Starting phenix.real_space_refine on Thu Feb 13 22:25:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xa3_33086/02_2025/7xa3_33086.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xa3_33086/02_2025/7xa3_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xa3_33086/02_2025/7xa3_33086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xa3_33086/02_2025/7xa3_33086.map" model { file = "/net/cci-nas-00/data/ceres_data/7xa3_33086/02_2025/7xa3_33086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xa3_33086/02_2025/7xa3_33086.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.74, per 1000 atoms: 0.60 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: 2.39 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.08 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: 2.70 Time building geometry restraints manager: 2.72 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: 0.490 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.280 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:10.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.490 ------------------------------------------------------------------------------- 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 9793 Z= 0.304 Angle : 0.850 10.720 13255 Z= 0.486 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.043 0.004 TRP E 110 HIS 0.009 0.002 HIS B 230 PHE 0.032 0.003 PHE A 354 TYR 0.031 0.003 TYR E 93 ARG 0.012 0.001 ARG B 319 *********************** 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 : 1.086 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: 0.7749 (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: 1.0757 time to fit residues: 329.1150 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 : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 35 optimal weight: 0.0270 chunk 56 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 A 346 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.149156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.127211 restraints weight = 14141.843| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.98 r_work: 0.3539 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9793 Z= 0.201 Angle : 0.564 7.407 13255 Z= 0.301 Chirality : 0.043 0.303 1503 Planarity : 0.004 0.042 1674 Dihedral : 4.250 18.411 1316 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.85 % Allowed : 10.84 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.23), residues: 1204 helix: 2.39 (0.24), residues: 431 sheet: 1.27 (0.29), residues: 282 loop : -0.68 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 174 HIS 0.003 0.001 HIS B 67 PHE 0.023 0.002 PHE R 53 TYR 0.018 0.002 TYR R 124 ARG 0.007 0.001 ARG R 231 *********************** 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 274 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 244 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 66 ILE cc_start: 0.8329 (mt) cc_final: 0.8027 (tp) REVERT: R 156 PHE cc_start: 0.7124 (t80) cc_final: 0.6917 (t80) REVERT: R 205 MET cc_start: 0.7988 (tpp) cc_final: 0.7655 (tpp) REVERT: R 254 LEU cc_start: 0.8246 (mt) cc_final: 0.7949 (mt) REVERT: R 312 PHE cc_start: 0.7561 (t80) cc_final: 0.7076 (t80) REVERT: A 197 LYS cc_start: 0.8766 (mtpt) cc_final: 0.8495 (mtpp) REVERT: A 245 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7272 (mm-30) REVERT: A 276 GLU cc_start: 0.6725 (tp30) cc_final: 0.6488 (tp30) REVERT: A 332 VAL cc_start: 0.8466 (t) cc_final: 0.8246 (m) REVERT: A 349 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7763 (ttmm) REVERT: B 24 ARG cc_start: 0.6614 (ttp80) cc_final: 0.6361 (ttp80) REVERT: B 27 ARG cc_start: 0.7183 (mtt180) cc_final: 0.6949 (mtt180) REVERT: B 148 THR cc_start: 0.8596 (p) cc_final: 0.8216 (m) REVERT: B 180 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7509 (mm-40) REVERT: B 193 MET cc_start: 0.8245 (mmm) cc_final: 0.7591 (mmm) REVERT: B 270 SER cc_start: 0.7817 (t) cc_final: 0.7538 (m) REVERT: B 272 ASP cc_start: 0.8024 (m-30) cc_final: 0.7754 (m-30) REVERT: B 281 VAL cc_start: 0.8509 (t) cc_final: 0.8154 (p) REVERT: B 319 ARG cc_start: 0.8274 (ttt90) cc_final: 0.8049 (ttm-80) REVERT: B 343 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8414 (mm) REVERT: B 345 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7661 (m-40) REVERT: E 20 SER cc_start: 0.8341 (p) cc_final: 0.8127 (m) REVERT: E 158 SER cc_start: 0.8634 (t) cc_final: 0.8394 (m) REVERT: E 191 ARG cc_start: 0.7811 (mtt180) cc_final: 0.7592 (mtm180) outliers start: 30 outliers final: 16 residues processed: 256 average time/residue: 1.1428 time to fit residues: 315.3344 Evaluate side-chains 256 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 238 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 191 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 343 ILE 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 29 SER 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 0.0670 chunk 39 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.148522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.126270 restraints weight = 14235.616| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.08 r_work: 0.3510 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9793 Z= 0.190 Angle : 0.538 8.627 13255 Z= 0.285 Chirality : 0.043 0.362 1503 Planarity : 0.004 0.040 1674 Dihedral : 4.161 18.041 1316 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.76 % Allowed : 12.83 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.23), residues: 1204 helix: 2.65 (0.24), residues: 426 sheet: 1.18 (0.29), residues: 288 loop : -0.60 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 174 HIS 0.003 0.001 HIS B 67 PHE 0.013 0.001 PHE A 189 TYR 0.015 0.002 TYR R 124 ARG 0.008 0.000 ARG B 142 *********************** 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 278 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 249 time to evaluate : 1.213 Fit side-chains revert: symmetry clash REVERT: R 61 MET cc_start: 0.7152 (tpp) cc_final: 0.6939 (tpp) REVERT: R 90 LEU cc_start: 0.8035 (mt) cc_final: 0.7720 (tm) REVERT: R 147 PHE cc_start: 0.8511 (t80) cc_final: 0.7987 (t80) REVERT: R 156 PHE cc_start: 0.7132 (t80) cc_final: 0.6916 (t80) REVERT: R 205 MET cc_start: 0.8028 (tpp) cc_final: 0.7529 (tpp) REVERT: R 254 LEU cc_start: 0.8326 (mt) cc_final: 0.7987 (mt) REVERT: R 312 PHE cc_start: 0.7502 (t80) cc_final: 0.6948 (t80) REVERT: A 10 LYS cc_start: 0.8230 (mttp) cc_final: 0.8015 (mmtm) REVERT: A 197 LYS cc_start: 0.8777 (mtpt) cc_final: 0.8493 (mtpp) REVERT: A 245 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7270 (mm-30) REVERT: A 276 GLU cc_start: 0.6814 (tp30) cc_final: 0.6602 (tp30) REVERT: A 312 LYS cc_start: 0.8061 (mmtt) cc_final: 0.7796 (mtmm) REVERT: A 332 VAL cc_start: 0.8512 (t) cc_final: 0.8248 (m) REVERT: A 349 LYS cc_start: 0.7960 (ttmm) cc_final: 0.7741 (ttmm) REVERT: B 27 ARG cc_start: 0.7081 (mtt180) cc_final: 0.6671 (mtt180) REVERT: B 148 THR cc_start: 0.8578 (p) cc_final: 0.8228 (m) REVERT: B 180 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7712 (mm-40) REVERT: B 217 ASP cc_start: 0.7765 (t0) cc_final: 0.7337 (p0) REVERT: B 256 ARG cc_start: 0.8463 (mtt90) cc_final: 0.8177 (mtt-85) REVERT: B 263 ASP cc_start: 0.7044 (t70) cc_final: 0.6636 (t70) REVERT: B 270 SER cc_start: 0.7861 (t) cc_final: 0.7558 (m) REVERT: B 272 ASP cc_start: 0.8005 (m-30) cc_final: 0.7741 (m-30) REVERT: B 281 VAL cc_start: 0.8505 (t) cc_final: 0.8165 (p) REVERT: B 343 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8434 (mm) REVERT: E 158 SER cc_start: 0.8709 (t) cc_final: 0.8456 (m) outliers start: 29 outliers final: 15 residues processed: 258 average time/residue: 1.1378 time to fit residues: 315.8332 Evaluate side-chains 257 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 241 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 66 MET 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 45 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 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 285 GLN L 6 ASN A 346 ASN B 264 GLN B 271 HIS B 345 ASN E 232 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.145603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.123273 restraints weight = 13958.485| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.06 r_work: 0.3480 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9793 Z= 0.218 Angle : 0.548 9.779 13255 Z= 0.289 Chirality : 0.043 0.353 1503 Planarity : 0.004 0.041 1674 Dihedral : 4.178 15.537 1316 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.23 % Allowed : 13.88 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.23), residues: 1204 helix: 2.70 (0.24), residues: 424 sheet: 1.09 (0.28), residues: 288 loop : -0.55 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 174 HIS 0.005 0.001 HIS B 67 PHE 0.017 0.002 PHE R 53 TYR 0.016 0.002 TYR R 120 ARG 0.006 0.000 ARG B 142 *********************** 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 267 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 1.029 Fit side-chains REVERT: R 66 ILE cc_start: 0.8449 (mm) cc_final: 0.8124 (tp) REVERT: R 90 LEU cc_start: 0.8014 (mt) cc_final: 0.7733 (tm) REVERT: R 156 PHE cc_start: 0.7155 (t80) cc_final: 0.6937 (t80) REVERT: R 254 LEU cc_start: 0.8358 (mt) cc_final: 0.8012 (mt) REVERT: R 263 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7611 (tt) REVERT: R 312 PHE cc_start: 0.7409 (t80) cc_final: 0.7032 (t80) REVERT: A 197 LYS cc_start: 0.8783 (mtpt) cc_final: 0.8481 (mtpp) REVERT: A 245 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7356 (mm-30) REVERT: A 251 ASP cc_start: 0.8163 (t0) cc_final: 0.7941 (t0) REVERT: A 276 GLU cc_start: 0.6951 (tp30) cc_final: 0.6703 (tp30) REVERT: A 309 ASP cc_start: 0.7545 (t0) cc_final: 0.7342 (t70) REVERT: A 312 LYS cc_start: 0.8065 (mmtt) cc_final: 0.7782 (mtmm) REVERT: A 332 VAL cc_start: 0.8510 (t) cc_final: 0.8209 (m) REVERT: A 349 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7755 (ttmm) REVERT: B 24 ARG cc_start: 0.6569 (ttp80) cc_final: 0.6161 (mtp-110) REVERT: B 27 ARG cc_start: 0.7090 (mtt180) cc_final: 0.6742 (mtt180) REVERT: B 148 THR cc_start: 0.8566 (p) cc_final: 0.8222 (m) REVERT: B 202 ARG cc_start: 0.7931 (mtp-110) cc_final: 0.7649 (mmm160) REVERT: B 263 ASP cc_start: 0.7162 (t70) cc_final: 0.6810 (t70) REVERT: B 270 SER cc_start: 0.7915 (t) cc_final: 0.7637 (m) REVERT: B 281 VAL cc_start: 0.8536 (t) cc_final: 0.8219 (p) REVERT: B 343 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8403 (mm) REVERT: E 37 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8217 (ptt180) REVERT: E 158 SER cc_start: 0.8747 (t) cc_final: 0.8474 (m) outliers start: 34 outliers final: 15 residues processed: 245 average time/residue: 1.1304 time to fit residues: 297.6234 Evaluate side-chains 230 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 212 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 267 MET Chi-restraints excluded: chain B residue 268 THR 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 210 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 116 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 104 ASN R 285 GLN A 346 ASN B 264 GLN B 271 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.145332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.123214 restraints weight = 14081.982| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.07 r_work: 0.3479 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9793 Z= 0.196 Angle : 0.536 10.692 13255 Z= 0.281 Chirality : 0.043 0.335 1503 Planarity : 0.003 0.042 1674 Dihedral : 4.129 19.578 1316 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.14 % Allowed : 16.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.24), residues: 1204 helix: 2.72 (0.24), residues: 424 sheet: 0.96 (0.28), residues: 300 loop : -0.47 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 216 HIS 0.003 0.001 HIS E 34 PHE 0.021 0.001 PHE R 53 TYR 0.014 0.002 TYR R 120 ARG 0.010 0.000 ARG R 231 *********************** 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 248 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 1.110 Fit side-chains REVERT: R 156 PHE cc_start: 0.7142 (t80) cc_final: 0.6921 (t80) REVERT: R 254 LEU cc_start: 0.8352 (mt) cc_final: 0.8004 (mt) REVERT: R 312 PHE cc_start: 0.7496 (t80) cc_final: 0.6943 (t80) REVERT: A 197 LYS cc_start: 0.8793 (mtpt) cc_final: 0.8509 (mtpp) REVERT: A 245 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7308 (mm-30) REVERT: A 251 ASP cc_start: 0.8164 (t0) cc_final: 0.7961 (t0) REVERT: A 270 LYS cc_start: 0.8234 (mttt) cc_final: 0.7952 (mttm) REVERT: A 276 GLU cc_start: 0.7065 (tp30) cc_final: 0.6825 (tp30) REVERT: A 309 ASP cc_start: 0.7576 (t0) cc_final: 0.7362 (t70) REVERT: A 312 LYS cc_start: 0.8058 (mmtt) cc_final: 0.7821 (mttp) REVERT: A 332 VAL cc_start: 0.8440 (t) cc_final: 0.8125 (m) REVERT: A 345 LYS cc_start: 0.8306 (mtpt) cc_final: 0.8029 (mtmm) REVERT: A 349 LYS cc_start: 0.8013 (ttmm) cc_final: 0.7797 (ttmm) REVERT: B 24 ARG cc_start: 0.6531 (ttp80) cc_final: 0.6239 (ttp80) REVERT: B 27 ARG cc_start: 0.7070 (mtt180) cc_final: 0.6725 (mtt180) REVERT: B 148 THR cc_start: 0.8569 (p) cc_final: 0.8236 (m) REVERT: B 202 ARG cc_start: 0.7963 (mtp-110) cc_final: 0.7671 (mmm160) REVERT: B 217 ASP cc_start: 0.7784 (t0) cc_final: 0.7374 (p0) REVERT: B 263 ASP cc_start: 0.7203 (t70) cc_final: 0.6830 (t70) REVERT: B 270 SER cc_start: 0.7950 (t) cc_final: 0.7600 (m) REVERT: B 281 VAL cc_start: 0.8548 (t) cc_final: 0.8240 (p) REVERT: E 37 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8252 (ptt180) outliers start: 33 outliers final: 18 residues processed: 230 average time/residue: 1.0896 time to fit residues: 270.6327 Evaluate side-chains 234 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 215 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 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 B residue 133 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 67 optimal weight: 0.0980 chunk 45 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 34 optimal weight: 0.0570 chunk 96 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 60 optimal weight: 0.0020 chunk 104 optimal weight: 0.8980 overall best weight: 0.1906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.147959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.125933 restraints weight = 14218.921| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.07 r_work: 0.3515 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 9793 Z= 0.128 Angle : 0.490 10.290 13255 Z= 0.256 Chirality : 0.041 0.327 1503 Planarity : 0.003 0.040 1674 Dihedral : 3.866 19.146 1316 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.47 % Allowed : 16.83 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1204 helix: 2.87 (0.25), residues: 427 sheet: 0.98 (0.28), residues: 303 loop : -0.33 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 216 HIS 0.003 0.000 HIS R 100 PHE 0.032 0.001 PHE R 53 TYR 0.010 0.001 TYR B 294 ARG 0.008 0.000 ARG R 231 *********************** 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 253 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 79 ILE cc_start: 0.8025 (mt) cc_final: 0.7661 (mt) REVERT: R 90 LEU cc_start: 0.7949 (mt) cc_final: 0.7619 (tm) REVERT: R 156 PHE cc_start: 0.6989 (t80) cc_final: 0.6767 (t80) REVERT: R 177 ILE cc_start: 0.8170 (mm) cc_final: 0.7954 (mm) REVERT: R 254 LEU cc_start: 0.8361 (mt) cc_final: 0.7978 (mt) REVERT: R 312 PHE cc_start: 0.7505 (t80) cc_final: 0.6951 (t80) REVERT: A 197 LYS cc_start: 0.8756 (mtpt) cc_final: 0.8450 (ttmm) REVERT: A 245 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7314 (mm-30) REVERT: A 251 ASP cc_start: 0.8142 (t0) cc_final: 0.7919 (t0) REVERT: A 276 GLU cc_start: 0.6924 (tp30) cc_final: 0.6706 (tp30) REVERT: A 309 ASP cc_start: 0.7532 (t0) cc_final: 0.7322 (t70) REVERT: A 312 LYS cc_start: 0.7999 (mmtt) cc_final: 0.7765 (mttp) REVERT: A 345 LYS cc_start: 0.8210 (mtpt) cc_final: 0.7948 (mtmm) REVERT: A 349 LYS cc_start: 0.8010 (ttmm) cc_final: 0.7793 (ttmm) REVERT: B 24 ARG cc_start: 0.6557 (ttp80) cc_final: 0.6098 (mtp-110) REVERT: B 27 ARG cc_start: 0.6933 (mtt180) cc_final: 0.6649 (mtt180) REVERT: B 94 LYS cc_start: 0.8624 (mttm) cc_final: 0.8418 (mtmt) REVERT: B 148 THR cc_start: 0.8541 (p) cc_final: 0.8230 (m) REVERT: B 193 MET cc_start: 0.8187 (mmm) cc_final: 0.7598 (mmm) REVERT: B 217 ASP cc_start: 0.7730 (t0) cc_final: 0.7345 (p0) REVERT: B 256 ARG cc_start: 0.8410 (mtt90) cc_final: 0.8145 (mtt-85) REVERT: B 263 ASP cc_start: 0.7068 (t70) cc_final: 0.6696 (t70) REVERT: B 270 SER cc_start: 0.7820 (t) cc_final: 0.7530 (m) REVERT: B 281 VAL cc_start: 0.8551 (t) cc_final: 0.8256 (p) REVERT: E 158 SER cc_start: 0.8720 (t) cc_final: 0.8508 (m) outliers start: 26 outliers final: 16 residues processed: 237 average time/residue: 1.1053 time to fit residues: 281.9817 Evaluate side-chains 239 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 223 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain R residue 281 SER 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 B residue 133 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 29 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 66 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 78 optimal weight: 0.0970 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN B 264 GLN B 345 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.143331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.121250 restraints weight = 14095.799| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.06 r_work: 0.3454 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9793 Z= 0.293 Angle : 0.577 11.263 13255 Z= 0.306 Chirality : 0.045 0.340 1503 Planarity : 0.004 0.042 1674 Dihedral : 4.241 19.840 1316 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.14 % Allowed : 17.21 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.24), residues: 1204 helix: 2.60 (0.25), residues: 425 sheet: 0.90 (0.28), residues: 300 loop : -0.33 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 87 HIS 0.006 0.002 HIS B 230 PHE 0.030 0.002 PHE R 53 TYR 0.021 0.002 TYR R 120 ARG 0.006 0.000 ARG B 309 *********************** 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 266 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 233 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: R 90 LEU cc_start: 0.8106 (mt) cc_final: 0.7752 (tm) REVERT: R 156 PHE cc_start: 0.7241 (t80) cc_final: 0.7014 (t80) REVERT: R 249 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7350 (mpp) REVERT: R 254 LEU cc_start: 0.8406 (mt) cc_final: 0.8056 (mt) REVERT: A 197 LYS cc_start: 0.8788 (mtpt) cc_final: 0.8504 (mtpp) REVERT: A 245 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7297 (mm-30) REVERT: A 251 ASP cc_start: 0.8108 (t0) cc_final: 0.7870 (t0) REVERT: A 276 GLU cc_start: 0.7125 (tp30) cc_final: 0.6925 (tp30) REVERT: A 309 ASP cc_start: 0.7609 (t0) cc_final: 0.7405 (t70) REVERT: A 312 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7858 (mttp) REVERT: A 332 VAL cc_start: 0.8513 (t) cc_final: 0.8218 (m) REVERT: A 345 LYS cc_start: 0.8313 (mtpt) cc_final: 0.8038 (mtmm) REVERT: A 349 LYS cc_start: 0.8112 (ttmm) cc_final: 0.7900 (ttmm) REVERT: B 27 ARG cc_start: 0.7262 (mtt180) cc_final: 0.6905 (mtt180) REVERT: B 64 TYR cc_start: 0.8547 (m-80) cc_final: 0.8341 (m-80) REVERT: B 73 ARG cc_start: 0.8754 (ttt180) cc_final: 0.8504 (ttt180) REVERT: B 148 THR cc_start: 0.8594 (p) cc_final: 0.8288 (m) REVERT: B 186 THR cc_start: 0.8148 (p) cc_final: 0.7859 (m) REVERT: B 239 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: B 263 ASP cc_start: 0.7273 (t70) cc_final: 0.6902 (t70) REVERT: B 281 VAL cc_start: 0.8591 (t) cc_final: 0.8272 (p) REVERT: B 343 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8400 (mm) REVERT: E 230 MET cc_start: 0.8168 (tmm) cc_final: 0.7916 (ttm) outliers start: 33 outliers final: 18 residues processed: 248 average time/residue: 1.0348 time to fit residues: 277.8122 Evaluate side-chains 249 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 209 LYS 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 239 PHE 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 B residue 343 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 93 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 99 optimal weight: 0.4980 chunk 104 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.144903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.122900 restraints weight = 14288.445| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.07 r_work: 0.3475 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9793 Z= 0.181 Angle : 0.527 11.105 13255 Z= 0.277 Chirality : 0.043 0.320 1503 Planarity : 0.003 0.042 1674 Dihedral : 4.084 21.058 1316 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.85 % Allowed : 18.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.24), residues: 1204 helix: 2.72 (0.25), residues: 423 sheet: 0.97 (0.28), residues: 296 loop : -0.38 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 344 HIS 0.003 0.001 HIS B 67 PHE 0.030 0.002 PHE R 53 TYR 0.017 0.001 TYR B 294 ARG 0.006 0.000 ARG B 309 *********************** 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 261 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 231 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: R 90 LEU cc_start: 0.8104 (mt) cc_final: 0.7756 (tm) REVERT: R 112 MET cc_start: 0.4405 (ptt) cc_final: 0.3959 (ptt) REVERT: R 156 PHE cc_start: 0.7161 (t80) cc_final: 0.6937 (t80) REVERT: R 177 ILE cc_start: 0.8148 (mm) cc_final: 0.7891 (mm) REVERT: R 249 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7264 (mpp) REVERT: R 254 LEU cc_start: 0.8396 (mt) cc_final: 0.8080 (mt) REVERT: A 197 LYS cc_start: 0.8799 (mtpt) cc_final: 0.8483 (mtpp) REVERT: A 245 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7271 (mm-30) REVERT: A 251 ASP cc_start: 0.8082 (t0) cc_final: 0.7828 (t0) REVERT: A 276 GLU cc_start: 0.7041 (tp30) cc_final: 0.6828 (tp30) REVERT: A 309 ASP cc_start: 0.7569 (t0) cc_final: 0.7360 (t70) REVERT: A 312 LYS cc_start: 0.8045 (mmtt) cc_final: 0.7727 (mtmm) REVERT: A 332 VAL cc_start: 0.8429 (t) cc_final: 0.8150 (m) REVERT: A 349 LYS cc_start: 0.8104 (ttmm) cc_final: 0.7888 (ttmm) REVERT: B 24 ARG cc_start: 0.6562 (ttp80) cc_final: 0.6140 (mtp-110) REVERT: B 27 ARG cc_start: 0.7204 (mtt180) cc_final: 0.6885 (mtt180) REVERT: B 148 THR cc_start: 0.8594 (p) cc_final: 0.8263 (m) REVERT: B 160 ASN cc_start: 0.8512 (t0) cc_final: 0.8216 (t0) REVERT: B 193 MET cc_start: 0.8178 (mmm) cc_final: 0.7561 (mmm) REVERT: B 202 ARG cc_start: 0.7959 (mtp-110) cc_final: 0.7592 (mmm160) REVERT: B 239 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: B 263 ASP cc_start: 0.7281 (t70) cc_final: 0.6895 (t70) REVERT: B 281 VAL cc_start: 0.8577 (t) cc_final: 0.8268 (p) REVERT: B 343 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8391 (mm) outliers start: 30 outliers final: 22 residues processed: 244 average time/residue: 1.1311 time to fit residues: 296.8756 Evaluate side-chains 254 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 229 time to evaluate : 1.349 ------------------------------------------------------------------------------- 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 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 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 239 PHE 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 B residue 343 ILE 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 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 20 optimal weight: 0.0570 chunk 55 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.144717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.123038 restraints weight = 13934.123| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.04 r_work: 0.3481 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9793 Z= 0.195 Angle : 0.537 11.443 13255 Z= 0.282 Chirality : 0.043 0.314 1503 Planarity : 0.004 0.058 1674 Dihedral : 4.089 18.826 1316 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.47 % Allowed : 18.92 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.24), residues: 1204 helix: 2.72 (0.24), residues: 423 sheet: 0.95 (0.28), residues: 300 loop : -0.35 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 344 HIS 0.003 0.001 HIS B 59 PHE 0.028 0.002 PHE R 53 TYR 0.014 0.001 TYR R 120 ARG 0.014 0.000 ARG R 231 *********************** 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 256 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: R 90 LEU cc_start: 0.8123 (mt) cc_final: 0.7777 (tm) REVERT: R 112 MET cc_start: 0.4328 (ptt) cc_final: 0.3921 (ptt) REVERT: R 156 PHE cc_start: 0.7169 (t80) cc_final: 0.6945 (t80) REVERT: R 177 ILE cc_start: 0.8155 (mm) cc_final: 0.7923 (mm) REVERT: R 254 LEU cc_start: 0.8382 (mt) cc_final: 0.8077 (mt) REVERT: A 197 LYS cc_start: 0.8801 (mtpt) cc_final: 0.8482 (mtpp) REVERT: A 245 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7315 (mm-30) REVERT: A 251 ASP cc_start: 0.8085 (t0) cc_final: 0.7829 (t0) REVERT: A 277 LYS cc_start: 0.7555 (ttmm) cc_final: 0.7310 (ttmm) REVERT: A 309 ASP cc_start: 0.7615 (t0) cc_final: 0.7414 (t70) REVERT: A 312 LYS cc_start: 0.8062 (mmtt) cc_final: 0.7792 (mttm) REVERT: A 332 VAL cc_start: 0.8433 (t) cc_final: 0.8158 (m) REVERT: A 349 LYS cc_start: 0.8103 (ttmm) cc_final: 0.7899 (ttmm) REVERT: B 27 ARG cc_start: 0.7211 (mtt180) cc_final: 0.6879 (mtt180) REVERT: B 64 TYR cc_start: 0.8581 (m-80) cc_final: 0.8369 (m-80) REVERT: B 160 ASN cc_start: 0.8509 (t0) cc_final: 0.8193 (t0) REVERT: B 193 MET cc_start: 0.8183 (mmm) cc_final: 0.7550 (mmm) REVERT: B 202 ARG cc_start: 0.7922 (mtp-110) cc_final: 0.7563 (mmm160) REVERT: B 239 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.7843 (m-80) REVERT: B 263 ASP cc_start: 0.7209 (t70) cc_final: 0.6846 (t70) REVERT: B 272 ASP cc_start: 0.7889 (m-30) cc_final: 0.7668 (m-30) REVERT: B 281 VAL cc_start: 0.8583 (t) cc_final: 0.8270 (p) REVERT: B 343 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8417 (mm) REVERT: E 230 MET cc_start: 0.8159 (tmm) cc_final: 0.7903 (ttm) outliers start: 26 outliers final: 21 residues processed: 242 average time/residue: 1.1407 time to fit residues: 297.1310 Evaluate side-chains 253 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 230 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 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 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 217 ASP 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 343 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 11 VAL 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 18 optimal weight: 0.0770 chunk 68 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 110 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 109 optimal weight: 0.0070 chunk 74 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 overall best weight: 0.2956 ------------------------------------------------------------------------------- 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** ** B 345 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 = 0.3918 r_free = 0.3918 target = 0.146845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.125254 restraints weight = 14191.754| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.07 r_work: 0.3506 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9793 Z= 0.147 Angle : 0.526 12.685 13255 Z= 0.272 Chirality : 0.042 0.279 1503 Planarity : 0.003 0.055 1674 Dihedral : 3.906 17.442 1316 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.28 % Allowed : 19.11 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.24), residues: 1204 helix: 2.79 (0.25), residues: 425 sheet: 0.96 (0.28), residues: 300 loop : -0.29 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 216 HIS 0.002 0.000 HIS E 34 PHE 0.026 0.001 PHE R 53 TYR 0.016 0.001 TYR R 124 ARG 0.014 0.000 ARG R 231 ********************** 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 254 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 230 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: R 90 LEU cc_start: 0.8116 (mt) cc_final: 0.7776 (tm) REVERT: R 112 MET cc_start: 0.4192 (ptt) cc_final: 0.3862 (ptt) REVERT: R 156 PHE cc_start: 0.7072 (t80) cc_final: 0.6843 (t80) REVERT: R 177 ILE cc_start: 0.8116 (mm) cc_final: 0.7826 (mm) REVERT: R 254 LEU cc_start: 0.8354 (mt) cc_final: 0.7951 (mt) REVERT: R 295 MET cc_start: 0.7708 (mtm) cc_final: 0.7487 (mtm) REVERT: R 312 PHE cc_start: 0.7505 (t80) cc_final: 0.6938 (t80) REVERT: A 197 LYS cc_start: 0.8818 (mtpt) cc_final: 0.8495 (mtpp) REVERT: A 245 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7239 (mm-30) REVERT: A 251 ASP cc_start: 0.8072 (t0) cc_final: 0.7838 (t0) REVERT: A 277 LYS cc_start: 0.7582 (ttmm) cc_final: 0.7302 (ttmm) REVERT: A 309 ASP cc_start: 0.7581 (t0) cc_final: 0.7379 (t70) REVERT: A 312 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7724 (mtmm) REVERT: A 349 LYS cc_start: 0.8110 (ttmm) cc_final: 0.7907 (ttmm) REVERT: B 24 ARG cc_start: 0.6387 (ttp80) cc_final: 0.6141 (ttp80) REVERT: B 27 ARG cc_start: 0.7174 (mtt180) cc_final: 0.6868 (mtt180) REVERT: B 193 MET cc_start: 0.8162 (mmm) cc_final: 0.7664 (mmm) REVERT: B 202 ARG cc_start: 0.7902 (mtp-110) cc_final: 0.7550 (mmm160) REVERT: B 239 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.7769 (m-80) REVERT: B 256 ARG cc_start: 0.8408 (mtt90) cc_final: 0.8141 (mtt-85) REVERT: B 263 ASP cc_start: 0.7164 (t70) cc_final: 0.6776 (t70) REVERT: B 272 ASP cc_start: 0.7930 (m-30) cc_final: 0.7704 (m-30) REVERT: B 281 VAL cc_start: 0.8562 (t) cc_final: 0.8251 (p) REVERT: B 319 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8045 (ttm170) REVERT: B 343 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8417 (mm) outliers start: 24 outliers final: 18 residues processed: 241 average time/residue: 1.1298 time to fit residues: 292.7021 Evaluate side-chains 251 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 230 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 208 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 212 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 47 ARG 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 268 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 73 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.0170 chunk 66 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 71 optimal weight: 0.0270 chunk 88 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 ** 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 = 0.3902 r_free = 0.3902 target = 0.145345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.123834 restraints weight = 14050.566| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.03 r_work: 0.3491 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9793 Z= 0.179 Angle : 0.538 11.190 13255 Z= 0.280 Chirality : 0.042 0.269 1503 Planarity : 0.003 0.054 1674 Dihedral : 3.939 16.691 1316 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.57 % Allowed : 19.01 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.24), residues: 1204 helix: 2.74 (0.24), residues: 425 sheet: 0.94 (0.29), residues: 302 loop : -0.25 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 344 HIS 0.003 0.001 HIS B 59 PHE 0.024 0.001 PHE R 53 TYR 0.013 0.001 TYR B 294 ARG 0.013 0.000 ARG R 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8559.44 seconds wall clock time: 151 minutes 32.02 seconds (9092.02 seconds total)