Starting phenix.real_space_refine on Sun May 3 00:32:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n0e_48782/05_2026/9n0e_48782.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n0e_48782/05_2026/9n0e_48782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n0e_48782/05_2026/9n0e_48782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n0e_48782/05_2026/9n0e_48782.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n0e_48782/05_2026/9n0e_48782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n0e_48782/05_2026/9n0e_48782.map" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.054 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 56 5.16 5 C 5898 2.51 5 N 1636 2.21 5 O 1714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9304 Number of models: 1 Model: "" Number of chains: 8 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: "P" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 230 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 3161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3161 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 15, 'TRANS': 375} Chain breaks: 1 Chain: "A" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1894 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 1.99, per 1000 atoms: 0.21 Number of scatterers: 9304 At special positions: 0 Unit cell: (81.6, 99.45, 173.4, 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 56 16.00 O 1714 8.00 N 1636 7.00 C 5898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 67 " distance=2.04 Simple disulfide: pdb=" SG CYS R 58 " - pdb=" SG CYS R 100 " distance=2.03 Simple disulfide: pdb=" SG CYS R 81 " - pdb=" SG CYS R 121 " distance=2.03 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 407.9 milliseconds 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2190 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 11 sheets defined 45.2% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.514A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'P' and resid 2 through 27 Processing helix chain 'G' and resid 8 through 25 removed outlier: 4.159A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 27 through 46 removed outlier: 3.775A pdb=" N PHE R 31 " --> pdb=" O GLN R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 50 Processing helix chain 'R' and resid 87 through 92 removed outlier: 3.690A pdb=" N VAL R 91 " --> pdb=" O TRP R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 166 removed outlier: 3.900A pdb=" N ILE R 128 " --> pdb=" O ASP R 124 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU R 129 " --> pdb=" O GLY R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 203 Processing helix chain 'R' and resid 208 through 216 Processing helix chain 'R' and resid 217 through 220 Processing helix chain 'R' and resid 221 through 254 Processing helix chain 'R' and resid 263 through 273 Processing helix chain 'R' and resid 273 through 290 removed outlier: 3.780A pdb=" N LEU R 277 " --> pdb=" O GLY R 273 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE R 278 " --> pdb=" O ALA R 274 " (cutoff:3.500A) Proline residue: R 281 - end of helix Processing helix chain 'R' and resid 300 through 335 removed outlier: 3.755A pdb=" N ILE R 306 " --> pdb=" O GLY R 302 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU R 307 " --> pdb=" O PHE R 303 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG R 308 " --> pdb=" O TRP R 304 " (cutoff:3.500A) Proline residue: R 310 - end of helix Processing helix chain 'R' and resid 344 through 359 Proline residue: R 356 - end of helix Processing helix chain 'R' and resid 362 through 367 removed outlier: 4.516A pdb=" N PHE R 367 " --> pdb=" O VAL R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 374 through 401 removed outlier: 4.279A pdb=" N GLY R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 421 Processing helix chain 'A' and resid 10 through 39 removed outlier: 3.863A pdb=" N ASN A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 52 removed outlier: 4.236A pdb=" N GLY A 52 " --> pdb=" O GLY A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 52' Processing helix chain 'A' and resid 53 through 58 removed outlier: 3.727A pdb=" N LYS A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.733A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.633A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.563A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.614A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.598A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.920A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.771A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.679A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.544A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.765A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.975A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.625A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 76 through 80 Processing sheet with id=AB2, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.619A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3053 1.34 - 1.46: 2288 1.46 - 1.58: 4083 1.58 - 1.70: 0 1.70 - 1.81: 77 Bond restraints: 9501 Sorted by residual: bond pdb=" N ARG R 94 " pdb=" CA ARG R 94 " ideal model delta sigma weight residual 1.453 1.485 -0.031 1.22e-02 6.72e+03 6.56e+00 bond pdb=" N ALA R 26 " pdb=" CA ALA R 26 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.23e-02 6.61e+03 3.56e+00 bond pdb=" N SER B 2 " pdb=" CA SER B 2 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 bond pdb=" N THR A 9 " pdb=" CA THR A 9 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N HIS P 1 " pdb=" CA HIS P 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 ... (remaining 9496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.90: 12358 0.90 - 1.80: 396 1.80 - 2.70: 62 2.70 - 3.60: 39 3.60 - 4.50: 10 Bond angle restraints: 12865 Sorted by residual: angle pdb=" CA ARG R 94 " pdb=" C ARG R 94 " pdb=" O ARG R 94 " ideal model delta sigma weight residual 121.89 117.72 4.17 1.17e+00 7.31e-01 1.27e+01 angle pdb=" CA ALA R 26 " pdb=" C ALA R 26 " pdb=" O ALA R 26 " ideal model delta sigma weight residual 120.42 117.94 2.48 1.06e+00 8.90e-01 5.49e+00 angle pdb=" C VAL R 285 " pdb=" CA VAL R 285 " pdb=" CB VAL R 285 " ideal model delta sigma weight residual 112.26 108.50 3.76 1.62e+00 3.81e-01 5.40e+00 angle pdb=" C GLN R 42 " pdb=" N CYS R 43 " pdb=" CA CYS R 43 " ideal model delta sigma weight residual 121.14 117.09 4.05 1.75e+00 3.27e-01 5.35e+00 angle pdb=" CA TYR R 145 " pdb=" CB TYR R 145 " pdb=" CG TYR R 145 " ideal model delta sigma weight residual 113.90 118.00 -4.10 1.80e+00 3.09e-01 5.20e+00 ... (remaining 12860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 5154 17.52 - 35.04: 394 35.04 - 52.56: 56 52.56 - 70.08: 18 70.08 - 87.60: 13 Dihedral angle restraints: 5635 sinusoidal: 2247 harmonic: 3388 Sorted by residual: dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -158.17 -21.83 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CG ARG N 118 " pdb=" CD ARG N 118 " pdb=" NE ARG N 118 " pdb=" CZ ARG N 118 " ideal model delta sinusoidal sigma weight residual 180.00 136.66 43.34 2 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" CA CYS R 67 " pdb=" C CYS R 67 " pdb=" N TRP R 68 " pdb=" CA TRP R 68 " ideal model delta harmonic sigma weight residual 180.00 -164.18 -15.82 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 5632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 906 0.026 - 0.053: 323 0.053 - 0.079: 105 0.079 - 0.105: 36 0.105 - 0.132: 44 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA VAL N 93 " pdb=" N VAL N 93 " pdb=" C VAL N 93 " pdb=" CB VAL N 93 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.84e-01 ... (remaining 1411 not shown) Planarity restraints: 1646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 145 " 0.015 2.00e-02 2.50e+03 1.36e-02 3.70e+00 pdb=" CG TYR R 145 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR R 145 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR R 145 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR R 145 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR R 145 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR R 145 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR R 145 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP R 68 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO R 69 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO R 69 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 69 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN N 13 " 0.016 5.00e-02 4.00e+02 2.39e-02 9.14e-01 pdb=" N PRO N 14 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO N 14 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO N 14 " 0.013 5.00e-02 4.00e+02 ... (remaining 1643 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 463 2.73 - 3.27: 9443 3.27 - 3.82: 15545 3.82 - 4.36: 19029 4.36 - 4.90: 32566 Nonbonded interactions: 77046 Sorted by model distance: nonbonded pdb=" O ARG R 412 " pdb=" ND1 HIS R 416 " model vdw 2.189 3.120 nonbonded pdb=" O ARG A 283 " pdb=" ND1 HIS A 357 " model vdw 2.195 3.120 nonbonded pdb=" O GLN B 44 " pdb=" NH1 ARG B 46 " model vdw 2.211 3.120 nonbonded pdb=" O CYS R 43 " pdb=" NH2 ARG R 60 " model vdw 2.255 3.120 nonbonded pdb=" O SER G 57 " pdb=" NH2 ARG G 62 " model vdw 2.258 3.120 ... (remaining 77041 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.670 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 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 : 0.002 0.034 9507 Z= 0.101 Angle : 0.428 4.503 12877 Z= 0.237 Chirality : 0.037 0.132 1414 Planarity : 0.003 0.035 1646 Dihedral : 13.332 87.601 3427 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.20 % Allowed : 0.20 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.26), residues: 1151 helix: 2.98 (0.25), residues: 458 sheet: 1.31 (0.34), residues: 234 loop : 0.09 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 173 TYR 0.034 0.001 TYR R 145 PHE 0.011 0.001 PHE R 230 TRP 0.014 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 9501) covalent geometry : angle 0.42738 (12865) SS BOND : bond 0.00185 ( 6) SS BOND : angle 0.97035 ( 12) hydrogen bonds : bond 0.19287 ( 488) hydrogen bonds : angle 6.46105 ( 1392) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 176 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: B 217 MET cc_start: 0.7137 (pmm) cc_final: 0.6762 (pmm) REVERT: B 237 ASN cc_start: 0.6240 (t0) cc_final: 0.5869 (p0) REVERT: P 17 ARG cc_start: 0.5034 (tpt90) cc_final: 0.4328 (tpm170) REVERT: P 21 ASP cc_start: 0.5938 (m-30) cc_final: 0.5615 (m-30) REVERT: G 32 LYS cc_start: 0.7685 (ttpt) cc_final: 0.7187 (tttm) REVERT: N 46 GLU cc_start: 0.6606 (mm-30) cc_final: 0.6287 (mp0) REVERT: N 50 ASP cc_start: 0.7847 (p0) cc_final: 0.7622 (p0) REVERT: R 27 GLN cc_start: 0.5391 (OUTLIER) cc_final: 0.4853 (pt0) REVERT: R 94 ARG cc_start: 0.4732 (OUTLIER) cc_final: 0.4502 (mpp-170) REVERT: R 136 LYS cc_start: 0.6625 (mmtm) cc_final: 0.6360 (mmtt) REVERT: R 205 LYS cc_start: 0.6283 (mttt) cc_final: 0.5787 (pptt) REVERT: R 412 ARG cc_start: 0.4947 (mtt180) cc_final: 0.4224 (mmp-170) REVERT: A 16 GLU cc_start: 0.4169 (mm-30) cc_final: 0.3574 (mp0) REVERT: A 20 ARG cc_start: 0.4773 (mmt-90) cc_final: 0.4056 (ttp-110) REVERT: A 21 GLU cc_start: 0.4543 (tm-30) cc_final: 0.4144 (tm-30) REVERT: A 370 GLU cc_start: 0.6451 (pt0) cc_final: 0.6212 (pt0) outliers start: 2 outliers final: 0 residues processed: 178 average time/residue: 0.6909 time to fit residues: 129.9061 Evaluate side-chains 128 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 GLN Chi-restraints excluded: chain R residue 94 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 88 ASN B 266 HIS B 268 ASN R 170 HIS R 318 ASN R 327 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.211940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.174266 restraints weight = 7446.497| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 1.27 r_work: 0.3612 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9507 Z= 0.170 Angle : 0.599 9.389 12877 Z= 0.325 Chirality : 0.044 0.151 1414 Planarity : 0.004 0.047 1646 Dihedral : 4.927 58.107 1281 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.40 % Allowed : 7.00 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.25), residues: 1151 helix: 2.54 (0.24), residues: 462 sheet: 1.37 (0.33), residues: 223 loop : -0.07 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 314 TYR 0.030 0.002 TYR R 145 PHE 0.019 0.002 PHE B 151 TRP 0.018 0.002 TRP A 234 HIS 0.020 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9501) covalent geometry : angle 0.59792 (12865) SS BOND : bond 0.00213 ( 6) SS BOND : angle 1.19668 ( 12) hydrogen bonds : bond 0.06348 ( 488) hydrogen bonds : angle 5.01895 ( 1392) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: B 37 ILE cc_start: 0.7404 (OUTLIER) cc_final: 0.7130 (tp) REVERT: P 17 ARG cc_start: 0.7332 (tpt90) cc_final: 0.7112 (tpt170) REVERT: R 151 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7127 (mt) REVERT: R 277 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7709 (mt) REVERT: R 352 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7039 (mp) REVERT: R 412 ARG cc_start: 0.5700 (mtt180) cc_final: 0.5024 (mmp-170) REVERT: A 16 GLU cc_start: 0.5939 (mm-30) cc_final: 0.5429 (mp0) REVERT: A 20 ARG cc_start: 0.6457 (mmt-90) cc_final: 0.6135 (ptm-80) REVERT: A 31 GLN cc_start: 0.7680 (mm110) cc_final: 0.7231 (mm110) outliers start: 24 outliers final: 11 residues processed: 138 average time/residue: 0.6878 time to fit residues: 100.2207 Evaluate side-chains 133 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 290 GLU Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 363 VAL Chi-restraints excluded: chain A residue 224 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 39 optimal weight: 0.0040 chunk 62 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 58 optimal weight: 0.0050 overall best weight: 0.5006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 268 ASN R 327 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.215107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.175956 restraints weight = 7641.305| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.47 r_work: 0.3625 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9507 Z= 0.107 Angle : 0.478 7.901 12877 Z= 0.260 Chirality : 0.040 0.146 1414 Planarity : 0.003 0.030 1646 Dihedral : 3.996 20.087 1274 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.40 % Allowed : 8.80 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.25), residues: 1151 helix: 2.75 (0.24), residues: 462 sheet: 1.26 (0.33), residues: 225 loop : -0.04 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 46 TYR 0.027 0.001 TYR R 145 PHE 0.016 0.001 PHE R 230 TRP 0.015 0.001 TRP A 234 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 9501) covalent geometry : angle 0.47777 (12865) SS BOND : bond 0.00152 ( 6) SS BOND : angle 0.75968 ( 12) hydrogen bonds : bond 0.04899 ( 488) hydrogen bonds : angle 4.53141 ( 1392) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: B 37 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7183 (tp) REVERT: P 17 ARG cc_start: 0.7396 (tpt90) cc_final: 0.7119 (tpm170) REVERT: G 42 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7569 (tp30) REVERT: R 151 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7135 (mm) REVERT: R 277 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7709 (mt) REVERT: R 412 ARG cc_start: 0.5847 (mtt180) cc_final: 0.5160 (mmp-170) REVERT: A 16 GLU cc_start: 0.6078 (mm-30) cc_final: 0.5497 (mp0) REVERT: A 19 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7529 (mt0) REVERT: A 20 ARG cc_start: 0.6672 (mmt-90) cc_final: 0.6239 (ptm-80) REVERT: A 21 GLU cc_start: 0.6655 (tm-30) cc_final: 0.6252 (tp30) REVERT: A 31 GLN cc_start: 0.7677 (mm110) cc_final: 0.7285 (mm110) REVERT: A 209 GLU cc_start: 0.7455 (mp0) cc_final: 0.7115 (tt0) REVERT: A 283 ARG cc_start: 0.7620 (mtt-85) cc_final: 0.7407 (mtt-85) REVERT: A 389 ARG cc_start: 0.7570 (ttp-110) cc_final: 0.7339 (ttm-80) outliers start: 24 outliers final: 10 residues processed: 141 average time/residue: 0.6831 time to fit residues: 101.9773 Evaluate side-chains 135 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 224 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 75 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 239 ASN B 268 ASN R 327 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.210574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.172188 restraints weight = 7616.687| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.29 r_work: 0.3562 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9507 Z= 0.156 Angle : 0.564 9.927 12877 Z= 0.308 Chirality : 0.043 0.153 1414 Planarity : 0.004 0.043 1646 Dihedral : 4.370 20.720 1274 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.00 % Allowed : 10.10 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.25), residues: 1151 helix: 2.53 (0.24), residues: 463 sheet: 1.20 (0.33), residues: 226 loop : -0.15 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 46 TYR 0.024 0.002 TYR R 145 PHE 0.019 0.002 PHE B 151 TRP 0.018 0.002 TRP A 234 HIS 0.013 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9501) covalent geometry : angle 0.56365 (12865) SS BOND : bond 0.00271 ( 6) SS BOND : angle 1.03302 ( 12) hydrogen bonds : bond 0.05736 ( 488) hydrogen bonds : angle 4.69919 ( 1392) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: B 37 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.7102 (tp) REVERT: B 46 ARG cc_start: 0.8077 (mtm-85) cc_final: 0.7739 (mpt-90) REVERT: P 17 ARG cc_start: 0.7426 (tpt90) cc_final: 0.7139 (tpm170) REVERT: G 47 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: N 50 ASP cc_start: 0.8422 (p0) cc_final: 0.8170 (p0) REVERT: R 123 MET cc_start: 0.5329 (OUTLIER) cc_final: 0.4872 (ptt) REVERT: R 151 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7221 (mm) REVERT: R 277 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7748 (mt) REVERT: R 412 ARG cc_start: 0.5788 (mtt180) cc_final: 0.5117 (mmp-170) REVERT: A 16 GLU cc_start: 0.6029 (mm-30) cc_final: 0.5443 (mp0) REVERT: A 19 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7607 (mt0) REVERT: A 20 ARG cc_start: 0.6674 (mmt-90) cc_final: 0.6170 (ptm-80) REVERT: A 31 GLN cc_start: 0.7741 (mm110) cc_final: 0.7314 (mm110) REVERT: A 283 ARG cc_start: 0.7679 (mtt-85) cc_final: 0.7456 (mtt-85) REVERT: A 314 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.4999 (mp0) outliers start: 30 outliers final: 19 residues processed: 139 average time/residue: 0.6629 time to fit residues: 97.6206 Evaluate side-chains 145 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 290 GLU Chi-restraints excluded: chain R residue 360 VAL Chi-restraints excluded: chain R residue 363 VAL Chi-restraints excluded: chain R residue 376 THR Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 314 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 73 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 268 ASN ** A 292 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 = 0.4266 r_free = 0.4266 target = 0.210474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.172162 restraints weight = 7588.944| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.28 r_work: 0.3576 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9507 Z= 0.147 Angle : 0.550 9.759 12877 Z= 0.300 Chirality : 0.042 0.152 1414 Planarity : 0.004 0.048 1646 Dihedral : 4.384 22.262 1274 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.20 % Allowed : 10.80 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.25), residues: 1151 helix: 2.51 (0.24), residues: 462 sheet: 1.27 (0.32), residues: 223 loop : -0.14 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 232 TYR 0.023 0.002 TYR R 145 PHE 0.017 0.002 PHE B 151 TRP 0.018 0.002 TRP A 234 HIS 0.011 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9501) covalent geometry : angle 0.54936 (12865) SS BOND : bond 0.00212 ( 6) SS BOND : angle 0.97172 ( 12) hydrogen bonds : bond 0.05546 ( 488) hydrogen bonds : angle 4.64182 ( 1392) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: B 37 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.7123 (tp) REVERT: B 46 ARG cc_start: 0.8071 (mtm-85) cc_final: 0.7689 (mtp-110) REVERT: P 17 ARG cc_start: 0.7412 (tpt90) cc_final: 0.7162 (tpt170) REVERT: G 47 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6678 (mp0) REVERT: N 50 ASP cc_start: 0.8416 (p0) cc_final: 0.8176 (p0) REVERT: R 123 MET cc_start: 0.5336 (OUTLIER) cc_final: 0.4893 (ptt) REVERT: R 151 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7108 (mt) REVERT: R 277 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7735 (mt) REVERT: R 412 ARG cc_start: 0.5865 (mtt180) cc_final: 0.5201 (mmp-170) REVERT: A 16 GLU cc_start: 0.5990 (mm-30) cc_final: 0.5442 (mp0) REVERT: A 19 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7564 (mt0) REVERT: A 20 ARG cc_start: 0.6677 (mmt-90) cc_final: 0.6232 (ptm-80) REVERT: A 31 GLN cc_start: 0.7706 (mm110) cc_final: 0.7280 (mm110) REVERT: A 283 ARG cc_start: 0.7700 (mtt-85) cc_final: 0.7491 (mtt-85) REVERT: A 314 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.5027 (mp0) outliers start: 32 outliers final: 18 residues processed: 134 average time/residue: 0.6855 time to fit residues: 97.3153 Evaluate side-chains 142 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 290 GLU Chi-restraints excluded: chain R residue 360 VAL Chi-restraints excluded: chain R residue 363 VAL Chi-restraints excluded: chain R residue 376 THR Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 392 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 80 optimal weight: 0.5980 chunk 101 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 39 optimal weight: 0.0050 chunk 99 optimal weight: 0.4980 chunk 89 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 40.0000 chunk 95 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 268 ASN ** A 292 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 = 0.4252 r_free = 0.4252 target = 0.208963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.170937 restraints weight = 7577.046| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.30 r_work: 0.3536 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9507 Z= 0.175 Angle : 0.597 10.596 12877 Z= 0.327 Chirality : 0.044 0.157 1414 Planarity : 0.005 0.052 1646 Dihedral : 4.595 24.323 1274 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.00 % Allowed : 11.20 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.25), residues: 1151 helix: 2.30 (0.24), residues: 463 sheet: 1.26 (0.32), residues: 224 loop : -0.25 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 314 TYR 0.021 0.002 TYR R 145 PHE 0.020 0.002 PHE B 151 TRP 0.019 0.002 TRP A 234 HIS 0.011 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9501) covalent geometry : angle 0.59608 (12865) SS BOND : bond 0.00279 ( 6) SS BOND : angle 1.24718 ( 12) hydrogen bonds : bond 0.05995 ( 488) hydrogen bonds : angle 4.77191 ( 1392) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: B 37 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.7131 (tp) REVERT: B 46 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7604 (mtp-110) REVERT: P 17 ARG cc_start: 0.7474 (tpt90) cc_final: 0.7223 (tpt170) REVERT: G 21 MET cc_start: 0.6779 (mmm) cc_final: 0.6055 (mtp) REVERT: G 47 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6712 (mp0) REVERT: N 50 ASP cc_start: 0.8441 (p0) cc_final: 0.8194 (p0) REVERT: R 123 MET cc_start: 0.5476 (OUTLIER) cc_final: 0.5015 (ptt) REVERT: R 277 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7775 (mt) REVERT: A 16 GLU cc_start: 0.6105 (mm-30) cc_final: 0.5493 (mp0) REVERT: A 20 ARG cc_start: 0.6748 (mmt-90) cc_final: 0.6138 (ptm-80) REVERT: A 31 GLN cc_start: 0.7766 (mm110) cc_final: 0.7353 (mm110) REVERT: A 314 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.5226 (mp0) outliers start: 30 outliers final: 20 residues processed: 133 average time/residue: 0.6900 time to fit residues: 97.2923 Evaluate side-chains 135 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 206 ILE Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 290 GLU Chi-restraints excluded: chain R residue 360 VAL Chi-restraints excluded: chain R residue 363 VAL Chi-restraints excluded: chain R residue 376 THR Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 314 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 49 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 111 optimal weight: 0.3980 chunk 61 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 268 ASN A 292 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.211555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.173972 restraints weight = 7629.505| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.31 r_work: 0.3579 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9507 Z= 0.119 Angle : 0.509 9.369 12877 Z= 0.277 Chirality : 0.041 0.149 1414 Planarity : 0.004 0.038 1646 Dihedral : 4.263 22.234 1274 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.90 % Allowed : 11.30 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.25), residues: 1151 helix: 2.63 (0.24), residues: 460 sheet: 1.19 (0.33), residues: 226 loop : -0.12 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.021 0.002 TYR R 145 PHE 0.015 0.001 PHE R 230 TRP 0.016 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9501) covalent geometry : angle 0.50854 (12865) SS BOND : bond 0.00123 ( 6) SS BOND : angle 0.96418 ( 12) hydrogen bonds : bond 0.05045 ( 488) hydrogen bonds : angle 4.49726 ( 1392) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: B 37 ILE cc_start: 0.7404 (OUTLIER) cc_final: 0.7109 (tp) REVERT: B 46 ARG cc_start: 0.8126 (mtm-85) cc_final: 0.7683 (mtp-110) REVERT: P 17 ARG cc_start: 0.7453 (tpt90) cc_final: 0.7240 (tpt170) REVERT: N 50 ASP cc_start: 0.8378 (p0) cc_final: 0.8145 (p0) REVERT: R 123 MET cc_start: 0.5335 (OUTLIER) cc_final: 0.4850 (ptt) REVERT: R 277 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7748 (mt) REVERT: A 19 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7536 (mt0) REVERT: A 20 ARG cc_start: 0.6781 (mmt-90) cc_final: 0.6259 (ptm-80) REVERT: A 21 GLU cc_start: 0.6670 (tm-30) cc_final: 0.6316 (tp30) REVERT: A 31 GLN cc_start: 0.7674 (mm110) cc_final: 0.7256 (mm110) REVERT: A 314 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.5166 (mp0) outliers start: 29 outliers final: 19 residues processed: 141 average time/residue: 0.7022 time to fit residues: 104.6835 Evaluate side-chains 142 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 206 ILE Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 290 GLU Chi-restraints excluded: chain R residue 360 VAL Chi-restraints excluded: chain R residue 363 VAL Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 392 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 21 optimal weight: 0.1980 chunk 106 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 95 optimal weight: 0.0770 chunk 42 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 0.0010 chunk 82 optimal weight: 0.9980 overall best weight: 0.2544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.214814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.179600 restraints weight = 7670.405| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 1.17 r_work: 0.3682 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9507 Z= 0.097 Angle : 0.466 8.618 12877 Z= 0.252 Chirality : 0.039 0.146 1414 Planarity : 0.003 0.038 1646 Dihedral : 3.941 21.025 1274 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.70 % Allowed : 11.80 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.26), residues: 1151 helix: 2.92 (0.24), residues: 455 sheet: 1.20 (0.33), residues: 227 loop : -0.01 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.022 0.001 TYR R 145 PHE 0.017 0.001 PHE R 230 TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00189 ( 9501) covalent geometry : angle 0.46488 (12865) SS BOND : bond 0.00184 ( 6) SS BOND : angle 1.01882 ( 12) hydrogen bonds : bond 0.04287 ( 488) hydrogen bonds : angle 4.23216 ( 1392) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: B 37 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7154 (tp) REVERT: B 46 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7635 (mtp-110) REVERT: P 17 ARG cc_start: 0.7292 (tpt90) cc_final: 0.7042 (tpt170) REVERT: P 21 ASP cc_start: 0.7684 (m-30) cc_final: 0.7433 (m-30) REVERT: G 42 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7549 (tp30) REVERT: R 151 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7115 (mm) REVERT: R 412 ARG cc_start: 0.5892 (mtt180) cc_final: 0.5218 (mmp-170) REVERT: A 19 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7492 (mt0) REVERT: A 20 ARG cc_start: 0.6633 (mmt-90) cc_final: 0.6262 (ptm-80) REVERT: A 21 GLU cc_start: 0.6457 (tm-30) cc_final: 0.6146 (tp30) REVERT: A 314 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.5041 (mp0) REVERT: A 325 THR cc_start: 0.6454 (OUTLIER) cc_final: 0.6247 (p) outliers start: 27 outliers final: 14 residues processed: 143 average time/residue: 0.6623 time to fit residues: 100.5009 Evaluate side-chains 141 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 206 ILE Chi-restraints excluded: chain R residue 363 VAL Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 75 optimal weight: 0.0670 chunk 37 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.213548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.177146 restraints weight = 7634.313| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.23 r_work: 0.3656 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9507 Z= 0.106 Angle : 0.489 9.009 12877 Z= 0.263 Chirality : 0.040 0.145 1414 Planarity : 0.004 0.040 1646 Dihedral : 3.991 20.794 1274 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.20 % Allowed : 12.90 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.25), residues: 1151 helix: 2.82 (0.24), residues: 461 sheet: 1.24 (0.33), residues: 227 loop : -0.08 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 283 TYR 0.021 0.001 TYR R 145 PHE 0.016 0.001 PHE R 230 TRP 0.014 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 9501) covalent geometry : angle 0.48858 (12865) SS BOND : bond 0.00122 ( 6) SS BOND : angle 1.00645 ( 12) hydrogen bonds : bond 0.04483 ( 488) hydrogen bonds : angle 4.23352 ( 1392) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: B 37 ILE cc_start: 0.7378 (OUTLIER) cc_final: 0.7087 (tp) REVERT: B 46 ARG cc_start: 0.8027 (mtm-85) cc_final: 0.7607 (mtp-110) REVERT: P 17 ARG cc_start: 0.7302 (tpt90) cc_final: 0.7092 (tpt170) REVERT: G 42 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7594 (tp30) REVERT: R 151 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7128 (mm) REVERT: R 412 ARG cc_start: 0.5862 (mtt180) cc_final: 0.5180 (mmp-170) REVERT: A 19 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7482 (mt0) REVERT: A 20 ARG cc_start: 0.6515 (mmt-90) cc_final: 0.6192 (ptm-80) REVERT: A 21 GLU cc_start: 0.6491 (tm-30) cc_final: 0.6128 (tp30) REVERT: A 314 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.5097 (mp0) outliers start: 22 outliers final: 14 residues processed: 136 average time/residue: 0.6879 time to fit residues: 98.9477 Evaluate side-chains 141 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 206 ILE Chi-restraints excluded: chain R residue 363 VAL Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 392 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 58 optimal weight: 0.0870 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.212255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.173165 restraints weight = 7644.880| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.44 r_work: 0.3605 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9507 Z= 0.120 Angle : 0.518 9.434 12877 Z= 0.279 Chirality : 0.041 0.146 1414 Planarity : 0.004 0.038 1646 Dihedral : 4.115 20.978 1274 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.10 % Allowed : 13.00 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.25), residues: 1151 helix: 2.75 (0.24), residues: 461 sheet: 1.37 (0.32), residues: 223 loop : -0.15 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 17 TYR 0.022 0.002 TYR R 145 PHE 0.017 0.001 PHE R 230 TRP 0.015 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9501) covalent geometry : angle 0.51732 (12865) SS BOND : bond 0.00147 ( 6) SS BOND : angle 0.99220 ( 12) hydrogen bonds : bond 0.04809 ( 488) hydrogen bonds : angle 4.33718 ( 1392) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: B 37 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.7116 (tp) REVERT: B 46 ARG cc_start: 0.8093 (mtm-85) cc_final: 0.7643 (mtp-110) REVERT: R 151 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7150 (mm) REVERT: A 20 ARG cc_start: 0.6637 (mmt-90) cc_final: 0.6221 (ptm-80) REVERT: A 21 GLU cc_start: 0.6570 (tm-30) cc_final: 0.6202 (tp30) REVERT: A 314 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.5130 (mp0) outliers start: 21 outliers final: 14 residues processed: 134 average time/residue: 0.6768 time to fit residues: 95.9762 Evaluate side-chains 136 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 206 ILE Chi-restraints excluded: chain R residue 363 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 392 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 74 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN P 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.212137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.174157 restraints weight = 7523.408| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 1.38 r_work: 0.3601 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9507 Z= 0.121 Angle : 0.528 9.703 12877 Z= 0.284 Chirality : 0.041 0.147 1414 Planarity : 0.004 0.049 1646 Dihedral : 4.178 21.180 1274 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.90 % Allowed : 13.50 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.25), residues: 1151 helix: 2.75 (0.24), residues: 461 sheet: 1.13 (0.32), residues: 233 loop : -0.12 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 283 TYR 0.022 0.002 TYR R 145 PHE 0.017 0.001 PHE R 230 TRP 0.015 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9501) covalent geometry : angle 0.52534 (12865) SS BOND : bond 0.00230 ( 6) SS BOND : angle 1.67437 ( 12) hydrogen bonds : bond 0.04858 ( 488) hydrogen bonds : angle 4.37151 ( 1392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4656.66 seconds wall clock time: 79 minutes 47.53 seconds (4787.53 seconds total)