 345 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.142825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.121026 restraints weight = 14112.713| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.05 r_work: 0.3451 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9798 Z= 0.180 Angle : 0.570 11.735 13265 Z= 0.301 Chirality : 0.044 0.334 1503 Planarity : 0.004 0.044 1674 Dihedral : 4.350 24.328 1316 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.52 % Allowed : 17.11 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.36 (0.24), residues: 1204 helix: 2.42 (0.25), residues: 424 sheet: 0.87 (0.28), residues: 300 loop : -0.47 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 208 TYR 0.019 0.002 TYR R 120 PHE 0.034 0.002 PHE R 53 TRP 0.013 0.002 TRP E 46 HIS 0.005 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 9793) covalent geometry : angle 0.56946 (13255) SS BOND : bond 0.00446 ( 5) SS BOND : angle 1.14063 ( 10) hydrogen bonds : bond 0.04624 ( 496) hydrogen bonds : angle 4.75033 ( 1416) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 221 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: R 90 LEU cc_start: 0.8130 (mt) cc_final: 0.7771 (tm) REVERT: R 249 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7422 (mpp) REVERT: R 254 LEU cc_start: 0.8386 (mt) cc_final: 0.8076 (mt) REVERT: A 197 LYS cc_start: 0.8770 (mtpt) cc_final: 0.8492 (mtpp) REVERT: A 225 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8408 (m) REVERT: A 245 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7315 (mm-30) REVERT: A 270 LYS cc_start: 0.8245 (mttt) cc_final: 0.7959 (mttp) REVERT: A 332 VAL cc_start: 0.8530 (t) cc_final: 0.8166 (m) REVERT: A 345 LYS cc_start: 0.8327 (mtpt) cc_final: 0.8049 (mtmm) REVERT: A 349 LYS cc_start: 0.8092 (ttmm) cc_final: 0.7883 (ttmm) REVERT: B 27 ARG cc_start: 0.7230 (mtt180) cc_final: 0.6868 (mtt180) REVERT: B 64 TYR cc_start: 0.8549 (m-80) cc_final: 0.8322 (m-80) REVERT: B 160 ASN cc_start: 0.8463 (t0) cc_final: 0.8214 (t0) REVERT: B 202 ARG cc_start: 0.7985 (mtp-110) cc_final: 0.7642 (mmm160) REVERT: B 239 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.7779 (m-80) REVERT: B 263 ASP cc_start: 0.7280 (t70) cc_final: 0.6914 (t70) REVERT: B 281 VAL cc_start: 0.8581 (t) cc_final: 0.8264 (p) REVERT: E 37 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8422 (ptt180) outliers start: 37 outliers final: 22 residues processed: 239 average time/residue: 0.4685 time to fit residues: 120.8932 Evaluate side-chains 243 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 179 THR Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 249 MET Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 8 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 ASN A 346 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.143930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.122392 restraints weight = 14056.019| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.06 r_work: 0.3458 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9798 Z= 0.152 Angle : 0.554 11.840 13265 Z= 0.291 Chirality : 0.043 0.350 1503 Planarity : 0.004 0.044 1674 Dihedral : 4.259 21.926 1316 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.23 % Allowed : 17.78 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.40 (0.24), residues: 1204 helix: 2.44 (0.25), residues: 424 sheet: 0.87 (0.29), residues: 300 loop : -0.40 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 142 TYR 0.017 0.002 TYR R 120 PHE 0.032 0.002 PHE R 53 TRP 0.015 0.002 TRP B 216 HIS 0.004 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9793) covalent geometry : angle 0.55330 (13255) SS BOND : bond 0.00381 ( 5) SS BOND : angle 1.03352 ( 10) hydrogen bonds : bond 0.04439 ( 496) hydrogen bonds : angle 4.71063 ( 1416) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: R 66 ILE cc_start: 0.8410 (mm) cc_final: 0.8030 (tp) REVERT: R 249 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7514 (mmm) REVERT: R 254 LEU cc_start: 0.8355 (mt) cc_final: 0.8046 (mt) REVERT: R 300 ILE cc_start: 0.7763 (tp) cc_final: 0.7546 (tp) REVERT: A 197 LYS cc_start: 0.8814 (mtpt) cc_final: 0.8521 (mtpp) REVERT: A 225 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8417 (m) REVERT: A 245 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7245 (mm-30) REVERT: A 270 LYS cc_start: 0.8273 (mttt) cc_final: 0.7993 (mttm) REVERT: A 332 VAL cc_start: 0.8537 (t) cc_final: 0.8189 (m) REVERT: A 345 LYS cc_start: 0.8274 (mtpt) cc_final: 0.7989 (mtmm) REVERT: A 349 LYS cc_start: 0.8091 (ttmm) cc_final: 0.7889 (ttmm) REVERT: B 27 ARG cc_start: 0.7284 (mtt180) cc_final: 0.6944 (mtt180) REVERT: B 64 TYR cc_start: 0.8572 (m-80) cc_final: 0.8372 (m-80) REVERT: B 160 ASN cc_start: 0.8470 (t0) cc_final: 0.8206 (t0) REVERT: B 202 ARG cc_start: 0.8035 (mtp-110) cc_final: 0.7687 (mmm160) REVERT: B 239 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: B 263 ASP cc_start: 0.7233 (t70) cc_final: 0.6848 (t70) REVERT: B 281 VAL cc_start: 0.8573 (t) cc_final: 0.8243 (p) REVERT: B 319 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8093 (ttm170) REVERT: E 37 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8430 (ptt180) outliers start: 34 outliers final: 24 residues processed: 230 average time/residue: 0.4760 time to fit residues: 118.0664 Evaluate side-chains 242 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 213 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 179 THR Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain R residue 220 ILE Chi-restraints excluded: chain R residue 249 MET Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 6 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 ASN A 346 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.143789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.122300 restraints weight = 13983.322| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.06 r_work: 0.3466 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9798 Z= 0.145 Angle : 0.554 11.703 13265 Z= 0.290 Chirality : 0.043 0.330 1503 Planarity : 0.004 0.044 1674 Dihedral : 4.211 21.095 1316 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.14 % Allowed : 18.54 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.24), residues: 1204 helix: 2.41 (0.25), residues: 426 sheet: 0.89 (0.29), residues: 300 loop : -0.31 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 142 TYR 0.016 0.002 TYR R 120 PHE 0.031 0.002 PHE R 53 TRP 0.015 0.002 TRP B 216 HIS 0.004 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9793) covalent geometry : angle 0.55317 (13255) SS BOND : bond 0.00377 ( 5) SS BOND : angle 1.05010 ( 10) hydrogen bonds : bond 0.04345 ( 496) hydrogen bonds : angle 4.66570 ( 1416) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 228 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: R 66 ILE cc_start: 0.8424 (mm) cc_final: 0.8049 (tp) REVERT: R 254 LEU cc_start: 0.8349 (mt) cc_final: 0.8055 (mt) REVERT: R 300 ILE cc_start: 0.7724 (tp) cc_final: 0.7519 (tp) REVERT: A 197 LYS cc_start: 0.8811 (mtpt) cc_final: 0.8518 (mtpp) REVERT: A 225 VAL cc_start: 0.8797 (OUTLIER) cc_final: 0.8425 (m) REVERT: A 245 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7231 (mm-30) REVERT: A 270 LYS cc_start: 0.8276 (mttt) cc_final: 0.7995 (mttp) REVERT: A 332 VAL cc_start: 0.8521 (t) cc_final: 0.8169 (m) REVERT: A 345 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7998 (mtmm) REVERT: B 27 ARG cc_start: 0.7291 (mtt180) cc_final: 0.6963 (mtt180) REVERT: B 64 TYR cc_start: 0.8570 (m-80) cc_final: 0.8365 (m-80) REVERT: B 160 ASN cc_start: 0.8466 (t0) cc_final: 0.8181 (t0) REVERT: B 202 ARG cc_start: 0.8011 (mtp-110) cc_final: 0.7624 (mmm160) REVERT: B 225 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7783 (tt0) REVERT: B 239 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.7742 (m-80) REVERT: B 263 ASP cc_start: 0.7242 (t70) cc_final: 0.6872 (t70) REVERT: B 272 ASP cc_start: 0.7889 (m-30) cc_final: 0.7682 (m-30) REVERT: B 281 VAL cc_start: 0.8570 (t) cc_final: 0.8247 (p) REVERT: B 319 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8078 (ttm170) REVERT: E 37 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8430 (ptt180) REVERT: E 219 LEU cc_start: 0.8251 (tp) cc_final: 0.7960 (tm) outliers start: 33 outliers final: 23 residues processed: 242 average time/residue: 0.4779 time to fit residues: 124.5466 Evaluate side-chains 251 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 179 THR Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain R residue 220 ILE Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 55 optimal weight: 0.6980 chunk 20 optimal weight: 0.0770 chunk 66 optimal weight: 0.4980 chunk 6 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 82 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 ASN A 346 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.144938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.123501 restraints weight = 13998.860| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.03 r_work: 0.3487 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9798 Z= 0.117 Angle : 0.539 11.362 13265 Z= 0.280 Chirality : 0.042 0.316 1503 Planarity : 0.003 0.044 1674 Dihedral : 4.089 20.130 1316 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.85 % Allowed : 19.30 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.24), residues: 1204 helix: 2.49 (0.25), residues: 427 sheet: 0.90 (0.29), residues: 302 loop : -0.26 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 142 TYR 0.014 0.001 TYR B 294 PHE 0.029 0.001 PHE R 156 TRP 0.018 0.001 TRP B 216 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9793) covalent geometry : angle 0.53821 (13255) SS BOND : bond 0.00286 ( 5) SS BOND : angle 0.93065 ( 10) hydrogen bonds : bond 0.04000 ( 496) hydrogen bonds : angle 4.58844 ( 1416) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 232 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 61 MET cc_start: 0.7265 (tpp) cc_final: 0.6865 (mmm) REVERT: R 66 ILE cc_start: 0.8456 (mm) cc_final: 0.8093 (tp) REVERT: R 231 ARG cc_start: 0.6756 (mtm-85) cc_final: 0.6355 (mtm-85) REVERT: R 249 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7338 (mpp) REVERT: R 254 LEU cc_start: 0.8359 (mt) cc_final: 0.8064 (mt) REVERT: R 295 MET cc_start: 0.7844 (mtm) cc_final: 0.7607 (mtm) REVERT: R 300 ILE cc_start: 0.7600 (tp) cc_final: 0.7392 (tp) REVERT: A 197 LYS cc_start: 0.8819 (mtpt) cc_final: 0.8503 (mtpp) REVERT: A 225 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8427 (m) REVERT: A 245 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7255 (mm-30) REVERT: A 277 LYS cc_start: 0.7624 (ttmm) cc_final: 0.7223 (ttmm) REVERT: B 27 ARG cc_start: 0.7225 (mtt180) cc_final: 0.6910 (mtt180) REVERT: B 160 ASN cc_start: 0.8463 (t0) cc_final: 0.8179 (t0) REVERT: B 225 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: B 239 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: B 263 ASP cc_start: 0.7213 (t70) cc_final: 0.6843 (t70) REVERT: B 272 ASP cc_start: 0.7870 (m-30) cc_final: 0.7656 (m-30) REVERT: B 281 VAL cc_start: 0.8570 (t) cc_final: 0.8252 (p) REVERT: B 319 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8038 (ttm170) REVERT: E 37 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8317 (ptt180) REVERT: E 219 LEU cc_start: 0.8282 (tp) cc_final: 0.7956 (tm) outliers start: 30 outliers final: 23 residues processed: 245 average time/residue: 0.5113 time to fit residues: 134.6537 Evaluate side-chains 262 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 233 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 179 THR Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain R residue 220 ILE Chi-restraints excluded: chain R residue 249 MET Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 1 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 96 optimal weight: 0.3980 chunk 104 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 ASN A 346 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.144323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.122985 restraints weight = 13897.634| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.02 r_work: 0.3479 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9798 Z= 0.133 Angle : 0.548 10.633 13265 Z= 0.285 Chirality : 0.043 0.294 1503 Planarity : 0.003 0.044 1674 Dihedral : 4.107 19.440 1316 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.04 % Allowed : 18.92 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.50 (0.24), residues: 1204 helix: 2.48 (0.25), residues: 427 sheet: 0.93 (0.29), residues: 300 loop : -0.33 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 142 TYR 0.014 0.001 TYR R 120 PHE 0.029 0.002 PHE R 156 TRP 0.015 0.002 TRP B 344 HIS 0.003 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9793) covalent geometry : angle 0.54744 (13255) SS BOND : bond 0.00333 ( 5) SS BOND : angle 0.91724 ( 10) hydrogen bonds : bond 0.04131 ( 496) hydrogen bonds : angle 4.59157 ( 1416) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4125.18 seconds wall clock time: 70 minutes 52.53 seconds (4252.53 seconds total)