Starting phenix.real_space_refine on Tue Mar 3 18:35:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ffo_31570/03_2026/7ffo_31570_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ffo_31570/03_2026/7ffo_31570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ffo_31570/03_2026/7ffo_31570_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ffo_31570/03_2026/7ffo_31570_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ffo_31570/03_2026/7ffo_31570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ffo_31570/03_2026/7ffo_31570.map" } resolution = 3.5 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.007 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 60 5.16 5 C 5237 2.51 5 N 1413 2.21 5 O 1545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8255 Number of models: 1 Model: "" Number of chains: 4 Chain: "K" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "L" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "N" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3229 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 30, 'TRANS': 381} Chain breaks: 1 Chain: "O" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Time building chain proxies: 2.10, per 1000 atoms: 0.25 Number of scatterers: 8255 At special positions: 0 Unit cell: (76.56, 149.16, 174.24, 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 60 16.00 O 1545 8.00 N 1413 7.00 C 5237 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS L 7 " - pdb=" SG CYS L 16 " distance=2.03 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 123 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 27 " distance=2.03 Simple disulfide: pdb=" SG CYS N 90 " - pdb=" SG CYS N 104 " distance=2.02 Simple disulfide: pdb=" SG CYS N 151 " - pdb=" SG CYS N 266 " distance=2.03 Simple disulfide: pdb=" SG CYS N 200 " - pdb=" SG CYS N 226 " distance=2.02 Simple disulfide: pdb=" SG CYS N 202 " - pdb=" SG CYS N 220 " distance=2.02 Simple disulfide: pdb=" SG CYS O 62 " - pdb=" SG CYS O 94 " distance=2.04 Simple disulfide: pdb=" SG CYS O 63 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 259 " - pdb=" SG CYS O 271 " distance=2.03 Simple disulfide: pdb=" SG CYS O 301 " - pdb=" SG CYS O 376 " distance=2.03 Simple disulfide: pdb=" SG CYS O 306 " - pdb=" SG CYS O 380 " distance=2.03 Simple disulfide: pdb=" SG CYS O 328 " - pdb=" SG CYS O 370 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 352.0 milliseconds 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1986 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 30 sheets defined 17.4% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'K' and resid 113 through 123 removed outlier: 3.801A pdb=" N ARG K 117 " --> pdb=" O GLY K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 164 removed outlier: 3.874A pdb=" N ALA K 164 " --> pdb=" O ASP K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 185 removed outlier: 3.590A pdb=" N ARG K 185 " --> pdb=" O GLN K 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 37 removed outlier: 3.786A pdb=" N THR L 30 " --> pdb=" O LYS L 26 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU L 31 " --> pdb=" O PRO L 27 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL L 36 " --> pdb=" O ALA L 32 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASN L 37 " --> pdb=" O MET L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 52 removed outlier: 4.141A pdb=" N LYS L 52 " --> pdb=" O GLU L 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 5 removed outlier: 3.729A pdb=" N LEU N 5 " --> pdb=" O THR N 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 2 through 5' Processing helix chain 'N' and resid 6 through 11 Processing helix chain 'N' and resid 80 through 82 No H-bonds generated for 'chain 'N' and resid 80 through 82' Processing helix chain 'N' and resid 351 through 363 removed outlier: 3.803A pdb=" N VAL N 355 " --> pdb=" O LEU N 351 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE N 356 " --> pdb=" O PRO N 352 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR N 357 " --> pdb=" O HIS N 353 " (cutoff:3.500A) Processing helix chain 'N' and resid 363 through 402 removed outlier: 3.514A pdb=" N THR N 367 " --> pdb=" O TYR N 363 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE N 368 " --> pdb=" O PRO N 364 " (cutoff:3.500A) Proline residue: N 399 - end of helix removed outlier: 3.617A pdb=" N LEU N 402 " --> pdb=" O THR N 398 " (cutoff:3.500A) Processing helix chain 'N' and resid 409 through 415 removed outlier: 4.118A pdb=" N VAL N 414 " --> pdb=" O PHE N 410 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 246 Processing helix chain 'O' and resid 250 through 255 Processing helix chain 'O' and resid 256 through 259 removed outlier: 3.504A pdb=" N CYS O 259 " --> pdb=" O PRO O 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 256 through 259' Processing helix chain 'O' and resid 283 through 287 removed outlier: 3.573A pdb=" N LEU O 286 " --> pdb=" O PRO O 283 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE O 287 " --> pdb=" O ASP O 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 283 through 287' Processing helix chain 'O' and resid 289 through 293 removed outlier: 3.582A pdb=" N GLU O 292 " --> pdb=" O ARG O 289 " (cutoff:3.500A) Processing helix chain 'O' and resid 403 through 415 removed outlier: 3.901A pdb=" N LEU O 413 " --> pdb=" O TRP O 409 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 440 removed outlier: 3.538A pdb=" N LYS O 440 " --> pdb=" O LEU O 436 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 135 through 139 removed outlier: 5.657A pdb=" N ILE K 136 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU K 132 " --> pdb=" O ILE K 136 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY K 138 " --> pdb=" O ILE K 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 141 through 143 Processing sheet with id=AA3, first strand: chain 'K' and resid 168 through 170 Processing sheet with id=AA4, first strand: chain 'K' and resid 190 through 191 removed outlier: 6.706A pdb=" N LYS K 190 " --> pdb=" O VAL K 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'K' and resid 198 through 202 removed outlier: 8.493A pdb=" N ALA K 206 " --> pdb=" O PRO K 217 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N PHE K 214 " --> pdb=" O LEU K 253 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL K 256 " --> pdb=" O VAL K 241 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL K 241 " --> pdb=" O VAL K 256 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 229 through 230 removed outlier: 3.864A pdb=" N ALA K 239 " --> pdb=" O ILE K 230 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL K 241 " --> pdb=" O VAL K 256 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL K 256 " --> pdb=" O VAL K 241 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 6 through 8 Processing sheet with id=AA8, first strand: chain 'N' and resid 17 through 19 removed outlier: 3.928A pdb=" N CYS N 27 " --> pdb=" O CYS N 19 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 33 through 37 removed outlier: 6.554A pdb=" N GLN N 48 " --> pdb=" O GLU N 34 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL N 36 " --> pdb=" O ARG N 46 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG N 46 " --> pdb=" O VAL N 36 " (cutoff:3.500A) removed outlier: 9.536A pdb=" N SER N 50 " --> pdb=" O ASP N 69 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP N 69 " --> pdb=" O SER N 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 33 through 37 removed outlier: 6.554A pdb=" N GLN N 48 " --> pdb=" O GLU N 34 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL N 36 " --> pdb=" O ARG N 46 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG N 46 " --> pdb=" O VAL N 36 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR N 98 " --> pdb=" O THR N 49 " (cutoff:3.500A) removed outlier: 10.196A pdb=" N SER N 51 " --> pdb=" O HIS N 96 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N HIS N 96 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N TYR N 53 " --> pdb=" O ASP N 94 " (cutoff:3.500A) removed outlier: 10.082A pdb=" N ASP N 94 " --> pdb=" O TYR N 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 83 through 85 Processing sheet with id=AB3, first strand: chain 'N' and resid 147 through 154 Processing sheet with id=AB4, first strand: chain 'N' and resid 237 through 238 Processing sheet with id=AB5, first strand: chain 'N' and resid 173 through 174 removed outlier: 3.715A pdb=" N GLU N 173 " --> pdb=" O ARG N 230 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU N 197 " --> pdb=" O TYR N 229 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 179 through 181 removed outlier: 3.683A pdb=" N VAL N 186 " --> pdb=" O PHE N 217 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 275 through 279 Processing sheet with id=AB8, first strand: chain 'N' and resid 275 through 279 Processing sheet with id=AB9, first strand: chain 'N' and resid 307 through 311 Processing sheet with id=AC1, first strand: chain 'O' and resid 2 through 8 Processing sheet with id=AC2, first strand: chain 'O' and resid 15 through 19 removed outlier: 5.370A pdb=" N ILE O 31 " --> pdb=" O THR O 136 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR O 136 " --> pdb=" O ILE O 31 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASN O 134 " --> pdb=" O PRO O 33 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS O 35 " --> pdb=" O PHE O 132 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR O 41 " --> pdb=" O THR O 126 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N THR O 126 " --> pdb=" O THR O 41 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 46 through 48 removed outlier: 3.641A pdb=" N TYR O 46 " --> pdb=" O ALA O 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 51 through 55 removed outlier: 3.715A pdb=" N ALA O 59 " --> pdb=" O VAL O 103 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 51 through 55 Processing sheet with id=AC6, first strand: chain 'O' and resid 87 through 88 removed outlier: 3.890A pdb=" N GLY O 91 " --> pdb=" O MET O 88 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 203 through 205 Processing sheet with id=AC8, first strand: chain 'O' and resid 220 through 221 Processing sheet with id=AC9, first strand: chain 'O' and resid 260 through 262 Processing sheet with id=AD1, first strand: chain 'O' and resid 296 through 306 removed outlier: 5.013A pdb=" N ALA O 298 " --> pdb=" O SER O 321 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER O 321 " --> pdb=" O ALA O 298 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE O 315 " --> pdb=" O ASN O 304 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY O 350 " --> pdb=" O TYR O 320 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 326 through 328 Processing sheet with id=AD3, first strand: chain 'O' and resid 364 through 369 306 hydrogen bonds defined for protein. 789 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: 1.20 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2608 1.34 - 1.46: 2052 1.46 - 1.59: 3729 1.59 - 1.71: 2 1.71 - 1.84: 80 Bond restraints: 8471 Sorted by residual: bond pdb=" CA ASP N 175 " pdb=" C ASP N 175 " ideal model delta sigma weight residual 1.526 1.614 -0.088 1.08e-02 8.57e+03 6.64e+01 bond pdb=" C ASP N 175 " pdb=" O ASP N 175 " ideal model delta sigma weight residual 1.235 1.311 -0.076 1.21e-02 6.83e+03 3.99e+01 bond pdb=" N VAL N 179 " pdb=" CA VAL N 179 " ideal model delta sigma weight residual 1.457 1.528 -0.071 1.32e-02 5.74e+03 2.88e+01 bond pdb=" CA VAL N 179 " pdb=" C VAL N 179 " ideal model delta sigma weight residual 1.525 1.589 -0.064 1.22e-02 6.72e+03 2.74e+01 bond pdb=" N ASP N 175 " pdb=" CA ASP N 175 " ideal model delta sigma weight residual 1.464 1.507 -0.043 1.25e-02 6.40e+03 1.18e+01 ... (remaining 8466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 11375 3.17 - 6.34: 136 6.34 - 9.51: 18 9.51 - 12.68: 2 12.68 - 15.86: 2 Bond angle restraints: 11533 Sorted by residual: angle pdb=" N ASP N 175 " pdb=" CA ASP N 175 " pdb=" C ASP N 175 " ideal model delta sigma weight residual 107.44 123.30 -15.86 1.93e+00 2.68e-01 6.75e+01 angle pdb=" CA VAL N 179 " pdb=" C VAL N 179 " pdb=" N SER N 180 " ideal model delta sigma weight residual 115.77 123.03 -7.26 1.25e+00 6.40e-01 3.37e+01 angle pdb=" N VAL N 179 " pdb=" CA VAL N 179 " pdb=" C VAL N 179 " ideal model delta sigma weight residual 109.80 117.18 -7.38 1.33e+00 5.65e-01 3.08e+01 angle pdb=" C VAL N 174 " pdb=" N ASP N 175 " pdb=" CA ASP N 175 " ideal model delta sigma weight residual 122.47 129.62 -7.15 1.50e+00 4.44e-01 2.27e+01 angle pdb=" C CYS N 22 " pdb=" N ALA N 23 " pdb=" CA ALA N 23 " ideal model delta sigma weight residual 121.54 130.31 -8.77 1.91e+00 2.74e-01 2.11e+01 ... (remaining 11528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 4899 17.61 - 35.22: 158 35.22 - 52.83: 29 52.83 - 70.44: 4 70.44 - 88.05: 5 Dihedral angle restraints: 5095 sinusoidal: 1995 harmonic: 3100 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 27 " pdb=" CB CYS N 27 " ideal model delta sinusoidal sigma weight residual 93.00 173.62 -80.62 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CA ILE O 369 " pdb=" C ILE O 369 " pdb=" N CYS O 370 " pdb=" CA CYS O 370 " ideal model delta harmonic sigma weight residual 180.00 -135.76 -44.24 0 5.00e+00 4.00e-02 7.83e+01 dihedral pdb=" CA ASN O 264 " pdb=" C ASN O 264 " pdb=" N PRO O 265 " pdb=" CA PRO O 265 " ideal model delta harmonic sigma weight residual 180.00 137.36 42.64 0 5.00e+00 4.00e-02 7.27e+01 ... (remaining 5092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1062 0.072 - 0.145: 199 0.145 - 0.217: 22 0.217 - 0.289: 1 0.289 - 0.362: 1 Chirality restraints: 1285 Sorted by residual: chirality pdb=" CA ASP N 175 " pdb=" N ASP N 175 " pdb=" C ASP N 175 " pdb=" CB ASP N 175 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CA HIS N 156 " pdb=" N HIS N 156 " pdb=" C HIS N 156 " pdb=" CB HIS N 156 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB VAL O 80 " pdb=" CA VAL O 80 " pdb=" CG1 VAL O 80 " pdb=" CG2 VAL O 80 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.87e-01 ... (remaining 1282 not shown) Planarity restraints: 1483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN O 264 " -0.066 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO O 265 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO O 265 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO O 265 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG N 13 " -0.046 5.00e-02 4.00e+02 6.98e-02 7.80e+00 pdb=" N PRO N 14 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO N 14 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO N 14 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG N 88 " 0.046 5.00e-02 4.00e+02 6.92e-02 7.65e+00 pdb=" N PRO N 89 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO N 89 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO N 89 " 0.038 5.00e-02 4.00e+02 ... (remaining 1480 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 878 2.75 - 3.29: 7017 3.29 - 3.82: 12940 3.82 - 4.36: 14704 4.36 - 4.90: 26617 Nonbonded interactions: 62156 Sorted by model distance: nonbonded pdb=" NZ LYS K 146 " pdb=" O ARG N 401 " model vdw 2.211 3.120 nonbonded pdb=" OH TYR N 359 " pdb=" O ALA O 401 " model vdw 2.257 3.040 nonbonded pdb=" OE1 GLU O 120 " pdb=" OH TYR O 122 " model vdw 2.279 3.040 nonbonded pdb=" O GLY O 182 " pdb=" OG1 THR O 263 " model vdw 2.312 3.040 nonbonded pdb=" OG1 THR N 12 " pdb=" NE2 GLN N 52 " model vdw 2.327 3.120 ... (remaining 62151 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 group one per residue 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.540 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 : 0.008 0.137 8485 Z= 0.368 Angle : 0.950 15.856 11559 Z= 0.518 Chirality : 0.057 0.362 1285 Planarity : 0.008 0.099 1483 Dihedral : 9.499 88.052 3070 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.62 % Favored : 93.28 % Rotamer: Outliers : 0.33 % Allowed : 2.66 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.20 % 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: -2.95 (0.22), residues: 1057 helix: -1.88 (0.34), residues: 134 sheet: -1.26 (0.26), residues: 340 loop : -2.46 (0.21), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 230 TYR 0.031 0.003 TYR O 122 PHE 0.023 0.003 PHE N 328 TRP 0.016 0.003 TRP K 202 HIS 0.010 0.002 HIS N 28 Details of bonding type rmsd covalent geometry : bond 0.00749 ( 8471) covalent geometry : angle 0.94475 (11533) SS BOND : bond 0.00458 ( 13) SS BOND : angle 2.27213 ( 26) hydrogen bonds : bond 0.20677 ( 291) hydrogen bonds : angle 8.79673 ( 789) Misc. bond : bond 0.13702 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 228 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 166 LYS cc_start: 0.5536 (tttt) cc_final: 0.5250 (ptmt) REVERT: K 231 LEU cc_start: 0.5389 (mt) cc_final: 0.5151 (mt) REVERT: K 238 VAL cc_start: 0.4926 (m) cc_final: 0.4245 (p) REVERT: N 152 GLN cc_start: 0.7739 (mt0) cc_final: 0.7409 (mt0) REVERT: N 365 MET cc_start: 0.7162 (ttt) cc_final: 0.6920 (pmm) REVERT: O 88 MET cc_start: 0.8872 (mmm) cc_final: 0.8396 (mmm) REVERT: O 143 VAL cc_start: 0.9188 (t) cc_final: 0.8892 (m) REVERT: O 147 TYR cc_start: 0.8366 (m-10) cc_final: 0.8093 (m-80) REVERT: O 266 ILE cc_start: 0.9008 (mt) cc_final: 0.8721 (mp) outliers start: 3 outliers final: 0 residues processed: 228 average time/residue: 0.1117 time to fit residues: 33.0915 Evaluate side-chains 124 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 156 HIS N 160 ASN N 358 HIS O 264 ASN O 360 ASN O 394 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.142468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.111516 restraints weight = 11568.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.109931 restraints weight = 13677.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.111506 restraints weight = 13094.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.111306 restraints weight = 8541.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.111758 restraints weight = 9976.649| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8485 Z= 0.163 Angle : 0.647 8.484 11559 Z= 0.339 Chirality : 0.046 0.157 1285 Planarity : 0.006 0.086 1483 Dihedral : 5.497 38.684 1156 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.88 % Allowed : 10.42 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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 (0.24), residues: 1057 helix: -0.11 (0.44), residues: 141 sheet: -0.65 (0.27), residues: 336 loop : -2.01 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 115 TYR 0.020 0.002 TYR O 308 PHE 0.013 0.002 PHE N 328 TRP 0.009 0.001 TRP K 202 HIS 0.009 0.001 HIS N 156 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 8471) covalent geometry : angle 0.64216 (11533) SS BOND : bond 0.00319 ( 13) SS BOND : angle 1.75118 ( 26) hydrogen bonds : bond 0.03592 ( 291) hydrogen bonds : angle 5.78570 ( 789) Misc. bond : bond 0.00288 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 174 ASP cc_start: 0.8382 (t0) cc_final: 0.8105 (t0) REVERT: N 16 MET cc_start: 0.7719 (mtm) cc_final: 0.7094 (mtt) REVERT: N 52 GLN cc_start: 0.8129 (mt0) cc_final: 0.7894 (mt0) REVERT: N 302 ASP cc_start: 0.8315 (p0) cc_final: 0.8084 (p0) REVERT: N 324 LYS cc_start: 0.8264 (mtmt) cc_final: 0.7911 (mtpp) REVERT: O 85 TYR cc_start: 0.8664 (t80) cc_final: 0.8392 (t80) REVERT: O 143 VAL cc_start: 0.9264 (t) cc_final: 0.9037 (m) REVERT: O 266 ILE cc_start: 0.9129 (mt) cc_final: 0.8884 (mp) REVERT: O 421 ILE cc_start: 0.8598 (tp) cc_final: 0.8260 (mt) outliers start: 17 outliers final: 9 residues processed: 153 average time/residue: 0.0775 time to fit residues: 16.8749 Evaluate side-chains 130 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 205 THR Chi-restraints excluded: chain N residue 342 GLU Chi-restraints excluded: chain N residue 398 THR Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 213 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 66 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 79 optimal weight: 0.3980 chunk 76 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.138712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.109012 restraints weight = 11350.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.107481 restraints weight = 19218.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.108786 restraints weight = 17360.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.108982 restraints weight = 11192.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.109885 restraints weight = 9576.071| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8485 Z= 0.170 Angle : 0.639 8.115 11559 Z= 0.329 Chirality : 0.046 0.154 1285 Planarity : 0.005 0.077 1483 Dihedral : 5.449 57.299 1156 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.77 % Allowed : 11.97 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -1.34 (0.25), residues: 1057 helix: 0.95 (0.47), residues: 141 sheet: -0.52 (0.27), residues: 337 loop : -1.61 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 115 TYR 0.022 0.002 TYR O 308 PHE 0.022 0.002 PHE L 14 TRP 0.010 0.001 TRP N 330 HIS 0.006 0.001 HIS N 305 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 8471) covalent geometry : angle 0.63411 (11533) SS BOND : bond 0.00401 ( 13) SS BOND : angle 1.74621 ( 26) hydrogen bonds : bond 0.03183 ( 291) hydrogen bonds : angle 5.17675 ( 789) Misc. bond : bond 0.00064 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 174 ASP cc_start: 0.8370 (t0) cc_final: 0.8101 (t0) REVERT: L 30 THR cc_start: 0.8830 (m) cc_final: 0.8046 (m) REVERT: N 231 LEU cc_start: 0.7749 (mt) cc_final: 0.7511 (mt) REVERT: N 256 HIS cc_start: 0.6992 (p-80) cc_final: 0.6665 (p90) REVERT: N 324 LYS cc_start: 0.8567 (mtmt) cc_final: 0.8226 (mtpp) REVERT: O 2 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7030 (mp0) REVERT: O 143 VAL cc_start: 0.9187 (t) cc_final: 0.8947 (m) outliers start: 34 outliers final: 21 residues processed: 156 average time/residue: 0.0832 time to fit residues: 18.2815 Evaluate side-chains 141 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 160 ASP Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 180 SER Chi-restraints excluded: chain N residue 198 VAL Chi-restraints excluded: chain N residue 205 THR Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 342 GLU Chi-restraints excluded: chain N residue 385 SER Chi-restraints excluded: chain N residue 398 THR Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 346 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 60 optimal weight: 7.9990 chunk 105 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 0.0570 chunk 78 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 overall best weight: 2.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.136830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.109169 restraints weight = 11649.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.108787 restraints weight = 21643.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.109834 restraints weight = 23186.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.110389 restraints weight = 12955.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.110846 restraints weight = 11543.701| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8485 Z= 0.157 Angle : 0.611 7.781 11559 Z= 0.314 Chirality : 0.046 0.160 1285 Planarity : 0.005 0.079 1483 Dihedral : 5.221 51.455 1156 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.77 % Allowed : 13.30 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.25), residues: 1057 helix: 1.25 (0.47), residues: 144 sheet: -0.33 (0.28), residues: 335 loop : -1.38 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 21 TYR 0.022 0.001 TYR O 308 PHE 0.012 0.001 PHE N 328 TRP 0.008 0.001 TRP K 202 HIS 0.005 0.001 HIS N 41 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 8471) covalent geometry : angle 0.60639 (11533) SS BOND : bond 0.00420 ( 13) SS BOND : angle 1.68540 ( 26) hydrogen bonds : bond 0.02900 ( 291) hydrogen bonds : angle 4.93288 ( 789) Misc. bond : bond 0.00537 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 174 ASP cc_start: 0.8409 (t0) cc_final: 0.8141 (t0) REVERT: K 225 ASP cc_start: 0.8398 (t0) cc_final: 0.8194 (t0) REVERT: N 324 LYS cc_start: 0.8554 (mtmt) cc_final: 0.8283 (mtpt) REVERT: N 342 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: O 2 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7060 (mp0) REVERT: O 88 MET cc_start: 0.8791 (mmm) cc_final: 0.8446 (mtp) REVERT: O 377 LYS cc_start: 0.8566 (mtpt) cc_final: 0.8361 (mtpt) outliers start: 25 outliers final: 16 residues processed: 131 average time/residue: 0.0804 time to fit residues: 15.1565 Evaluate side-chains 125 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 160 ASP Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain N residue 179 VAL Chi-restraints excluded: chain N residue 180 SER Chi-restraints excluded: chain N residue 198 VAL Chi-restraints excluded: chain N residue 205 THR Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 342 GLU Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 346 LEU Chi-restraints excluded: chain O residue 429 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 65 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 70 optimal weight: 0.2980 chunk 66 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN N 353 HIS O 140 HIS O 396 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.138481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.110005 restraints weight = 11490.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.108125 restraints weight = 17727.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.108841 restraints weight = 15990.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.109493 restraints weight = 11703.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.109397 restraints weight = 11597.610| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8485 Z= 0.099 Angle : 0.583 14.085 11559 Z= 0.297 Chirality : 0.044 0.190 1285 Planarity : 0.005 0.076 1483 Dihedral : 5.020 48.909 1156 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.22 % Allowed : 13.75 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.26), residues: 1057 helix: 1.62 (0.47), residues: 143 sheet: -0.17 (0.28), residues: 334 loop : -1.25 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 223 TYR 0.016 0.001 TYR O 308 PHE 0.009 0.001 PHE K 189 TRP 0.007 0.001 TRP N 326 HIS 0.005 0.001 HIS O 140 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8471) covalent geometry : angle 0.57623 (11533) SS BOND : bond 0.00345 ( 13) SS BOND : angle 1.89110 ( 26) hydrogen bonds : bond 0.02496 ( 291) hydrogen bonds : angle 4.68127 ( 789) Misc. bond : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 174 ASP cc_start: 0.8424 (t0) cc_final: 0.8085 (t0) REVERT: N 69 ASP cc_start: 0.7247 (t0) cc_final: 0.6953 (t0) REVERT: N 256 HIS cc_start: 0.6895 (p-80) cc_final: 0.6519 (p-80) REVERT: N 324 LYS cc_start: 0.8743 (mtmt) cc_final: 0.8300 (mtpp) REVERT: N 342 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: O 2 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7076 (mp0) REVERT: O 88 MET cc_start: 0.8850 (mmm) cc_final: 0.8559 (mtp) outliers start: 20 outliers final: 13 residues processed: 136 average time/residue: 0.0851 time to fit residues: 16.3643 Evaluate side-chains 128 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain N residue 6 PHE Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 205 THR Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 342 GLU Chi-restraints excluded: chain N residue 398 THR Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 346 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 40 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 95 optimal weight: 0.2980 chunk 22 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.137862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.109431 restraints weight = 11503.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.107973 restraints weight = 18834.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.108924 restraints weight = 19120.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.109702 restraints weight = 11663.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.109783 restraints weight = 10374.881| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8485 Z= 0.138 Angle : 0.605 10.043 11559 Z= 0.310 Chirality : 0.045 0.197 1285 Planarity : 0.005 0.091 1483 Dihedral : 4.972 46.979 1156 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.66 % Allowed : 13.75 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.26), residues: 1057 helix: 1.69 (0.47), residues: 143 sheet: -0.03 (0.28), residues: 332 loop : -1.16 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 117 TYR 0.021 0.001 TYR O 308 PHE 0.012 0.001 PHE N 328 TRP 0.006 0.001 TRP N 326 HIS 0.004 0.001 HIS N 305 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8471) covalent geometry : angle 0.59458 (11533) SS BOND : bond 0.00609 ( 13) SS BOND : angle 2.42918 ( 26) hydrogen bonds : bond 0.02760 ( 291) hydrogen bonds : angle 4.68673 ( 789) Misc. bond : bond 0.00171 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 174 ASP cc_start: 0.8456 (t0) cc_final: 0.8112 (t0) REVERT: K 225 ASP cc_start: 0.8545 (t0) cc_final: 0.8323 (t0) REVERT: N 69 ASP cc_start: 0.7291 (t0) cc_final: 0.7028 (t0) REVERT: N 324 LYS cc_start: 0.8579 (mtmt) cc_final: 0.8204 (mtpt) REVERT: O 2 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7089 (mp0) outliers start: 24 outliers final: 18 residues processed: 132 average time/residue: 0.0767 time to fit residues: 14.7829 Evaluate side-chains 129 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 160 ASP Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain N residue 6 PHE Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 342 GLU Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 219 LEU Chi-restraints excluded: chain O residue 346 LEU Chi-restraints excluded: chain O residue 377 LYS Chi-restraints excluded: chain O residue 397 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 46 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 54 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.139169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.109893 restraints weight = 11555.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.107859 restraints weight = 16419.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.109031 restraints weight = 18179.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.109685 restraints weight = 10577.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.110054 restraints weight = 9227.053| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8485 Z= 0.092 Angle : 0.550 10.276 11559 Z= 0.282 Chirality : 0.044 0.197 1285 Planarity : 0.005 0.081 1483 Dihedral : 4.751 45.838 1156 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.66 % Allowed : 14.19 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.26), residues: 1057 helix: 1.83 (0.47), residues: 143 sheet: 0.09 (0.28), residues: 332 loop : -1.11 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 149 TYR 0.015 0.001 TYR O 308 PHE 0.009 0.001 PHE K 189 TRP 0.008 0.001 TRP N 326 HIS 0.003 0.000 HIS N 256 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 8471) covalent geometry : angle 0.54541 (11533) SS BOND : bond 0.00326 ( 13) SS BOND : angle 1.66217 ( 26) hydrogen bonds : bond 0.02400 ( 291) hydrogen bonds : angle 4.47285 ( 789) Misc. bond : bond 0.00138 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 324 LYS cc_start: 0.8688 (mtmt) cc_final: 0.8281 (mtpt) REVERT: O 2 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7108 (mp0) outliers start: 24 outliers final: 16 residues processed: 132 average time/residue: 0.0720 time to fit residues: 14.0174 Evaluate side-chains 124 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain N residue 6 PHE Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 180 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 219 LEU Chi-restraints excluded: chain O residue 370 CYS Chi-restraints excluded: chain O residue 397 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 7 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.137455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.108894 restraints weight = 11556.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.105599 restraints weight = 17244.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.106652 restraints weight = 16143.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.107627 restraints weight = 10498.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.107575 restraints weight = 9732.467| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8485 Z= 0.116 Angle : 0.573 10.507 11559 Z= 0.294 Chirality : 0.044 0.188 1285 Planarity : 0.005 0.088 1483 Dihedral : 4.753 45.128 1156 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.88 % Allowed : 14.41 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.26), residues: 1057 helix: 1.84 (0.47), residues: 142 sheet: 0.11 (0.29), residues: 332 loop : -1.12 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 149 TYR 0.018 0.001 TYR O 308 PHE 0.010 0.001 PHE N 328 TRP 0.007 0.001 TRP N 326 HIS 0.003 0.001 HIS N 305 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8471) covalent geometry : angle 0.56872 (11533) SS BOND : bond 0.00309 ( 13) SS BOND : angle 1.58644 ( 26) hydrogen bonds : bond 0.02457 ( 291) hydrogen bonds : angle 4.45725 ( 789) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 324 LYS cc_start: 0.8774 (mtmt) cc_final: 0.8454 (mtpt) REVERT: O 2 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7021 (mp0) outliers start: 26 outliers final: 22 residues processed: 131 average time/residue: 0.0655 time to fit residues: 13.0270 Evaluate side-chains 129 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain N residue 6 PHE Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 180 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 7 MET Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 219 LEU Chi-restraints excluded: chain O residue 370 CYS Chi-restraints excluded: chain O residue 397 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 13 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 89 optimal weight: 0.3980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.138871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.110735 restraints weight = 11531.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.109112 restraints weight = 18421.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.110023 restraints weight = 18185.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.110640 restraints weight = 11415.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.110744 restraints weight = 10403.557| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8485 Z= 0.102 Angle : 0.570 9.947 11559 Z= 0.293 Chirality : 0.044 0.197 1285 Planarity : 0.005 0.081 1483 Dihedral : 4.762 45.423 1156 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.66 % Allowed : 15.30 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.26), residues: 1057 helix: 2.02 (0.48), residues: 139 sheet: 0.13 (0.28), residues: 341 loop : -1.02 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 149 TYR 0.017 0.001 TYR O 308 PHE 0.010 0.001 PHE K 189 TRP 0.008 0.001 TRP N 326 HIS 0.003 0.001 HIS N 353 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8471) covalent geometry : angle 0.56592 (11533) SS BOND : bond 0.00307 ( 13) SS BOND : angle 1.47661 ( 26) hydrogen bonds : bond 0.02428 ( 291) hydrogen bonds : angle 4.43807 ( 789) Misc. bond : bond 0.00049 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 160 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7721 (p0) REVERT: N 324 LYS cc_start: 0.8711 (mtmt) cc_final: 0.8317 (mtpt) REVERT: O 2 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7033 (mp0) outliers start: 24 outliers final: 23 residues processed: 127 average time/residue: 0.0584 time to fit residues: 11.3843 Evaluate side-chains 132 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 160 ASP Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain N residue 6 PHE Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain N residue 180 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 7 MET Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 219 LEU Chi-restraints excluded: chain O residue 370 CYS Chi-restraints excluded: chain O residue 397 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 56 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 8 optimal weight: 0.4980 chunk 82 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN N 52 GLN O 130 GLN O 392 GLN O 396 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.131680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.102750 restraints weight = 11606.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.100136 restraints weight = 17670.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.101361 restraints weight = 18773.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.102194 restraints weight = 11215.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.102444 restraints weight = 9736.840| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 8485 Z= 0.263 Angle : 0.700 9.318 11559 Z= 0.363 Chirality : 0.049 0.181 1285 Planarity : 0.006 0.087 1483 Dihedral : 5.305 40.549 1156 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.66 % Allowed : 15.19 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.26), residues: 1057 helix: 1.58 (0.47), residues: 141 sheet: -0.12 (0.29), residues: 329 loop : -1.28 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 362 TYR 0.029 0.002 TYR O 308 PHE 0.015 0.002 PHE O 240 TRP 0.011 0.002 TRP K 202 HIS 0.008 0.002 HIS N 305 Details of bonding type rmsd covalent geometry : bond 0.00653 ( 8471) covalent geometry : angle 0.69418 (11533) SS BOND : bond 0.00382 ( 13) SS BOND : angle 2.02909 ( 26) hydrogen bonds : bond 0.03220 ( 291) hydrogen bonds : angle 4.83175 ( 789) Misc. bond : bond 0.00049 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: N 324 LYS cc_start: 0.8799 (mtmt) cc_final: 0.8364 (mtpp) REVERT: N 347 ASN cc_start: 0.8378 (t0) cc_final: 0.8145 (t0) REVERT: O 2 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7135 (mt-10) REVERT: O 88 MET cc_start: 0.8609 (mtp) cc_final: 0.8398 (mtt) outliers start: 24 outliers final: 18 residues processed: 138 average time/residue: 0.0729 time to fit residues: 14.8739 Evaluate side-chains 130 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain N residue 180 SER Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 219 LEU Chi-restraints excluded: chain O residue 397 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 46 optimal weight: 0.2980 chunk 59 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 87 optimal weight: 0.0020 chunk 44 optimal weight: 9.9990 chunk 47 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN O 392 GLN O 396 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.135700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.106736 restraints weight = 11558.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.104601 restraints weight = 17266.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.105829 restraints weight = 17080.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.106433 restraints weight = 10346.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.106602 restraints weight = 9567.327| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8485 Z= 0.101 Angle : 0.579 9.696 11559 Z= 0.299 Chirality : 0.044 0.170 1285 Planarity : 0.005 0.082 1483 Dihedral : 4.975 44.024 1156 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.88 % Allowed : 16.96 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.26), residues: 1057 helix: 2.00 (0.48), residues: 139 sheet: 0.09 (0.28), residues: 344 loop : -1.06 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 149 TYR 0.021 0.001 TYR K 267 PHE 0.011 0.001 PHE K 189 TRP 0.008 0.001 TRP N 326 HIS 0.005 0.001 HIS K 193 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 8471) covalent geometry : angle 0.57519 (11533) SS BOND : bond 0.00320 ( 13) SS BOND : angle 1.48905 ( 26) hydrogen bonds : bond 0.02519 ( 291) hydrogen bonds : angle 4.55056 ( 789) Misc. bond : bond 0.00059 ( 1) =============================================================================== Job complete usr+sys time: 1497.02 seconds wall clock time: 26 minutes 27.22 seconds (1587.22 seconds total)