Starting phenix.real_space_refine on Wed Mar 12 15:40:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ffo_31570/03_2025/7ffo_31570_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ffo_31570/03_2025/7ffo_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ffo_31570/03_2025/7ffo_31570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ffo_31570/03_2025/7ffo_31570.map" model { file = "/net/cci-nas-00/data/ceres_data/7ffo_31570/03_2025/7ffo_31570_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ffo_31570/03_2025/7ffo_31570_neut.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.10, per 1000 atoms: 0.62 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: 2.00 Conformation dependent library (CDL) restraints added in 984.5 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: 1.21 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: 2.43 Time building geometry restraints manager: 2.38 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: 1.170 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.040 Find NCS groups from input model: 0.110 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.650 ------------------------------------------------------------------------------- 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 : 0.007 0.098 8471 Z= 0.500 Angle : 0.945 15.856 11533 Z= 0.516 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.016 0.003 TRP K 202 HIS 0.010 0.002 HIS N 28 PHE 0.023 0.003 PHE N 328 TYR 0.031 0.003 TYR O 122 ARG 0.009 0.001 ARG N 230 *********************** 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 : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 166 LYS cc_start: 0.5536 (tttt) cc_final: 0.5251 (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: 0.7738 (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: 0.9007 (mt) cc_final: 0.8721 (mp) outliers start: 3 outliers final: 0 residues processed: 228 average time/residue: 0.2539 time to fit residues: 75.6283 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 : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 121 HIS 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.147422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.118090 restraints weight = 11292.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.116686 restraints weight = 22151.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.117868 restraints weight = 20230.794| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8471 Z= 0.177 Angle : 0.625 8.577 11533 Z= 0.324 Chirality : 0.045 0.167 1285 Planarity : 0.006 0.082 1483 Dihedral : 5.536 39.186 1156 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.77 % Allowed : 9.76 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.24), residues: 1057 helix: 0.31 (0.45), residues: 133 sheet: -0.66 (0.27), residues: 342 loop : -2.01 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 202 HIS 0.007 0.001 HIS N 156 PHE 0.010 0.001 PHE N 328 TYR 0.018 0.001 TYR O 308 ARG 0.003 0.000 ARG N 64 *********************** 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 158 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: N 324 LYS cc_start: 0.8211 (mtmt) cc_final: 0.7918 (mtpp) REVERT: O 266 ILE cc_start: 0.9125 (mt) cc_final: 0.8835 (mp) REVERT: O 377 LYS cc_start: 0.8197 (mtpt) cc_final: 0.7914 (mtpt) REVERT: O 421 ILE cc_start: 0.8467 (tp) cc_final: 0.8219 (mp) outliers start: 16 outliers final: 10 residues processed: 152 average time/residue: 0.2148 time to fit residues: 45.8673 Evaluate side-chains 134 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 160 ASP 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 64 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.135654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.107389 restraints weight = 11673.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.105648 restraints weight = 21511.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.107187 restraints weight = 21070.969| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8471 Z= 0.386 Angle : 0.696 8.415 11533 Z= 0.361 Chirality : 0.048 0.151 1285 Planarity : 0.006 0.079 1483 Dihedral : 5.707 65.335 1156 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.32 % Allowed : 11.31 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.25), residues: 1057 helix: 0.72 (0.45), residues: 144 sheet: -0.46 (0.27), residues: 335 loop : -1.64 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 330 HIS 0.009 0.002 HIS N 41 PHE 0.017 0.002 PHE N 328 TYR 0.028 0.002 TYR O 308 ARG 0.006 0.001 ARG K 115 *********************** 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 173 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: K 174 ASP cc_start: 0.8370 (t0) cc_final: 0.8103 (t0) REVERT: L 30 THR cc_start: 0.8817 (m) cc_final: 0.8152 (m) REVERT: N 7 ASN cc_start: 0.4284 (OUTLIER) cc_final: 0.3675 (t0) REVERT: N 173 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6709 (pt0) REVERT: N 256 HIS cc_start: 0.6963 (p-80) cc_final: 0.6743 (p-80) REVERT: N 324 LYS cc_start: 0.8669 (mtmt) cc_final: 0.8295 (mtpp) REVERT: O 2 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6958 (mp0) REVERT: O 88 MET cc_start: 0.8747 (mmm) cc_final: 0.8423 (mtp) outliers start: 39 outliers final: 24 residues processed: 164 average time/residue: 0.1985 time to fit residues: 45.9078 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 : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 160 ASP Chi-restraints excluded: chain K residue 238 VAL 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 7 ASN Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 167 MET Chi-restraints excluded: chain N residue 179 VAL Chi-restraints excluded: chain N residue 205 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 342 GLU Chi-restraints excluded: chain N residue 394 VAL 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 51 TYR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 97 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 chunk 87 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 396 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.138139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.109750 restraints weight = 11390.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.107943 restraints weight = 19278.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.109021 restraints weight = 18777.708| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8471 Z= 0.177 Angle : 0.597 11.261 11533 Z= 0.307 Chirality : 0.045 0.180 1285 Planarity : 0.005 0.071 1483 Dihedral : 5.288 58.855 1156 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.77 % Allowed : 13.53 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.25), residues: 1057 helix: 1.44 (0.47), residues: 140 sheet: -0.34 (0.28), residues: 329 loop : -1.35 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 202 HIS 0.003 0.001 HIS N 256 PHE 0.010 0.001 PHE O 365 TYR 0.020 0.001 TYR O 308 ARG 0.004 0.001 ARG K 115 *********************** 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 148 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 174 ASP cc_start: 0.8372 (t0) cc_final: 0.8041 (t0) REVERT: N 69 ASP cc_start: 0.7264 (t0) cc_final: 0.7058 (t0) REVERT: N 70 MET cc_start: 0.7584 (tpp) cc_final: 0.7331 (tpp) REVERT: N 324 LYS cc_start: 0.8820 (mtmt) cc_final: 0.8419 (mtpp) REVERT: N 342 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: O 2 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6929 (mp0) REVERT: O 88 MET cc_start: 0.8843 (mmm) cc_final: 0.8494 (mtp) outliers start: 25 outliers final: 13 residues processed: 141 average time/residue: 0.1834 time to fit residues: 36.4846 Evaluate side-chains 127 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 160 ASP Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 167 MET Chi-restraints excluded: chain N residue 205 THR Chi-restraints excluded: chain N residue 302 ASP 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 174 ASP Chi-restraints excluded: chain O residue 213 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 70 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 50 optimal weight: 0.0060 chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN O 130 GLN O 140 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.135061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.105777 restraints weight = 11446.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.102930 restraints weight = 17196.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.104028 restraints weight = 18389.001| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8471 Z= 0.288 Angle : 0.640 10.786 11533 Z= 0.328 Chirality : 0.047 0.151 1285 Planarity : 0.005 0.076 1483 Dihedral : 5.466 64.408 1156 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.77 % Allowed : 13.86 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.26), residues: 1057 helix: 1.60 (0.47), residues: 143 sheet: -0.22 (0.28), residues: 328 loop : -1.25 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 258 HIS 0.006 0.001 HIS O 441 PHE 0.014 0.001 PHE N 328 TYR 0.024 0.002 TYR O 308 ARG 0.004 0.001 ARG O 223 *********************** 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 142 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 231 LEU cc_start: 0.8487 (mt) cc_final: 0.8268 (mt) REVERT: N 324 LYS cc_start: 0.8622 (mtmt) cc_final: 0.8127 (mtpp) REVERT: O 2 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7061 (mp0) REVERT: O 88 MET cc_start: 0.8944 (mmm) cc_final: 0.8699 (mtp) REVERT: O 95 PHE cc_start: 0.7371 (p90) cc_final: 0.7145 (p90) outliers start: 25 outliers final: 20 residues processed: 135 average time/residue: 0.2127 time to fit residues: 40.7243 Evaluate side-chains 134 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 160 ASP Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 167 MET Chi-restraints excluded: chain N residue 205 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 302 ASP 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 143 VAL Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 219 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 79 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 101 optimal weight: 0.2980 chunk 39 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.135255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.105318 restraints weight = 11414.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.103218 restraints weight = 18021.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.104360 restraints weight = 17073.670| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8471 Z= 0.240 Angle : 0.599 10.773 11533 Z= 0.309 Chirality : 0.045 0.181 1285 Planarity : 0.005 0.071 1483 Dihedral : 5.225 59.725 1156 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.88 % Allowed : 13.08 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.26), residues: 1057 helix: 1.71 (0.47), residues: 142 sheet: -0.13 (0.28), residues: 330 loop : -1.22 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 326 HIS 0.004 0.001 HIS N 256 PHE 0.011 0.001 PHE N 328 TYR 0.020 0.001 TYR O 308 ARG 0.008 0.001 ARG K 149 *********************** 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 156 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 324 LYS cc_start: 0.8907 (mtmt) cc_final: 0.8458 (mtpp) REVERT: O 2 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7040 (mp0) outliers start: 35 outliers final: 23 residues processed: 143 average time/residue: 0.1962 time to fit residues: 39.7380 Evaluate side-chains 136 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 137 GLU Chi-restraints excluded: chain N residue 167 MET Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 302 ASP Chi-restraints excluded: chain N residue 342 GLU Chi-restraints excluded: chain N residue 382 VAL 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 143 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 219 LEU Chi-restraints excluded: chain O residue 275 SER Chi-restraints excluded: chain O residue 346 LEU 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 57 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 49 optimal weight: 0.0870 chunk 66 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 overall best weight: 1.1364 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.136594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.107215 restraints weight = 11467.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.104775 restraints weight = 18565.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.105873 restraints weight = 15780.542| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8471 Z= 0.149 Angle : 0.569 10.010 11533 Z= 0.294 Chirality : 0.044 0.191 1285 Planarity : 0.005 0.071 1483 Dihedral : 5.025 62.809 1156 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.33 % Allowed : 14.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.26), residues: 1057 helix: 1.95 (0.47), residues: 142 sheet: -0.02 (0.28), residues: 342 loop : -1.08 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 326 HIS 0.006 0.001 HIS N 256 PHE 0.011 0.001 PHE K 189 TYR 0.016 0.001 TYR O 308 ARG 0.006 0.001 ARG K 149 *********************** 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 143 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 324 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8236 (mtpp) REVERT: O 2 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6976 (mp0) REVERT: O 88 MET cc_start: 0.8635 (mtp) cc_final: 0.8428 (mtp) REVERT: O 377 LYS cc_start: 0.8553 (mtpt) cc_final: 0.8058 (mtpt) outliers start: 21 outliers final: 16 residues processed: 137 average time/residue: 0.1932 time to fit residues: 37.7293 Evaluate side-chains 129 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain N residue 6 PHE Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 137 GLU 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 346 LEU 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 49 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.131901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.102762 restraints weight = 11725.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.100710 restraints weight = 19410.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.101835 restraints weight = 18345.616| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8471 Z= 0.362 Angle : 0.664 10.271 11533 Z= 0.344 Chirality : 0.048 0.175 1285 Planarity : 0.005 0.088 1483 Dihedral : 5.259 53.056 1156 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.44 % Allowed : 14.86 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.26), residues: 1057 helix: 1.68 (0.47), residues: 143 sheet: -0.08 (0.29), residues: 331 loop : -1.26 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 202 HIS 0.007 0.002 HIS O 441 PHE 0.014 0.002 PHE N 328 TYR 0.027 0.002 TYR O 308 ARG 0.006 0.001 ARG K 149 *********************** 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 145 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 303 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7773 (mm-30) REVERT: N 324 LYS cc_start: 0.8881 (mtmt) cc_final: 0.8399 (mtpp) REVERT: N 347 ASN cc_start: 0.8320 (t0) cc_final: 0.8083 (t0) REVERT: O 2 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6925 (mp0) REVERT: O 88 MET cc_start: 0.8682 (mtp) cc_final: 0.8371 (mtt) REVERT: O 377 LYS cc_start: 0.8608 (mtpt) cc_final: 0.8171 (mtpt) outliers start: 31 outliers final: 26 residues processed: 138 average time/residue: 0.1743 time to fit residues: 34.7144 Evaluate side-chains 138 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 238 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 11 LEU Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 137 GLU Chi-restraints excluded: chain N residue 200 CYS Chi-restraints excluded: chain N residue 273 GLU Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 302 ASP Chi-restraints excluded: chain N residue 303 GLU Chi-restraints excluded: chain N residue 342 GLU Chi-restraints excluded: chain N residue 382 VAL 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 143 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 219 LEU Chi-restraints excluded: chain O residue 275 SER Chi-restraints excluded: chain O residue 346 LEU 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 65 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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** N 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.129412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.100734 restraints weight = 11881.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.097703 restraints weight = 17913.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.098734 restraints weight = 19873.643| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 8471 Z= 0.552 Angle : 0.759 10.736 11533 Z= 0.395 Chirality : 0.052 0.192 1285 Planarity : 0.006 0.082 1483 Dihedral : 5.676 43.042 1156 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.99 % Allowed : 14.75 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.25), residues: 1057 helix: 1.24 (0.47), residues: 142 sheet: -0.30 (0.29), residues: 331 loop : -1.49 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 202 HIS 0.010 0.002 HIS N 305 PHE 0.017 0.002 PHE K 189 TYR 0.030 0.002 TYR O 308 ARG 0.007 0.001 ARG N 362 *********************** 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 152 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 239 ASN cc_start: 0.8841 (t0) cc_final: 0.8422 (t0) REVERT: N 303 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7822 (mm-30) REVERT: N 324 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8305 (mtpp) REVERT: N 347 ASN cc_start: 0.8440 (t0) cc_final: 0.8203 (t0) REVERT: O 88 MET cc_start: 0.8754 (mtp) cc_final: 0.8446 (mtt) REVERT: O 377 LYS cc_start: 0.8605 (mtpt) cc_final: 0.8127 (mtpt) outliers start: 36 outliers final: 28 residues processed: 143 average time/residue: 0.1867 time to fit residues: 37.8611 Evaluate side-chains 139 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 238 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain N residue 6 PHE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 137 GLU Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain N residue 200 CYS Chi-restraints excluded: chain N residue 273 GLU Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 302 ASP Chi-restraints excluded: chain N residue 303 GLU Chi-restraints excluded: chain N residue 342 GLU Chi-restraints excluded: chain N residue 382 VAL 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 143 VAL 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 275 SER 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 18 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 50 optimal weight: 0.0000 chunk 67 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 overall best weight: 4.5992 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.130709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.101461 restraints weight = 11685.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.099570 restraints weight = 16960.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.100587 restraints weight = 18039.775| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8471 Z= 0.369 Angle : 0.694 11.089 11533 Z= 0.359 Chirality : 0.048 0.184 1285 Planarity : 0.005 0.077 1483 Dihedral : 5.653 46.670 1156 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.77 % Allowed : 15.52 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.26), residues: 1057 helix: 1.33 (0.47), residues: 141 sheet: -0.29 (0.29), residues: 333 loop : -1.48 (0.24), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 202 HIS 0.007 0.001 HIS N 41 PHE 0.015 0.002 PHE K 189 TYR 0.025 0.002 TYR O 308 ARG 0.005 0.001 ARG K 185 ********************** 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 148 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 303 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7737 (mm-30) REVERT: N 324 LYS cc_start: 0.8899 (mtmt) cc_final: 0.8365 (mtpp) REVERT: N 347 ASN cc_start: 0.8385 (t0) cc_final: 0.8177 (t0) REVERT: O 88 MET cc_start: 0.8753 (mtp) cc_final: 0.8488 (mtt) REVERT: O 377 LYS cc_start: 0.8581 (mtpt) cc_final: 0.8126 (mtpt) REVERT: O 396 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7185 (tm-30) outliers start: 34 outliers final: 26 residues processed: 142 average time/residue: 0.2708 time to fit residues: 53.4146 Evaluate side-chains 135 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 238 VAL Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain N residue 6 PHE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 137 GLU Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain N residue 200 CYS Chi-restraints excluded: chain N residue 273 GLU Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 303 GLU Chi-restraints excluded: chain N residue 382 VAL 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 143 VAL Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 219 LEU Chi-restraints excluded: chain O residue 275 SER Chi-restraints excluded: chain O residue 396 GLN 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 61 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.132372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.102919 restraints weight = 11698.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.101015 restraints weight = 16130.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.102296 restraints weight = 16531.101| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8471 Z= 0.243 Angle : 0.640 10.616 11533 Z= 0.331 Chirality : 0.046 0.168 1285 Planarity : 0.005 0.075 1483 Dihedral : 5.487 48.413 1156 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.77 % Allowed : 16.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.26), residues: 1057 helix: 1.61 (0.47), residues: 140 sheet: -0.30 (0.28), residues: 337 loop : -1.36 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 258 HIS 0.005 0.001 HIS N 256 PHE 0.014 0.001 PHE K 189 TYR 0.020 0.001 TYR O 308 ARG 0.009 0.001 ARG N 362 =============================================================================== Job complete usr+sys time: 3080.71 seconds wall clock time: 55 minutes 12.38 seconds (3312.38 seconds total)