Starting phenix.real_space_refine on Sat Aug 23 14:06:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ti9_41282/08_2025/8ti9_41282.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ti9_41282/08_2025/8ti9_41282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ti9_41282/08_2025/8ti9_41282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ti9_41282/08_2025/8ti9_41282.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ti9_41282/08_2025/8ti9_41282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ti9_41282/08_2025/8ti9_41282.map" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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 24 5.16 5 C 8048 2.51 5 N 2038 2.21 5 O 2382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12492 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1620 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain breaks: 1 Chain: "F" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1499 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain breaks: 1 Chain: "G" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1507 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 6, 'TRANS': 179} Chain breaks: 1 Chain: "H" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1620 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain breaks: 1 Chain: "A" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1620 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain breaks: 1 Chain: "B" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1499 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain breaks: 1 Chain: "C" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1507 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 6, 'TRANS': 179} Chain breaks: 1 Chain: "D" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1620 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain breaks: 1 Time building chain proxies: 3.80, per 1000 atoms: 0.30 Number of scatterers: 12492 At special positions: 0 Unit cell: (87.89, 95.37, 158.015, 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 24 16.00 O 2382 8.00 N 2038 7.00 C 8048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 770.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2980 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 8 sheets defined 58.6% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'E' and resid 173 through 197 removed outlier: 3.599A pdb=" N ASN E 197 " --> pdb=" O VAL E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 213 removed outlier: 3.719A pdb=" N GLU E 213 " --> pdb=" O SER E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 223 removed outlier: 3.919A pdb=" N LEU E 218 " --> pdb=" O ASN E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 254 Processing helix chain 'E' and resid 255 through 258 removed outlier: 3.531A pdb=" N LYS E 258 " --> pdb=" O PRO E 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 255 through 258' Processing helix chain 'E' and resid 286 through 318 Processing helix chain 'E' and resid 336 through 340 removed outlier: 3.861A pdb=" N THR E 339 " --> pdb=" O MET E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 354 Processing helix chain 'E' and resid 363 through 379 Processing helix chain 'F' and resid 184 through 197 Processing helix chain 'F' and resid 203 through 214 removed outlier: 3.615A pdb=" N TRP F 207 " --> pdb=" O SER F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 220 Processing helix chain 'F' and resid 230 through 235 removed outlier: 3.997A pdb=" N VAL F 235 " --> pdb=" O GLU F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 306 removed outlier: 3.541A pdb=" N THR F 290 " --> pdb=" O HIS F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 317 Processing helix chain 'F' and resid 336 through 340 removed outlier: 3.525A pdb=" N THR F 339 " --> pdb=" O MET F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 356 removed outlier: 3.580A pdb=" N LEU F 356 " --> pdb=" O TYR F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 379 removed outlier: 3.728A pdb=" N VAL F 371 " --> pdb=" O LEU F 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 198 Processing helix chain 'G' and resid 203 through 214 removed outlier: 3.510A pdb=" N TRP G 207 " --> pdb=" O SER G 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN G 214 " --> pdb=" O VAL G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 220 removed outlier: 4.386A pdb=" N LEU G 218 " --> pdb=" O ASN G 214 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN G 220 " --> pdb=" O TRP G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 306 removed outlier: 3.542A pdb=" N THR G 290 " --> pdb=" O HIS G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 317 Processing helix chain 'G' and resid 336 through 340 removed outlier: 3.629A pdb=" N THR G 339 " --> pdb=" O MET G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 355 Processing helix chain 'G' and resid 363 through 379 Processing helix chain 'H' and resid 174 through 197 Processing helix chain 'H' and resid 203 through 213 removed outlier: 3.597A pdb=" N GLU H 213 " --> pdb=" O SER H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 222 removed outlier: 4.078A pdb=" N LEU H 218 " --> pdb=" O ASN H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 254 removed outlier: 3.535A pdb=" N PHE H 250 " --> pdb=" O LYS H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 318 Processing helix chain 'H' and resid 336 through 340 removed outlier: 3.575A pdb=" N THR H 339 " --> pdb=" O MET H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 354 Processing helix chain 'H' and resid 363 through 379 Processing helix chain 'A' and resid 174 through 197 removed outlier: 3.500A pdb=" N LEU A 181 " --> pdb=" O GLN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.593A pdb=" N GLU A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 222 removed outlier: 3.775A pdb=" N LEU A 218 " --> pdb=" O ASN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 254 Processing helix chain 'A' and resid 255 through 258 removed outlier: 3.610A pdb=" N LYS A 258 " --> pdb=" O PRO A 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 255 through 258' Processing helix chain 'A' and resid 286 through 318 Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.667A pdb=" N THR A 339 " --> pdb=" O MET A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 Processing helix chain 'A' and resid 363 through 379 Processing helix chain 'B' and resid 184 through 197 Processing helix chain 'B' and resid 203 through 214 removed outlier: 3.558A pdb=" N TRP B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 220 Processing helix chain 'B' and resid 286 through 306 Processing helix chain 'B' and resid 306 through 318 Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.549A pdb=" N THR B 339 " --> pdb=" O MET B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.639A pdb=" N GLU B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 379 removed outlier: 3.743A pdb=" N ARG B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 198 Processing helix chain 'C' and resid 203 through 214 removed outlier: 3.670A pdb=" N TRP C 207 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 214 " --> pdb=" O VAL C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'C' and resid 286 through 306 removed outlier: 3.523A pdb=" N THR C 290 " --> pdb=" O HIS C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 318 Processing helix chain 'C' and resid 336 through 340 Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 363 through 379 removed outlier: 3.882A pdb=" N VAL C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 197 Processing helix chain 'D' and resid 203 through 213 removed outlier: 3.624A pdb=" N GLU D 213 " --> pdb=" O SER D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 222 removed outlier: 3.855A pdb=" N LEU D 218 " --> pdb=" O ASN D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 254 removed outlier: 3.552A pdb=" N PHE D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 318 Processing helix chain 'D' and resid 336 through 340 removed outlier: 3.858A pdb=" N THR D 339 " --> pdb=" O MET D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 354 Processing helix chain 'D' and resid 363 through 379 Processing sheet with id=AA1, first strand: chain 'E' and resid 238 through 239 removed outlier: 7.010A pdb=" N THR E 226 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE E 263 " --> pdb=" O THR E 226 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU E 228 " --> pdb=" O ILE E 263 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE E 265 " --> pdb=" O LEU E 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 227 through 228 removed outlier: 7.135A pdb=" N CYS F 330 " --> pdb=" O THR F 360 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE F 362 " --> pdb=" O CYS F 330 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL F 332 " --> pdb=" O ILE F 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 227 through 228 removed outlier: 6.873A pdb=" N CYS G 330 " --> pdb=" O THR G 360 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE G 362 " --> pdb=" O CYS G 330 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL G 332 " --> pdb=" O ILE G 362 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 238 through 239 removed outlier: 6.402A pdb=" N LEU H 262 " --> pdb=" O VAL H 331 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE H 333 " --> pdb=" O LEU H 262 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ALA H 264 " --> pdb=" O ILE H 333 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 239 removed outlier: 3.542A pdb=" N VAL A 261 " --> pdb=" O THR A 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 227 through 228 removed outlier: 8.538A pdb=" N VAL B 331 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU B 262 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ILE B 333 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA B 264 " --> pdb=" O ILE B 333 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N CYS B 330 " --> pdb=" O THR B 360 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE B 362 " --> pdb=" O CYS B 330 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL B 332 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 227 through 228 removed outlier: 3.524A pdb=" N ILE C 263 " --> pdb=" O PHE C 250 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N CYS C 330 " --> pdb=" O THR C 360 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE C 362 " --> pdb=" O CYS C 330 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL C 332 " --> pdb=" O ILE C 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 238 through 239 697 hydrogen bonds defined for protein. 2004 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: 2.03 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3931 1.34 - 1.46: 2859 1.46 - 1.58: 5914 1.58 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 12736 Sorted by residual: bond pdb=" C THR A 327 " pdb=" O THR A 327 " ideal model delta sigma weight residual 1.235 1.231 0.004 4.70e-03 4.53e+04 5.86e-01 bond pdb=" N THR D 327 " pdb=" CA THR D 327 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.41e-02 5.03e+03 5.01e-01 bond pdb=" N ASN A 224 " pdb=" CA ASN A 224 " ideal model delta sigma weight residual 1.457 1.447 0.010 1.41e-02 5.03e+03 4.81e-01 bond pdb=" N ASN A 230 " pdb=" CA ASN A 230 " ideal model delta sigma weight residual 1.457 1.466 -0.009 1.29e-02 6.01e+03 4.70e-01 bond pdb=" CB ARG E 370 " pdb=" CG ARG E 370 " ideal model delta sigma weight residual 1.520 1.501 0.019 3.00e-02 1.11e+03 4.00e-01 ... (remaining 12731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 17091 1.18 - 2.37: 163 2.37 - 3.55: 55 3.55 - 4.74: 2 4.74 - 5.92: 3 Bond angle restraints: 17314 Sorted by residual: angle pdb=" C ASN A 230 " pdb=" CA ASN A 230 " pdb=" CB ASN A 230 " ideal model delta sigma weight residual 110.42 115.77 -5.35 1.99e+00 2.53e-01 7.24e+00 angle pdb=" C ILE D 326 " pdb=" N THR D 327 " pdb=" CA THR D 327 " ideal model delta sigma weight residual 121.80 127.72 -5.92 2.44e+00 1.68e-01 5.90e+00 angle pdb=" N ILE F 333 " pdb=" CA ILE F 333 " pdb=" C ILE F 333 " ideal model delta sigma weight residual 106.53 109.47 -2.94 1.41e+00 5.03e-01 4.35e+00 angle pdb=" C LYS A 266 " pdb=" N THR A 267 " pdb=" CA THR A 267 " ideal model delta sigma weight residual 120.97 115.44 5.53 2.84e+00 1.24e-01 3.80e+00 angle pdb=" CA ASN A 230 " pdb=" C ASN A 230 " pdb=" N ASP A 231 " ideal model delta sigma weight residual 116.84 119.96 -3.12 1.71e+00 3.42e-01 3.32e+00 ... (remaining 17309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.01: 7144 14.01 - 28.03: 366 28.03 - 42.04: 75 42.04 - 56.05: 20 56.05 - 70.07: 5 Dihedral angle restraints: 7610 sinusoidal: 3024 harmonic: 4586 Sorted by residual: dihedral pdb=" N PHE E 337 " pdb=" CA PHE E 337 " pdb=" CB PHE E 337 " pdb=" CG PHE E 337 " ideal model delta sinusoidal sigma weight residual -60.00 -119.05 59.05 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LYS A 287 " pdb=" CB LYS A 287 " pdb=" CG LYS A 287 " pdb=" CD LYS A 287 " ideal model delta sinusoidal sigma weight residual 60.00 118.61 -58.61 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N ASN E 224 " pdb=" CA ASN E 224 " pdb=" CB ASN E 224 " pdb=" CG ASN E 224 " ideal model delta sinusoidal sigma weight residual -60.00 -116.28 56.28 3 1.50e+01 4.44e-03 9.39e+00 ... (remaining 7607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1261 0.027 - 0.053: 465 0.053 - 0.080: 177 0.080 - 0.106: 130 0.106 - 0.133: 35 Chirality restraints: 2068 Sorted by residual: chirality pdb=" CA PHE E 368 " pdb=" N PHE E 368 " pdb=" C PHE E 368 " pdb=" CB PHE E 368 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA PHE H 368 " pdb=" N PHE H 368 " pdb=" C PHE H 368 " pdb=" CB PHE H 368 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA ILE E 333 " pdb=" N ILE E 333 " pdb=" C ILE E 333 " pdb=" CB ILE E 333 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 ... (remaining 2065 not shown) Planarity restraints: 2146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 267 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO F 268 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO F 268 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO F 268 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 267 " -0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO B 268 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 268 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 268 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 327 " -0.019 5.00e-02 4.00e+02 2.80e-02 1.25e+00 pdb=" N PRO G 328 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO G 328 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 328 " -0.015 5.00e-02 4.00e+02 ... (remaining 2143 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1029 2.74 - 3.28: 12779 3.28 - 3.82: 21131 3.82 - 4.36: 24900 4.36 - 4.90: 43118 Nonbonded interactions: 102957 Sorted by model distance: nonbonded pdb=" OH TYR E 315 " pdb=" OD1 ASN H 313 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR G 363 " pdb=" OD1 ASP G 365 " model vdw 2.235 3.040 nonbonded pdb=" OE1 GLU H 232 " pdb=" OH TYR H 234 " model vdw 2.268 3.040 nonbonded pdb=" OG1 THR F 363 " pdb=" OD1 ASP F 365 " model vdw 2.281 3.040 nonbonded pdb=" NH1 ARG E 370 " pdb=" O PHE F 222 " model vdw 2.289 3.120 ... (remaining 102952 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 183 through 235 or resid 248 through 379)) selection = (chain 'B' and (resid 183 through 318 or resid 324 through 379)) selection = (chain 'C' and (resid 183 through 235 or resid 248 through 318 or resid 324 thro \ ugh 379)) selection = (chain 'D' and (resid 183 through 235 or resid 248 through 379)) selection = (chain 'E' and (resid 183 through 235 or resid 248 through 379)) selection = (chain 'F' and (resid 183 through 318 or resid 324 through 379)) selection = (chain 'G' and (resid 183 through 235 or resid 248 through 318 or resid 324 thro \ ugh 379)) selection = (chain 'H' and (resid 183 through 235 or resid 248 through 379)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.280 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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.120 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 12736 Z= 0.100 Angle : 0.371 5.924 17314 Z= 0.202 Chirality : 0.040 0.133 2068 Planarity : 0.003 0.030 2146 Dihedral : 9.320 70.067 4630 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.27 % Allowed : 4.02 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.23), residues: 1518 helix: 2.69 (0.18), residues: 834 sheet: -0.36 (0.43), residues: 164 loop : 0.31 (0.31), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 370 TYR 0.007 0.001 TYR G 234 PHE 0.015 0.001 PHE E 368 TRP 0.009 0.001 TRP C 207 HIS 0.001 0.000 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00216 (12736) covalent geometry : angle 0.37105 (17314) hydrogen bonds : bond 0.14192 ( 697) hydrogen bonds : angle 4.54252 ( 2004) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 425 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 192 SER cc_start: 0.9476 (t) cc_final: 0.9180 (p) REVERT: E 198 LYS cc_start: 0.9099 (pttp) cc_final: 0.8780 (ptpt) REVERT: E 269 SER cc_start: 0.8979 (m) cc_final: 0.8771 (p) REVERT: E 317 GLN cc_start: 0.8327 (tp40) cc_final: 0.7730 (tm-30) REVERT: E 336 MET cc_start: 0.7152 (mtm) cc_final: 0.6843 (mtm) REVERT: F 312 TYR cc_start: 0.8365 (t80) cc_final: 0.7574 (t80) REVERT: F 317 GLN cc_start: 0.8474 (mt0) cc_final: 0.8119 (tm-30) REVERT: G 212 LYS cc_start: 0.7827 (tttt) cc_final: 0.7435 (ttmm) REVERT: G 259 ASP cc_start: 0.7505 (t0) cc_final: 0.7247 (p0) REVERT: G 313 ASN cc_start: 0.9008 (m-40) cc_final: 0.8535 (m-40) REVERT: G 336 MET cc_start: 0.4964 (mtm) cc_final: 0.4503 (mtm) REVERT: G 372 LYS cc_start: 0.9125 (tttt) cc_final: 0.8921 (ptpt) REVERT: H 198 LYS cc_start: 0.9201 (pttt) cc_final: 0.8997 (ptpp) REVERT: H 207 TRP cc_start: 0.7634 (m100) cc_final: 0.7343 (m100) REVERT: H 257 SER cc_start: 0.8430 (m) cc_final: 0.8125 (p) REVERT: H 280 THR cc_start: 0.8301 (m) cc_final: 0.7982 (p) REVERT: H 304 GLN cc_start: 0.8018 (mt0) cc_final: 0.7700 (tm-30) REVERT: H 368 PHE cc_start: 0.8389 (m-80) cc_final: 0.7985 (m-80) REVERT: H 376 LYS cc_start: 0.9410 (tttt) cc_final: 0.9118 (pttp) REVERT: A 258 LYS cc_start: 0.6104 (mttt) cc_final: 0.5691 (tttt) REVERT: A 277 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7584 (mp0) REVERT: A 304 GLN cc_start: 0.8255 (mt0) cc_final: 0.8046 (mt0) REVERT: A 305 ARG cc_start: 0.7532 (tpt170) cc_final: 0.7291 (tpt170) REVERT: A 346 ARG cc_start: 0.7680 (mtt180) cc_final: 0.7177 (mtt-85) REVERT: B 304 GLN cc_start: 0.8386 (tt0) cc_final: 0.8144 (tp40) REVERT: C 192 SER cc_start: 0.9585 (t) cc_final: 0.9253 (p) REVERT: C 209 SER cc_start: 0.9023 (m) cc_final: 0.8621 (p) REVERT: C 226 THR cc_start: 0.7950 (p) cc_final: 0.7683 (p) REVERT: C 232 GLU cc_start: 0.8936 (pt0) cc_final: 0.8736 (pt0) REVERT: C 336 MET cc_start: 0.7488 (mtm) cc_final: 0.7070 (mtp) REVERT: D 202 THR cc_start: 0.9291 (p) cc_final: 0.8964 (p) REVERT: D 204 GLU cc_start: 0.7990 (tt0) cc_final: 0.7571 (tm-30) REVERT: D 212 LYS cc_start: 0.8571 (pttt) cc_final: 0.8250 (ptmt) REVERT: D 246 LYS cc_start: 0.8810 (mttt) cc_final: 0.8503 (mmmt) REVERT: D 256 PHE cc_start: 0.8195 (t80) cc_final: 0.7881 (p90) REVERT: D 259 ASP cc_start: 0.7036 (m-30) cc_final: 0.6448 (p0) REVERT: D 299 TYR cc_start: 0.8132 (t80) cc_final: 0.7800 (t80) REVERT: D 350 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8485 (mm-30) REVERT: D 369 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8210 (tp30) REVERT: D 376 LYS cc_start: 0.8734 (tttt) cc_final: 0.8239 (tmmt) outliers start: 18 outliers final: 8 residues processed: 441 average time/residue: 0.1436 time to fit residues: 85.8401 Evaluate side-chains 225 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 217 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 194 TRP Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain D residue 375 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 220 GLN E 313 ASN F 295 GLN G 197 ASN ** H 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 ASN A 220 GLN A 313 ASN B 197 ASN B 295 GLN B 345 HIS C 201 ASN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS D 179 ASN D 186 ASN D 220 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.106825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.089808 restraints weight = 28377.625| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.40 r_work: 0.3385 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12736 Z= 0.142 Angle : 0.546 12.895 17314 Z= 0.286 Chirality : 0.044 0.223 2068 Planarity : 0.004 0.047 2146 Dihedral : 4.426 58.190 1670 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.24 % Allowed : 12.20 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.23), residues: 1518 helix: 2.25 (0.18), residues: 844 sheet: 0.31 (0.47), residues: 148 loop : 0.21 (0.30), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 370 TYR 0.022 0.001 TYR B 278 PHE 0.016 0.002 PHE C 206 TRP 0.014 0.002 TRP G 216 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00326 (12736) covalent geometry : angle 0.54597 (17314) hydrogen bonds : bond 0.04158 ( 697) hydrogen bonds : angle 3.91092 ( 2004) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 252 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 317 GLN cc_start: 0.8199 (tp40) cc_final: 0.7576 (tm-30) REVERT: E 336 MET cc_start: 0.6981 (mtm) cc_final: 0.6586 (mtm) REVERT: G 195 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8893 (mp0) REVERT: G 206 PHE cc_start: 0.7355 (t80) cc_final: 0.6967 (t80) REVERT: G 212 LYS cc_start: 0.7685 (tttt) cc_final: 0.7421 (ttmt) REVERT: G 232 GLU cc_start: 0.8517 (pp20) cc_final: 0.8272 (pp20) REVERT: G 259 ASP cc_start: 0.7581 (t0) cc_final: 0.7323 (p0) REVERT: G 277 GLU cc_start: 0.8457 (pt0) cc_final: 0.8198 (pt0) REVERT: H 280 THR cc_start: 0.8304 (m) cc_final: 0.8019 (p) REVERT: H 304 GLN cc_start: 0.8038 (mt0) cc_final: 0.7673 (tm-30) REVERT: H 368 PHE cc_start: 0.8259 (m-80) cc_final: 0.7937 (m-80) REVERT: H 369 GLU cc_start: 0.8742 (tp30) cc_final: 0.8475 (tp30) REVERT: H 370 ARG cc_start: 0.7092 (tpt90) cc_final: 0.6871 (tpt90) REVERT: H 376 LYS cc_start: 0.9445 (tttt) cc_final: 0.9111 (pttp) REVERT: A 258 LYS cc_start: 0.6202 (mttt) cc_final: 0.5819 (tttt) REVERT: A 277 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7756 (mp0) REVERT: A 305 ARG cc_start: 0.7659 (tpt170) cc_final: 0.7453 (tpt170) REVERT: A 346 ARG cc_start: 0.7639 (mtt180) cc_final: 0.7284 (mtt-85) REVERT: B 336 MET cc_start: 0.8455 (mtm) cc_final: 0.7962 (mmm) REVERT: B 365 ASP cc_start: 0.7617 (p0) cc_final: 0.7347 (p0) REVERT: B 378 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8585 (mm) REVERT: C 192 SER cc_start: 0.9594 (t) cc_final: 0.9338 (p) REVERT: C 226 THR cc_start: 0.7964 (p) cc_final: 0.7734 (p) REVERT: C 308 GLN cc_start: 0.7684 (tt0) cc_final: 0.7433 (mm-40) REVERT: C 354 LYS cc_start: 0.7891 (mmmt) cc_final: 0.7624 (mmtm) REVERT: D 246 LYS cc_start: 0.8979 (mttt) cc_final: 0.8604 (mmmt) REVERT: D 256 PHE cc_start: 0.8376 (t80) cc_final: 0.7982 (p90) REVERT: D 259 ASP cc_start: 0.7156 (m-30) cc_final: 0.6264 (p0) REVERT: D 299 TYR cc_start: 0.8132 (t80) cc_final: 0.7705 (t80) REVERT: D 376 LYS cc_start: 0.8684 (tttt) cc_final: 0.8148 (tmmt) outliers start: 46 outliers final: 25 residues processed: 289 average time/residue: 0.1254 time to fit residues: 51.3330 Evaluate side-chains 234 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 256 PHE Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 375 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 116 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 32 optimal weight: 0.2980 chunk 98 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 59 optimal weight: 0.4980 chunk 28 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 220 GLN G 197 ASN H 197 ASN H 201 ASN H 208 GLN A 220 GLN C 208 GLN C 214 ASN D 186 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.106368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.089501 restraints weight = 28762.445| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 3.35 r_work: 0.3389 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12736 Z= 0.127 Angle : 0.519 11.063 17314 Z= 0.273 Chirality : 0.043 0.144 2068 Planarity : 0.003 0.050 2146 Dihedral : 4.443 58.069 1666 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.53 % Allowed : 13.54 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.23), residues: 1518 helix: 2.02 (0.18), residues: 848 sheet: -0.14 (0.40), residues: 184 loop : 0.34 (0.32), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 279 TYR 0.026 0.001 TYR B 283 PHE 0.019 0.002 PHE E 256 TRP 0.028 0.002 TRP G 216 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00289 (12736) covalent geometry : angle 0.51947 (17314) hydrogen bonds : bond 0.03802 ( 697) hydrogen bonds : angle 3.83521 ( 2004) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 234 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 317 GLN cc_start: 0.8199 (tp40) cc_final: 0.7580 (tm-30) REVERT: E 336 MET cc_start: 0.6988 (mtm) cc_final: 0.6599 (mtm) REVERT: F 259 ASP cc_start: 0.7969 (t0) cc_final: 0.7678 (t70) REVERT: F 322 ASP cc_start: 0.8795 (m-30) cc_final: 0.8340 (m-30) REVERT: G 197 ASN cc_start: 0.8366 (OUTLIER) cc_final: 0.7877 (t0) REVERT: G 206 PHE cc_start: 0.7449 (t80) cc_final: 0.6952 (t80) REVERT: G 212 LYS cc_start: 0.7604 (tttt) cc_final: 0.7332 (mtmt) REVERT: G 277 GLU cc_start: 0.8513 (pt0) cc_final: 0.8305 (pt0) REVERT: H 198 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8344 (ptpt) REVERT: H 280 THR cc_start: 0.8267 (m) cc_final: 0.7983 (p) REVERT: H 304 GLN cc_start: 0.8085 (mt0) cc_final: 0.7706 (tm-30) REVERT: H 326 ILE cc_start: 0.6244 (mm) cc_final: 0.5954 (mt) REVERT: H 368 PHE cc_start: 0.8270 (m-80) cc_final: 0.8009 (m-80) REVERT: H 370 ARG cc_start: 0.7054 (tpt90) cc_final: 0.6811 (tpt90) REVERT: H 376 LYS cc_start: 0.9447 (tttt) cc_final: 0.9160 (pttp) REVERT: A 177 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8457 (mm-40) REVERT: A 258 LYS cc_start: 0.6484 (mttt) cc_final: 0.5985 (tttt) REVERT: A 277 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7729 (mp0) REVERT: A 346 ARG cc_start: 0.7678 (mtt180) cc_final: 0.7354 (mtt-85) REVERT: B 312 TYR cc_start: 0.8362 (t80) cc_final: 0.7873 (t80) REVERT: B 336 MET cc_start: 0.8464 (mtm) cc_final: 0.8035 (mmm) REVERT: B 365 ASP cc_start: 0.7670 (p0) cc_final: 0.7431 (p0) REVERT: B 378 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8555 (mm) REVERT: C 192 SER cc_start: 0.9562 (t) cc_final: 0.9307 (p) REVERT: C 226 THR cc_start: 0.7941 (p) cc_final: 0.7710 (p) REVERT: D 188 LYS cc_start: 0.8391 (mmtm) cc_final: 0.8013 (mmmt) REVERT: D 246 LYS cc_start: 0.8968 (mttt) cc_final: 0.8598 (mmmt) REVERT: D 256 PHE cc_start: 0.8422 (t80) cc_final: 0.7992 (p90) REVERT: D 259 ASP cc_start: 0.7203 (m-30) cc_final: 0.6313 (p0) REVERT: D 336 MET cc_start: 0.7626 (mtm) cc_final: 0.7301 (mtm) REVERT: D 376 LYS cc_start: 0.8743 (tttt) cc_final: 0.8188 (tmmt) outliers start: 50 outliers final: 30 residues processed: 266 average time/residue: 0.1227 time to fit residues: 46.5482 Evaluate side-chains 247 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 329 CYS Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 256 PHE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 337 PHE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 375 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 108 optimal weight: 0.0370 chunk 135 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 56 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 177 GLN E 220 GLN ** G 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.107023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.090038 restraints weight = 28569.195| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.35 r_work: 0.3398 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12736 Z= 0.119 Angle : 0.515 8.791 17314 Z= 0.270 Chirality : 0.043 0.286 2068 Planarity : 0.003 0.051 2146 Dihedral : 4.441 57.748 1666 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.75 % Allowed : 15.16 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.22), residues: 1518 helix: 2.00 (0.18), residues: 846 sheet: -0.04 (0.40), residues: 186 loop : 0.34 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 370 TYR 0.017 0.001 TYR B 278 PHE 0.020 0.001 PHE E 256 TRP 0.029 0.002 TRP G 216 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00271 (12736) covalent geometry : angle 0.51547 (17314) hydrogen bonds : bond 0.03595 ( 697) hydrogen bonds : angle 3.76087 ( 2004) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 228 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 317 GLN cc_start: 0.8186 (tp40) cc_final: 0.7564 (tm-30) REVERT: E 336 MET cc_start: 0.6974 (mtm) cc_final: 0.6578 (mtm) REVERT: F 187 LEU cc_start: 0.8849 (mm) cc_final: 0.8546 (mm) REVERT: F 259 ASP cc_start: 0.7898 (t0) cc_final: 0.7601 (t70) REVERT: F 322 ASP cc_start: 0.8840 (m-30) cc_final: 0.8399 (m-30) REVERT: G 195 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8221 (mp0) REVERT: G 212 LYS cc_start: 0.7510 (tttt) cc_final: 0.7256 (ttmm) REVERT: G 232 GLU cc_start: 0.8696 (pp20) cc_final: 0.8426 (pp20) REVERT: G 306 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7047 (mp0) REVERT: H 198 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8299 (ptpt) REVERT: H 280 THR cc_start: 0.8245 (m) cc_final: 0.7959 (p) REVERT: H 304 GLN cc_start: 0.8078 (mt0) cc_final: 0.7684 (tm-30) REVERT: H 306 GLU cc_start: 0.8454 (tp30) cc_final: 0.7938 (tp30) REVERT: H 326 ILE cc_start: 0.6173 (mm) cc_final: 0.5946 (mm) REVERT: H 368 PHE cc_start: 0.8223 (m-80) cc_final: 0.7944 (m-80) REVERT: H 376 LYS cc_start: 0.9455 (tttt) cc_final: 0.9164 (pttp) REVERT: A 176 ASP cc_start: 0.8913 (p0) cc_final: 0.8477 (p0) REVERT: A 177 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8523 (mm-40) REVERT: A 258 LYS cc_start: 0.6538 (mttt) cc_final: 0.6041 (tttt) REVERT: A 277 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7735 (mp0) REVERT: A 346 ARG cc_start: 0.7709 (mtt180) cc_final: 0.7388 (mtt-85) REVERT: B 336 MET cc_start: 0.8443 (mtm) cc_final: 0.8094 (mmm) REVERT: B 365 ASP cc_start: 0.7700 (p0) cc_final: 0.7487 (p0) REVERT: B 378 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8611 (mm) REVERT: C 192 SER cc_start: 0.9553 (t) cc_final: 0.9303 (p) REVERT: C 226 THR cc_start: 0.7940 (p) cc_final: 0.7697 (p) REVERT: C 366 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8411 (mt-10) REVERT: D 188 LYS cc_start: 0.8424 (mmtm) cc_final: 0.8059 (mmmt) REVERT: D 246 LYS cc_start: 0.8971 (mttt) cc_final: 0.8610 (mmmt) REVERT: D 256 PHE cc_start: 0.8436 (t80) cc_final: 0.7924 (p90) REVERT: D 259 ASP cc_start: 0.7187 (m-30) cc_final: 0.6310 (p0) REVERT: D 336 MET cc_start: 0.7586 (mtm) cc_final: 0.7350 (mtm) REVERT: D 376 LYS cc_start: 0.8770 (tttt) cc_final: 0.8193 (tmmt) outliers start: 39 outliers final: 26 residues processed: 253 average time/residue: 0.1214 time to fit residues: 43.9613 Evaluate side-chains 231 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 329 CYS Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 256 PHE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 337 PHE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 379 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 115 optimal weight: 0.9980 chunk 131 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 88 optimal weight: 0.2980 chunk 118 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN H 197 ASN H 208 GLN A 220 GLN C 208 GLN D 186 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.107245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.090423 restraints weight = 28610.914| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.33 r_work: 0.3409 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12736 Z= 0.120 Angle : 0.512 11.999 17314 Z= 0.266 Chirality : 0.043 0.249 2068 Planarity : 0.003 0.051 2146 Dihedral : 4.430 57.519 1666 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.96 % Allowed : 15.73 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.22), residues: 1518 helix: 2.02 (0.18), residues: 844 sheet: -0.01 (0.40), residues: 186 loop : 0.35 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 316 TYR 0.017 0.001 TYR B 278 PHE 0.021 0.001 PHE G 206 TRP 0.033 0.002 TRP G 216 HIS 0.002 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00269 (12736) covalent geometry : angle 0.51151 (17314) hydrogen bonds : bond 0.03502 ( 697) hydrogen bonds : angle 3.68811 ( 2004) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 317 GLN cc_start: 0.8258 (tp40) cc_final: 0.7589 (tm-30) REVERT: E 336 MET cc_start: 0.6929 (mtm) cc_final: 0.6652 (mtm) REVERT: F 187 LEU cc_start: 0.8839 (mm) cc_final: 0.8556 (mm) REVERT: F 259 ASP cc_start: 0.7864 (t0) cc_final: 0.7546 (t70) REVERT: F 322 ASP cc_start: 0.8836 (m-30) cc_final: 0.8390 (m-30) REVERT: G 206 PHE cc_start: 0.7272 (t80) cc_final: 0.6864 (t80) REVERT: G 212 LYS cc_start: 0.7459 (tttt) cc_final: 0.7239 (ttmm) REVERT: G 232 GLU cc_start: 0.8751 (pp20) cc_final: 0.8437 (pp20) REVERT: G 306 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7063 (mp0) REVERT: G 360 THR cc_start: 0.7863 (m) cc_final: 0.7646 (p) REVERT: G 372 LYS cc_start: 0.8867 (pttt) cc_final: 0.8623 (pttm) REVERT: H 198 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8295 (ptpt) REVERT: H 280 THR cc_start: 0.8269 (m) cc_final: 0.7960 (p) REVERT: H 304 GLN cc_start: 0.8098 (mt0) cc_final: 0.7698 (tm-30) REVERT: H 306 GLU cc_start: 0.8541 (tp30) cc_final: 0.8017 (tp30) REVERT: H 326 ILE cc_start: 0.6206 (mm) cc_final: 0.5989 (mm) REVERT: H 368 PHE cc_start: 0.8186 (m-80) cc_final: 0.7957 (m-80) REVERT: H 376 LYS cc_start: 0.9461 (tttt) cc_final: 0.9175 (pttp) REVERT: A 176 ASP cc_start: 0.8893 (p0) cc_final: 0.8450 (p0) REVERT: A 177 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8592 (mm-40) REVERT: A 258 LYS cc_start: 0.6535 (mttt) cc_final: 0.6033 (tttt) REVERT: A 273 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7772 (pt) REVERT: A 277 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7697 (mp0) REVERT: A 279 ARG cc_start: 0.7351 (mmt-90) cc_final: 0.7055 (mtt-85) REVERT: A 346 ARG cc_start: 0.7695 (mtt180) cc_final: 0.7383 (mtt-85) REVERT: B 312 TYR cc_start: 0.8241 (t80) cc_final: 0.7855 (t80) REVERT: B 378 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8629 (mm) REVERT: C 192 SER cc_start: 0.9547 (t) cc_final: 0.9294 (p) REVERT: C 203 SER cc_start: 0.7572 (t) cc_final: 0.7345 (p) REVERT: C 208 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7353 (tp40) REVERT: C 226 THR cc_start: 0.7964 (p) cc_final: 0.7706 (p) REVERT: C 366 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8447 (mt-10) REVERT: D 188 LYS cc_start: 0.8428 (mmtm) cc_final: 0.8056 (mmmt) REVERT: D 246 LYS cc_start: 0.8975 (mttt) cc_final: 0.8621 (mmmt) REVERT: D 256 PHE cc_start: 0.8419 (t80) cc_final: 0.7918 (p90) REVERT: D 259 ASP cc_start: 0.7187 (m-30) cc_final: 0.6324 (p0) REVERT: D 305 ARG cc_start: 0.7970 (tpp-160) cc_final: 0.7643 (tpt170) REVERT: D 376 LYS cc_start: 0.8783 (tttt) cc_final: 0.8193 (tmmt) outliers start: 42 outliers final: 27 residues processed: 248 average time/residue: 0.1184 time to fit residues: 42.2651 Evaluate side-chains 231 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 329 CYS Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 256 PHE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 208 GLN Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain D residue 337 PHE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 379 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 148 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 63 optimal weight: 0.0050 chunk 91 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 99 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN D 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.107171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.090537 restraints weight = 28503.082| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.28 r_work: 0.3411 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12736 Z= 0.120 Angle : 0.521 11.261 17314 Z= 0.269 Chirality : 0.042 0.165 2068 Planarity : 0.003 0.051 2146 Dihedral : 4.401 57.485 1666 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.82 % Allowed : 16.93 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.22), residues: 1518 helix: 2.06 (0.18), residues: 844 sheet: 0.04 (0.40), residues: 186 loop : 0.38 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 279 TYR 0.021 0.001 TYR B 278 PHE 0.022 0.001 PHE E 256 TRP 0.035 0.002 TRP G 216 HIS 0.002 0.001 HIS H 286 Details of bonding type rmsd covalent geometry : bond 0.00276 (12736) covalent geometry : angle 0.52146 (17314) hydrogen bonds : bond 0.03416 ( 697) hydrogen bonds : angle 3.66200 ( 2004) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 225 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 317 GLN cc_start: 0.8195 (tp40) cc_final: 0.7535 (tm-30) REVERT: E 336 MET cc_start: 0.6897 (mtm) cc_final: 0.6505 (mtm) REVERT: F 187 LEU cc_start: 0.8846 (mm) cc_final: 0.8565 (mm) REVERT: F 259 ASP cc_start: 0.7842 (t0) cc_final: 0.7561 (t70) REVERT: F 322 ASP cc_start: 0.8847 (m-30) cc_final: 0.8337 (m-30) REVERT: F 372 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8907 (pptt) REVERT: G 206 PHE cc_start: 0.7312 (t80) cc_final: 0.6945 (t80) REVERT: G 212 LYS cc_start: 0.7344 (tttt) cc_final: 0.7076 (mttm) REVERT: G 277 GLU cc_start: 0.8588 (pt0) cc_final: 0.8307 (pt0) REVERT: H 198 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8288 (ptpp) REVERT: H 280 THR cc_start: 0.8271 (m) cc_final: 0.7963 (p) REVERT: H 304 GLN cc_start: 0.8075 (mt0) cc_final: 0.7667 (tm-30) REVERT: H 306 GLU cc_start: 0.8548 (tp30) cc_final: 0.8011 (tp30) REVERT: H 326 ILE cc_start: 0.6193 (mm) cc_final: 0.5977 (mm) REVERT: H 368 PHE cc_start: 0.8206 (m-80) cc_final: 0.7987 (m-80) REVERT: H 376 LYS cc_start: 0.9462 (tttt) cc_final: 0.9194 (pttp) REVERT: A 176 ASP cc_start: 0.8827 (p0) cc_final: 0.8322 (p0) REVERT: A 177 GLN cc_start: 0.8956 (mm-40) cc_final: 0.8586 (mm-40) REVERT: A 258 LYS cc_start: 0.6551 (mttt) cc_final: 0.6039 (tttt) REVERT: A 277 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7679 (mp0) REVERT: A 279 ARG cc_start: 0.7366 (mmt-90) cc_final: 0.7112 (mtt-85) REVERT: A 346 ARG cc_start: 0.7660 (mtt180) cc_final: 0.7360 (mtt-85) REVERT: B 378 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8627 (mm) REVERT: C 188 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.9200 (mttt) REVERT: C 192 SER cc_start: 0.9555 (t) cc_final: 0.9288 (p) REVERT: C 226 THR cc_start: 0.7985 (p) cc_final: 0.7720 (p) REVERT: D 231 ASP cc_start: 0.9032 (p0) cc_final: 0.8826 (p0) REVERT: D 246 LYS cc_start: 0.8982 (mttt) cc_final: 0.8661 (mmmt) REVERT: D 256 PHE cc_start: 0.8476 (t80) cc_final: 0.7952 (p90) REVERT: D 259 ASP cc_start: 0.7177 (m-30) cc_final: 0.6311 (p0) REVERT: D 305 ARG cc_start: 0.7991 (tpp-160) cc_final: 0.7656 (tpt170) REVERT: D 376 LYS cc_start: 0.8782 (tttt) cc_final: 0.8194 (tmmt) outliers start: 40 outliers final: 27 residues processed: 252 average time/residue: 0.1212 time to fit residues: 43.7305 Evaluate side-chains 236 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 372 LYS Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 256 PHE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain D residue 337 PHE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 379 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 86 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 88 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 142 optimal weight: 0.0170 chunk 43 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 ASN H 220 GLN A 220 GLN C 208 GLN D 186 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.107437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.090666 restraints weight = 28494.829| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 3.30 r_work: 0.3419 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12736 Z= 0.117 Angle : 0.527 11.085 17314 Z= 0.270 Chirality : 0.043 0.287 2068 Planarity : 0.003 0.050 2146 Dihedral : 4.392 57.379 1666 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.82 % Allowed : 17.00 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.22), residues: 1518 helix: 2.05 (0.18), residues: 844 sheet: 0.07 (0.40), residues: 186 loop : 0.40 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 279 TYR 0.021 0.001 TYR B 278 PHE 0.022 0.001 PHE E 256 TRP 0.038 0.002 TRP G 216 HIS 0.002 0.001 HIS H 286 Details of bonding type rmsd covalent geometry : bond 0.00267 (12736) covalent geometry : angle 0.52723 (17314) hydrogen bonds : bond 0.03442 ( 697) hydrogen bonds : angle 3.65069 ( 2004) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 227 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 317 GLN cc_start: 0.8213 (tp40) cc_final: 0.7451 (pp30) REVERT: E 336 MET cc_start: 0.6876 (mtm) cc_final: 0.6482 (mtm) REVERT: F 187 LEU cc_start: 0.8835 (mm) cc_final: 0.8576 (mm) REVERT: F 259 ASP cc_start: 0.7800 (t0) cc_final: 0.7583 (t70) REVERT: F 322 ASP cc_start: 0.8864 (m-30) cc_final: 0.8434 (m-30) REVERT: F 372 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8919 (pptt) REVERT: G 206 PHE cc_start: 0.7339 (t80) cc_final: 0.6996 (t80) REVERT: G 212 LYS cc_start: 0.7242 (tttt) cc_final: 0.6957 (mtmm) REVERT: G 277 GLU cc_start: 0.8597 (pt0) cc_final: 0.8309 (pt0) REVERT: G 360 THR cc_start: 0.7865 (m) cc_final: 0.7658 (p) REVERT: G 372 LYS cc_start: 0.8855 (pttt) cc_final: 0.8560 (pttm) REVERT: H 198 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8292 (ptpp) REVERT: H 280 THR cc_start: 0.8273 (m) cc_final: 0.7961 (p) REVERT: H 304 GLN cc_start: 0.8093 (mt0) cc_final: 0.7683 (tm-30) REVERT: H 306 GLU cc_start: 0.8576 (tp30) cc_final: 0.8038 (tp30) REVERT: H 326 ILE cc_start: 0.6168 (mm) cc_final: 0.5955 (mm) REVERT: H 368 PHE cc_start: 0.8181 (m-80) cc_final: 0.7945 (m-80) REVERT: H 376 LYS cc_start: 0.9455 (tttt) cc_final: 0.9207 (pttp) REVERT: A 176 ASP cc_start: 0.8828 (p0) cc_final: 0.8312 (p0) REVERT: A 177 GLN cc_start: 0.8965 (mm-40) cc_final: 0.8594 (mm-40) REVERT: A 232 GLU cc_start: 0.6351 (mp0) cc_final: 0.6088 (mp0) REVERT: A 258 LYS cc_start: 0.6532 (mttt) cc_final: 0.6027 (tttt) REVERT: A 277 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7698 (mp0) REVERT: A 279 ARG cc_start: 0.7351 (mmt-90) cc_final: 0.7100 (mtt-85) REVERT: A 346 ARG cc_start: 0.7687 (mtt180) cc_final: 0.7376 (mtt-85) REVERT: A 366 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6552 (mt-10) REVERT: B 278 TYR cc_start: 0.7790 (t80) cc_final: 0.7429 (t80) REVERT: C 188 LYS cc_start: 0.9429 (OUTLIER) cc_final: 0.9184 (mttt) REVERT: C 192 SER cc_start: 0.9551 (t) cc_final: 0.9283 (p) REVERT: C 208 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7460 (tp40) REVERT: C 226 THR cc_start: 0.7991 (p) cc_final: 0.7726 (p) REVERT: D 220 GLN cc_start: 0.8402 (tp40) cc_final: 0.8071 (tp40) REVERT: D 231 ASP cc_start: 0.9023 (p0) cc_final: 0.8814 (p0) REVERT: D 246 LYS cc_start: 0.8913 (mttt) cc_final: 0.8669 (mmmt) REVERT: D 256 PHE cc_start: 0.8455 (t80) cc_final: 0.7998 (p90) REVERT: D 259 ASP cc_start: 0.7168 (m-30) cc_final: 0.6375 (p0) REVERT: D 305 ARG cc_start: 0.7987 (tpp-160) cc_final: 0.7677 (tpt170) REVERT: D 376 LYS cc_start: 0.8786 (tttt) cc_final: 0.8196 (tmmt) outliers start: 40 outliers final: 30 residues processed: 255 average time/residue: 0.1174 time to fit residues: 43.5181 Evaluate side-chains 245 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 372 LYS Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 256 PHE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 208 GLN Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 337 PHE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 379 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 115 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 0.0470 chunk 103 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 220 GLN G 197 ASN ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.107581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.090794 restraints weight = 28196.330| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.27 r_work: 0.3420 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12736 Z= 0.121 Angle : 0.543 11.376 17314 Z= 0.279 Chirality : 0.043 0.294 2068 Planarity : 0.003 0.050 2146 Dihedral : 4.408 57.282 1666 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.89 % Allowed : 17.63 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.22), residues: 1518 helix: 2.01 (0.18), residues: 844 sheet: 0.10 (0.40), residues: 186 loop : 0.38 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 279 TYR 0.025 0.001 TYR F 312 PHE 0.023 0.001 PHE E 256 TRP 0.042 0.002 TRP G 216 HIS 0.002 0.001 HIS H 286 Details of bonding type rmsd covalent geometry : bond 0.00280 (12736) covalent geometry : angle 0.54262 (17314) hydrogen bonds : bond 0.03468 ( 697) hydrogen bonds : angle 3.68616 ( 2004) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 219 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 246 LYS cc_start: 0.3842 (OUTLIER) cc_final: 0.3431 (tptt) REVERT: E 317 GLN cc_start: 0.8293 (tp40) cc_final: 0.7489 (pp30) REVERT: E 336 MET cc_start: 0.6915 (mtm) cc_final: 0.6522 (mtm) REVERT: F 187 LEU cc_start: 0.8811 (mm) cc_final: 0.8571 (mm) REVERT: F 259 ASP cc_start: 0.7756 (t0) cc_final: 0.7534 (t70) REVERT: F 322 ASP cc_start: 0.8863 (m-30) cc_final: 0.8353 (m-30) REVERT: G 206 PHE cc_start: 0.7344 (t80) cc_final: 0.6929 (t80) REVERT: G 212 LYS cc_start: 0.7235 (tttt) cc_final: 0.6946 (mtmm) REVERT: G 277 GLU cc_start: 0.8584 (pt0) cc_final: 0.8302 (pt0) REVERT: G 372 LYS cc_start: 0.8865 (pttt) cc_final: 0.8634 (pttm) REVERT: H 198 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8280 (ptpp) REVERT: H 280 THR cc_start: 0.8273 (m) cc_final: 0.7965 (p) REVERT: H 304 GLN cc_start: 0.8093 (mt0) cc_final: 0.7679 (tm-30) REVERT: H 306 GLU cc_start: 0.8574 (tp30) cc_final: 0.8026 (tp30) REVERT: H 326 ILE cc_start: 0.6198 (mm) cc_final: 0.5993 (mm) REVERT: H 368 PHE cc_start: 0.8173 (m-80) cc_final: 0.7957 (m-80) REVERT: H 376 LYS cc_start: 0.9473 (tttt) cc_final: 0.9216 (pttp) REVERT: A 176 ASP cc_start: 0.8808 (p0) cc_final: 0.8276 (p0) REVERT: A 177 GLN cc_start: 0.8965 (mm-40) cc_final: 0.8614 (mm-40) REVERT: A 232 GLU cc_start: 0.6362 (mp0) cc_final: 0.6093 (mp0) REVERT: A 258 LYS cc_start: 0.6542 (mttt) cc_final: 0.6046 (tttt) REVERT: A 277 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7683 (mp0) REVERT: A 279 ARG cc_start: 0.7340 (mmt-90) cc_final: 0.7107 (mtt-85) REVERT: A 346 ARG cc_start: 0.7715 (mtt180) cc_final: 0.7412 (mtt-85) REVERT: A 366 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6748 (mt-10) REVERT: B 278 TYR cc_start: 0.7833 (t80) cc_final: 0.7576 (t80) REVERT: C 188 LYS cc_start: 0.9439 (OUTLIER) cc_final: 0.9186 (mttt) REVERT: C 192 SER cc_start: 0.9556 (t) cc_final: 0.9305 (p) REVERT: C 226 THR cc_start: 0.7992 (p) cc_final: 0.7725 (p) REVERT: D 220 GLN cc_start: 0.8404 (tp40) cc_final: 0.8130 (tp40) REVERT: D 231 ASP cc_start: 0.9007 (p0) cc_final: 0.8790 (p0) REVERT: D 246 LYS cc_start: 0.8862 (mttt) cc_final: 0.8610 (mmmt) REVERT: D 256 PHE cc_start: 0.8473 (t80) cc_final: 0.8093 (p90) REVERT: D 259 ASP cc_start: 0.7201 (m-30) cc_final: 0.6358 (p0) REVERT: D 305 ARG cc_start: 0.7988 (tpp-160) cc_final: 0.7687 (tpt170) REVERT: D 350 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8202 (mm-30) REVERT: D 376 LYS cc_start: 0.8805 (tttt) cc_final: 0.8212 (tmmt) outliers start: 41 outliers final: 31 residues processed: 249 average time/residue: 0.1211 time to fit residues: 43.2362 Evaluate side-chains 243 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 246 LYS Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 256 PHE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 337 PHE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 379 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 149 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 146 optimal weight: 0.7980 chunk 10 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.107464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.090837 restraints weight = 28518.105| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 3.28 r_work: 0.3420 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12736 Z= 0.123 Angle : 0.564 15.706 17314 Z= 0.288 Chirality : 0.044 0.284 2068 Planarity : 0.003 0.047 2146 Dihedral : 4.418 57.179 1666 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.75 % Allowed : 17.63 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.22), residues: 1518 helix: 1.97 (0.18), residues: 844 sheet: 0.14 (0.40), residues: 186 loop : 0.40 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 279 TYR 0.032 0.001 TYR F 312 PHE 0.024 0.001 PHE E 256 TRP 0.044 0.002 TRP G 216 HIS 0.002 0.001 HIS H 286 Details of bonding type rmsd covalent geometry : bond 0.00284 (12736) covalent geometry : angle 0.56419 (17314) hydrogen bonds : bond 0.03509 ( 697) hydrogen bonds : angle 3.70509 ( 2004) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 246 LYS cc_start: 0.3825 (OUTLIER) cc_final: 0.3338 (tptt) REVERT: E 317 GLN cc_start: 0.8301 (tp40) cc_final: 0.7479 (pp30) REVERT: E 336 MET cc_start: 0.6910 (mtm) cc_final: 0.6516 (mtm) REVERT: F 187 LEU cc_start: 0.8791 (mm) cc_final: 0.8561 (mm) REVERT: F 259 ASP cc_start: 0.7748 (t0) cc_final: 0.7544 (t70) REVERT: F 322 ASP cc_start: 0.8872 (m-30) cc_final: 0.8365 (m-30) REVERT: G 212 LYS cc_start: 0.7210 (tttt) cc_final: 0.6915 (mtmm) REVERT: G 232 GLU cc_start: 0.8896 (pp20) cc_final: 0.8695 (pp20) REVERT: H 280 THR cc_start: 0.8275 (m) cc_final: 0.7968 (p) REVERT: H 304 GLN cc_start: 0.8103 (mt0) cc_final: 0.7699 (tm-30) REVERT: H 306 GLU cc_start: 0.8575 (tp30) cc_final: 0.8070 (tp30) REVERT: H 368 PHE cc_start: 0.8116 (m-80) cc_final: 0.7897 (m-80) REVERT: H 376 LYS cc_start: 0.9482 (tttt) cc_final: 0.9224 (pttp) REVERT: A 176 ASP cc_start: 0.8771 (p0) cc_final: 0.8274 (p0) REVERT: A 177 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8553 (mm-40) REVERT: A 232 GLU cc_start: 0.6379 (mp0) cc_final: 0.6104 (mp0) REVERT: A 258 LYS cc_start: 0.6556 (mttt) cc_final: 0.6055 (tttt) REVERT: A 277 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7676 (mp0) REVERT: A 279 ARG cc_start: 0.7343 (mmt-90) cc_final: 0.7107 (mtt-85) REVERT: A 342 ASP cc_start: 0.6955 (m-30) cc_final: 0.6448 (m-30) REVERT: A 346 ARG cc_start: 0.7722 (mtt180) cc_final: 0.7418 (mtt-85) REVERT: A 366 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6745 (mt-10) REVERT: B 278 TYR cc_start: 0.7838 (t80) cc_final: 0.7586 (t80) REVERT: C 192 SER cc_start: 0.9550 (t) cc_final: 0.9300 (p) REVERT: C 208 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7312 (tp40) REVERT: C 226 THR cc_start: 0.7995 (p) cc_final: 0.7727 (p) REVERT: D 186 ASN cc_start: 0.8579 (m-40) cc_final: 0.8341 (m110) REVERT: D 220 GLN cc_start: 0.8423 (tp40) cc_final: 0.8162 (tp40) REVERT: D 231 ASP cc_start: 0.9003 (p0) cc_final: 0.8778 (p0) REVERT: D 246 LYS cc_start: 0.8831 (mttt) cc_final: 0.8575 (mmmt) REVERT: D 256 PHE cc_start: 0.8447 (t80) cc_final: 0.8115 (p90) REVERT: D 259 ASP cc_start: 0.7181 (m-30) cc_final: 0.6414 (p0) REVERT: D 305 ARG cc_start: 0.7985 (tpp-160) cc_final: 0.7692 (tpt170) REVERT: D 350 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8211 (mm-30) REVERT: D 376 LYS cc_start: 0.8803 (tttt) cc_final: 0.8198 (tmmt) outliers start: 39 outliers final: 32 residues processed: 249 average time/residue: 0.1207 time to fit residues: 43.0091 Evaluate side-chains 242 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 246 LYS Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain H residue 256 PHE Chi-restraints excluded: chain H residue 261 VAL Chi-restraints excluded: chain H residue 273 ILE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 208 GLN Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 337 PHE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 379 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 67 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 GLN A 220 GLN C 208 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.107294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.090582 restraints weight = 28579.692| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.30 r_work: 0.3414 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12736 Z= 0.135 Angle : 0.588 15.049 17314 Z= 0.302 Chirality : 0.044 0.268 2068 Planarity : 0.003 0.047 2146 Dihedral : 4.462 57.163 1666 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.54 % Allowed : 18.12 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.22), residues: 1518 helix: 1.90 (0.18), residues: 844 sheet: 0.15 (0.40), residues: 186 loop : 0.40 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 279 TYR 0.034 0.001 TYR F 312 PHE 0.024 0.001 PHE E 256 TRP 0.050 0.002 TRP G 216 HIS 0.002 0.001 HIS H 286 Details of bonding type rmsd covalent geometry : bond 0.00316 (12736) covalent geometry : angle 0.58799 (17314) hydrogen bonds : bond 0.03587 ( 697) hydrogen bonds : angle 3.76647 ( 2004) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 246 LYS cc_start: 0.3830 (OUTLIER) cc_final: 0.3376 (tptt) REVERT: E 317 GLN cc_start: 0.8309 (tp40) cc_final: 0.7483 (pp30) REVERT: E 336 MET cc_start: 0.6931 (mtm) cc_final: 0.6540 (mtm) REVERT: F 187 LEU cc_start: 0.8788 (mm) cc_final: 0.8569 (mm) REVERT: F 259 ASP cc_start: 0.7770 (t0) cc_final: 0.7543 (t70) REVERT: F 322 ASP cc_start: 0.8855 (m-30) cc_final: 0.8340 (m-30) REVERT: G 206 PHE cc_start: 0.7276 (t80) cc_final: 0.6963 (t80) REVERT: G 212 LYS cc_start: 0.7193 (tttt) cc_final: 0.6977 (mtmm) REVERT: G 232 GLU cc_start: 0.8921 (pp20) cc_final: 0.8713 (pp20) REVERT: H 204 GLU cc_start: 0.7921 (tt0) cc_final: 0.7667 (tt0) REVERT: H 280 THR cc_start: 0.8314 (m) cc_final: 0.7981 (p) REVERT: H 304 GLN cc_start: 0.8118 (mt0) cc_final: 0.7700 (tm-30) REVERT: H 306 GLU cc_start: 0.8590 (tp30) cc_final: 0.8088 (tp30) REVERT: H 368 PHE cc_start: 0.8109 (m-80) cc_final: 0.7887 (m-80) REVERT: H 376 LYS cc_start: 0.9490 (tttt) cc_final: 0.9234 (pttp) REVERT: A 176 ASP cc_start: 0.8779 (p0) cc_final: 0.8251 (p0) REVERT: A 177 GLN cc_start: 0.8973 (mm-40) cc_final: 0.8576 (mm-40) REVERT: A 232 GLU cc_start: 0.6383 (mp0) cc_final: 0.6104 (mp0) REVERT: A 258 LYS cc_start: 0.6575 (mttt) cc_final: 0.6062 (tttt) REVERT: A 277 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7698 (mp0) REVERT: A 279 ARG cc_start: 0.7377 (mmt-90) cc_final: 0.7115 (mtt-85) REVERT: A 336 MET cc_start: 0.6237 (mtp) cc_final: 0.5668 (mtp) REVERT: A 346 ARG cc_start: 0.7736 (mtt180) cc_final: 0.7428 (mtt-85) REVERT: C 192 SER cc_start: 0.9546 (t) cc_final: 0.9283 (p) REVERT: C 208 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7456 (tp40) REVERT: C 226 THR cc_start: 0.7994 (p) cc_final: 0.7725 (p) REVERT: D 186 ASN cc_start: 0.8589 (m-40) cc_final: 0.8351 (m110) REVERT: D 220 GLN cc_start: 0.8448 (tp40) cc_final: 0.8196 (tp40) REVERT: D 231 ASP cc_start: 0.8995 (p0) cc_final: 0.8780 (p0) REVERT: D 246 LYS cc_start: 0.8832 (mttt) cc_final: 0.8585 (mmmt) REVERT: D 256 PHE cc_start: 0.8493 (t80) cc_final: 0.8151 (p90) REVERT: D 259 ASP cc_start: 0.7198 (m-30) cc_final: 0.6434 (p0) REVERT: D 273 ILE cc_start: 0.8158 (pt) cc_final: 0.7938 (mm) REVERT: D 305 ARG cc_start: 0.7982 (tpp-160) cc_final: 0.7692 (tpt170) REVERT: D 350 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8218 (mm-30) REVERT: D 376 LYS cc_start: 0.8815 (tttt) cc_final: 0.8209 (tmmt) outliers start: 36 outliers final: 33 residues processed: 235 average time/residue: 0.1180 time to fit residues: 39.8469 Evaluate side-chains 240 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 246 LYS Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain H residue 256 PHE Chi-restraints excluded: chain H residue 261 VAL Chi-restraints excluded: chain H residue 273 ILE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 208 GLN Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 337 PHE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 379 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 0.0030 chunk 147 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.0870 overall best weight: 0.5568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.107886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.091168 restraints weight = 28706.134| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.28 r_work: 0.3424 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12736 Z= 0.125 Angle : 0.584 14.671 17314 Z= 0.300 Chirality : 0.044 0.369 2068 Planarity : 0.003 0.048 2146 Dihedral : 4.424 56.769 1666 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.54 % Allowed : 18.19 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.22), residues: 1518 helix: 1.90 (0.18), residues: 844 sheet: 0.19 (0.41), residues: 186 loop : 0.40 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 279 TYR 0.033 0.001 TYR F 312 PHE 0.024 0.001 PHE E 256 TRP 0.046 0.002 TRP G 216 HIS 0.002 0.001 HIS H 286 Details of bonding type rmsd covalent geometry : bond 0.00286 (12736) covalent geometry : angle 0.58389 (17314) hydrogen bonds : bond 0.03585 ( 697) hydrogen bonds : angle 3.78639 ( 2004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2903.25 seconds wall clock time: 51 minutes 6.29 seconds (3066.29 seconds total)