Starting phenix.real_space_refine on Wed Jul 30 16:50:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ti9_41282/07_2025/8ti9_41282.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ti9_41282/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ti9_41282/07_2025/8ti9_41282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ti9_41282/07_2025/8ti9_41282.map" model { file = "/net/cci-nas-00/data/ceres_data/8ti9_41282/07_2025/8ti9_41282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ti9_41282/07_2025/8ti9_41282.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 10.04, per 1000 atoms: 0.80 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: 3.32 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.43 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: 3.84 Time building geometry restraints manager: 3.89 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: 4.420 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: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 33.940 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.800 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (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 TRP 0.009 0.001 TRP C 207 HIS 0.001 0.000 HIS A 286 PHE 0.015 0.001 PHE E 368 TYR 0.007 0.001 TYR G 234 ARG 0.002 0.000 ARG E 370 Details of bonding type rmsd hydrogen bonds : bond 0.14192 ( 697) hydrogen bonds : angle 4.54252 ( 2004) covalent geometry : bond 0.00216 (12736) covalent geometry : angle 0.37105 (17314) *********************** 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 : 1.806 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: 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: 0.7575 (t80) REVERT: F 317 GLN cc_start: 0.8474 (mt0) cc_final: 0.8119 (tm-30) REVERT: F 375 ILE cc_start: 0.9146 (mt) cc_final: 0.8843 (mt) 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: H 198 LYS cc_start: 0.9201 (pttt) cc_final: 0.8996 (ptpp) REVERT: H 207 TRP cc_start: 0.7634 (m100) cc_final: 0.7339 (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: 0.7943 (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 346 ARG cc_start: 0.7680 (mtt180) cc_final: 0.7178 (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: 0.7069 (mtp) REVERT: D 202 THR cc_start: 0.9291 (p) cc_final: 0.8963 (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: 0.6447 (p0) REVERT: D 299 TYR cc_start: 0.8132 (t80) cc_final: 0.7799 (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: 0.3496 time to fit residues: 206.4361 Evaluate side-chains 227 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 219 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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 128 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 0.0010 chunk 39 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 0.0980 chunk 88 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.107826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.090809 restraints weight = 27862.541| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.37 r_work: 0.3405 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12736 Z= 0.127 Angle : 0.533 7.150 17314 Z= 0.282 Chirality : 0.044 0.220 2068 Planarity : 0.004 0.047 2146 Dihedral : 4.355 57.897 1670 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.75 % Allowed : 12.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.23), residues: 1518 helix: 2.30 (0.18), residues: 844 sheet: -0.04 (0.41), residues: 184 loop : 0.34 (0.32), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 216 HIS 0.005 0.001 HIS A 347 PHE 0.019 0.002 PHE C 206 TYR 0.022 0.001 TYR B 278 ARG 0.004 0.000 ARG D 370 Details of bonding type rmsd hydrogen bonds : bond 0.04138 ( 697) hydrogen bonds : angle 3.88413 ( 2004) covalent geometry : bond 0.00285 (12736) covalent geometry : angle 0.53299 (17314) *********************** 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 297 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 258 time to evaluate : 1.402 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 317 GLN cc_start: 0.8148 (tp40) cc_final: 0.7615 (tm-30) REVERT: E 336 MET cc_start: 0.6963 (mtm) cc_final: 0.6581 (mtm) REVERT: F 259 ASP cc_start: 0.7913 (t0) cc_final: 0.7699 (t70) REVERT: F 375 ILE cc_start: 0.9208 (mt) cc_final: 0.8853 (mt) REVERT: G 195 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8892 (mp0) REVERT: G 206 PHE cc_start: 0.7402 (t80) cc_final: 0.6965 (t80) REVERT: G 212 LYS cc_start: 0.7694 (tttt) cc_final: 0.7371 (ttmm) REVERT: G 232 GLU cc_start: 0.8486 (pp20) cc_final: 0.8283 (pp20) REVERT: G 259 ASP cc_start: 0.7571 (t0) cc_final: 0.7302 (p0) REVERT: G 277 GLU cc_start: 0.8493 (pt0) cc_final: 0.8266 (pt0) REVERT: G 372 LYS cc_start: 0.8880 (ptpt) cc_final: 0.8568 (pttm) REVERT: H 280 THR cc_start: 0.8264 (m) cc_final: 0.7984 (p) REVERT: H 304 GLN cc_start: 0.7973 (mt0) cc_final: 0.7635 (tm-30) REVERT: H 368 PHE cc_start: 0.8251 (m-80) cc_final: 0.7945 (m-80) REVERT: H 369 GLU cc_start: 0.8726 (tp30) cc_final: 0.8464 (tp30) REVERT: H 370 ARG cc_start: 0.7085 (tpt90) cc_final: 0.6854 (tpt90) REVERT: H 376 LYS cc_start: 0.9435 (tttt) cc_final: 0.9102 (pttp) REVERT: A 258 LYS cc_start: 0.6197 (mttt) cc_final: 0.5812 (tttt) REVERT: A 277 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7679 (mp0) REVERT: A 346 ARG cc_start: 0.7631 (mtt180) cc_final: 0.7278 (mtt-85) REVERT: B 312 TYR cc_start: 0.8318 (t80) cc_final: 0.7764 (t80) REVERT: B 336 MET cc_start: 0.8450 (mtm) cc_final: 0.7946 (mmm) REVERT: B 365 ASP cc_start: 0.7589 (p0) cc_final: 0.7309 (p0) REVERT: B 378 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8605 (mm) REVERT: C 192 SER cc_start: 0.9591 (t) cc_final: 0.9330 (p) REVERT: C 226 THR cc_start: 0.7948 (p) cc_final: 0.7710 (p) REVERT: C 308 GLN cc_start: 0.7666 (tt0) cc_final: 0.7412 (mm-40) REVERT: C 354 LYS cc_start: 0.7882 (mmmt) cc_final: 0.7673 (mmtm) REVERT: D 246 LYS cc_start: 0.8954 (mttt) cc_final: 0.8592 (mmmt) REVERT: D 256 PHE cc_start: 0.8417 (t80) cc_final: 0.7920 (p90) REVERT: D 259 ASP cc_start: 0.7139 (m-30) cc_final: 0.6257 (p0) REVERT: D 299 TYR cc_start: 0.8156 (t80) cc_final: 0.7754 (t80) REVERT: D 336 MET cc_start: 0.7842 (mtm) cc_final: 0.7555 (mtm) REVERT: D 365 ASP cc_start: 0.7793 (m-30) cc_final: 0.7494 (m-30) REVERT: D 376 LYS cc_start: 0.8673 (tttt) cc_final: 0.8110 (tmmt) outliers start: 39 outliers final: 23 residues processed: 288 average time/residue: 0.2544 time to fit residues: 103.6469 Evaluate side-chains 234 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 210 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 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 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 337 PHE 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 81 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 41 optimal weight: 0.0370 chunk 150 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 179 ASN H 197 ASN H 201 ASN A 220 GLN D 186 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.107053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.090021 restraints weight = 28610.577| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.38 r_work: 0.3395 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2766 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= 0.124 Angle : 0.510 11.710 17314 Z= 0.269 Chirality : 0.043 0.147 2068 Planarity : 0.003 0.050 2146 Dihedral : 4.363 57.690 1666 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.46 % Allowed : 13.75 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.23), residues: 1518 helix: 2.10 (0.18), residues: 848 sheet: -0.08 (0.41), residues: 184 loop : 0.34 (0.32), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP G 216 HIS 0.003 0.001 HIS A 347 PHE 0.020 0.001 PHE E 256 TYR 0.025 0.001 TYR B 283 ARG 0.003 0.000 ARG B 279 Details of bonding type rmsd hydrogen bonds : bond 0.03724 ( 697) hydrogen bonds : angle 3.80802 ( 2004) covalent geometry : bond 0.00282 (12736) covalent geometry : angle 0.51003 (17314) *********************** 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 280 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 1.855 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: E 181 LEU cc_start: 0.9288 (mt) cc_final: 0.9083 (pp) REVERT: E 317 GLN cc_start: 0.8203 (tp40) cc_final: 0.7595 (tm-30) REVERT: E 336 MET cc_start: 0.7000 (mtm) cc_final: 0.6606 (mtm) REVERT: F 259 ASP cc_start: 0.7974 (t0) cc_final: 0.7654 (t70) REVERT: F 312 TYR cc_start: 0.8650 (t80) cc_final: 0.8412 (t80) REVERT: F 316 ARG cc_start: 0.8236 (mtp85) cc_final: 0.7933 (mmp80) REVERT: F 322 ASP cc_start: 0.8807 (m-30) cc_final: 0.8363 (m-30) REVERT: F 375 ILE cc_start: 0.9129 (mt) cc_final: 0.8850 (mt) REVERT: G 197 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.7850 (t0) REVERT: G 206 PHE cc_start: 0.7435 (t80) cc_final: 0.6974 (t80) REVERT: G 212 LYS cc_start: 0.7515 (tttt) cc_final: 0.7211 (ttmm) REVERT: G 277 GLU cc_start: 0.8526 (pt0) cc_final: 0.8310 (pt0) REVERT: H 198 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8325 (ptpt) REVERT: H 280 THR cc_start: 0.8266 (m) cc_final: 0.7984 (p) REVERT: H 304 GLN cc_start: 0.8077 (mt0) cc_final: 0.7710 (tm-30) REVERT: H 336 MET cc_start: 0.7739 (tpp) cc_final: 0.7105 (mmm) REVERT: H 368 PHE cc_start: 0.8246 (m-80) cc_final: 0.7944 (m-80) REVERT: H 376 LYS cc_start: 0.9437 (tttt) cc_final: 0.9156 (pttp) REVERT: A 177 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8462 (mm-40) REVERT: A 258 LYS cc_start: 0.6424 (mttt) cc_final: 0.5989 (tttt) REVERT: A 277 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7701 (mp0) REVERT: A 346 ARG cc_start: 0.7691 (mtt180) cc_final: 0.7368 (mtt-85) REVERT: B 312 TYR cc_start: 0.8354 (t80) cc_final: 0.7973 (t80) REVERT: B 336 MET cc_start: 0.8465 (mtm) cc_final: 0.8022 (mmm) REVERT: B 365 ASP cc_start: 0.7664 (p0) cc_final: 0.7412 (p0) REVERT: B 378 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8564 (mm) REVERT: C 192 SER cc_start: 0.9560 (t) cc_final: 0.9303 (p) REVERT: C 226 THR cc_start: 0.7942 (p) cc_final: 0.7704 (p) REVERT: D 188 LYS cc_start: 0.8389 (mmtm) cc_final: 0.8011 (mmmt) REVERT: D 246 LYS cc_start: 0.8968 (mttt) cc_final: 0.8599 (mmmt) REVERT: D 256 PHE cc_start: 0.8438 (t80) cc_final: 0.7929 (p90) REVERT: D 259 ASP cc_start: 0.7194 (m-30) cc_final: 0.6302 (p0) REVERT: D 299 TYR cc_start: 0.8149 (t80) cc_final: 0.7693 (t80) REVERT: D 336 MET cc_start: 0.7811 (mtm) cc_final: 0.7592 (mtm) REVERT: D 365 ASP cc_start: 0.7784 (m-30) cc_final: 0.7487 (m-30) REVERT: D 376 LYS cc_start: 0.8729 (tttt) cc_final: 0.8161 (tmmt) outliers start: 49 outliers final: 26 residues processed: 267 average time/residue: 0.3239 time to fit residues: 125.3421 Evaluate side-chains 236 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 2.957 ------------------------------------------------------------------------------- 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 231 ASP Chi-restraints excluded: chain G residue 197 ASN 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 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 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 209 SER Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 343 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 24 optimal weight: 0.0000 chunk 88 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.107506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.090633 restraints weight = 28046.477| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.29 r_work: 0.3407 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12736 Z= 0.117 Angle : 0.505 8.007 17314 Z= 0.268 Chirality : 0.043 0.271 2068 Planarity : 0.003 0.051 2146 Dihedral : 4.387 57.419 1666 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.89 % Allowed : 14.74 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.23), residues: 1518 helix: 2.09 (0.18), residues: 846 sheet: -0.01 (0.40), residues: 186 loop : 0.33 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 216 HIS 0.003 0.001 HIS A 347 PHE 0.020 0.001 PHE E 256 TYR 0.016 0.001 TYR B 278 ARG 0.002 0.000 ARG D 370 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 697) hydrogen bonds : angle 3.76979 ( 2004) covalent geometry : bond 0.00263 (12736) covalent geometry : angle 0.50529 (17314) *********************** 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 265 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 224 time to evaluate : 1.891 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 317 GLN cc_start: 0.8236 (tp40) cc_final: 0.7596 (tm-30) REVERT: E 336 MET cc_start: 0.6967 (mtm) cc_final: 0.6568 (mtm) REVERT: F 259 ASP cc_start: 0.7862 (t0) cc_final: 0.7565 (t70) REVERT: F 312 TYR cc_start: 0.8663 (t80) cc_final: 0.8431 (t80) REVERT: F 322 ASP cc_start: 0.8826 (m-30) cc_final: 0.8378 (m-30) REVERT: G 195 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8214 (mp0) REVERT: G 197 ASN cc_start: 0.8181 (m-40) cc_final: 0.7926 (t0) REVERT: G 212 LYS cc_start: 0.7486 (tttt) cc_final: 0.7230 (mtmt) REVERT: H 280 THR cc_start: 0.8242 (m) cc_final: 0.7957 (p) REVERT: H 304 GLN cc_start: 0.8052 (mt0) cc_final: 0.7681 (tm-30) REVERT: H 306 GLU cc_start: 0.8453 (tp30) cc_final: 0.7937 (tp30) REVERT: H 326 ILE cc_start: 0.6205 (mm) cc_final: 0.5985 (mm) REVERT: H 336 MET cc_start: 0.7740 (tpp) cc_final: 0.7120 (mmm) REVERT: H 368 PHE cc_start: 0.8198 (m-80) cc_final: 0.7958 (m-80) REVERT: H 376 LYS cc_start: 0.9444 (tttt) cc_final: 0.9150 (pttp) REVERT: A 176 ASP cc_start: 0.8915 (p0) cc_final: 0.8476 (p0) REVERT: A 177 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8544 (mm-40) REVERT: A 258 LYS cc_start: 0.6519 (mttt) cc_final: 0.6023 (tttt) REVERT: A 277 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7723 (mp0) REVERT: A 346 ARG cc_start: 0.7677 (mtt180) cc_final: 0.7354 (mtt-85) REVERT: B 336 MET cc_start: 0.8464 (mtm) cc_final: 0.8108 (mmm) REVERT: B 365 ASP cc_start: 0.7746 (p0) cc_final: 0.7534 (p0) REVERT: B 378 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8594 (mm) REVERT: C 192 SER cc_start: 0.9556 (t) cc_final: 0.9283 (p) REVERT: C 203 SER cc_start: 0.7556 (t) cc_final: 0.7322 (p) REVERT: C 226 THR cc_start: 0.7944 (p) cc_final: 0.7700 (p) REVERT: D 188 LYS cc_start: 0.8436 (mmtm) cc_final: 0.8071 (mmmt) REVERT: D 246 LYS cc_start: 0.8930 (mttt) cc_final: 0.8573 (mmmt) REVERT: D 256 PHE cc_start: 0.8416 (t80) cc_final: 0.7905 (p90) REVERT: D 259 ASP cc_start: 0.7150 (m-30) cc_final: 0.6269 (p0) REVERT: D 365 ASP cc_start: 0.7779 (m-30) cc_final: 0.7453 (m-30) REVERT: D 376 LYS cc_start: 0.8738 (tttt) cc_final: 0.8149 (tmmt) outliers start: 41 outliers final: 25 residues processed: 252 average time/residue: 0.3778 time to fit residues: 138.0852 Evaluate side-chains 228 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 1.452 ------------------------------------------------------------------------------- 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 251 LEU Chi-restraints excluded: chain H residue 256 PHE Chi-restraints excluded: chain H residue 261 VAL Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 329 CYS 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 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 61 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 197 ASN ** G 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 197 ASN ** C 208 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 = 0.3837 r_free = 0.3837 target = 0.106753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.089953 restraints weight = 28481.868| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.29 r_work: 0.3398 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12736 Z= 0.134 Angle : 0.522 12.198 17314 Z= 0.274 Chirality : 0.043 0.173 2068 Planarity : 0.003 0.050 2146 Dihedral : 4.425 57.576 1666 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.03 % Allowed : 15.44 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.22), residues: 1518 helix: 2.03 (0.18), residues: 846 sheet: -0.03 (0.40), residues: 186 loop : 0.32 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP G 216 HIS 0.002 0.001 HIS A 347 PHE 0.021 0.001 PHE E 256 TYR 0.017 0.001 TYR B 278 ARG 0.002 0.000 ARG F 353 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 697) hydrogen bonds : angle 3.77365 ( 2004) covalent geometry : bond 0.00310 (12736) covalent geometry : angle 0.52167 (17314) *********************** 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 259 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 216 time to evaluate : 1.567 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: 0.8262 (tp40) cc_final: 0.7593 (tm-30) REVERT: E 336 MET cc_start: 0.6940 (mtm) cc_final: 0.6535 (mtm) REVERT: F 259 ASP cc_start: 0.7894 (t0) cc_final: 0.7581 (t70) REVERT: F 312 TYR cc_start: 0.8693 (t80) cc_final: 0.8493 (t80) REVERT: F 322 ASP cc_start: 0.8851 (m-30) cc_final: 0.8384 (m-30) REVERT: G 197 ASN cc_start: 0.8241 (OUTLIER) cc_final: 0.8019 (t0) REVERT: G 360 THR cc_start: 0.7872 (m) cc_final: 0.7625 (p) REVERT: H 280 THR cc_start: 0.8292 (m) cc_final: 0.7984 (p) REVERT: H 304 GLN cc_start: 0.8087 (mt0) cc_final: 0.7679 (tm-30) REVERT: H 306 GLU cc_start: 0.8542 (tp30) cc_final: 0.8012 (tp30) REVERT: H 326 ILE cc_start: 0.6220 (mm) cc_final: 0.6005 (mm) REVERT: H 368 PHE cc_start: 0.8202 (m-80) cc_final: 0.7951 (m-80) REVERT: H 376 LYS cc_start: 0.9451 (tttt) cc_final: 0.9165 (pttp) REVERT: A 176 ASP cc_start: 0.8873 (p0) cc_final: 0.8405 (p0) REVERT: A 177 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8558 (mm-40) REVERT: A 258 LYS cc_start: 0.6537 (mttt) cc_final: 0.6033 (tttt) REVERT: A 346 ARG cc_start: 0.7662 (mtt180) cc_final: 0.7342 (mtt-85) REVERT: B 378 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8631 (mm) REVERT: C 192 SER cc_start: 0.9558 (t) cc_final: 0.9297 (p) REVERT: C 203 SER cc_start: 0.7573 (t) cc_final: 0.7344 (p) REVERT: C 226 THR cc_start: 0.7986 (p) cc_final: 0.7737 (p) REVERT: D 188 LYS cc_start: 0.8443 (mmtm) cc_final: 0.8070 (mmmt) REVERT: D 246 LYS cc_start: 0.8944 (mttt) cc_final: 0.8596 (mmmt) REVERT: D 256 PHE cc_start: 0.8450 (t80) cc_final: 0.7925 (p90) REVERT: D 259 ASP cc_start: 0.7163 (m-30) cc_final: 0.6295 (p0) REVERT: D 305 ARG cc_start: 0.7969 (tpp-160) cc_final: 0.7726 (tpt170) REVERT: D 376 LYS cc_start: 0.8788 (tttt) cc_final: 0.8207 (tmmt) outliers start: 43 outliers final: 31 residues processed: 246 average time/residue: 0.2639 time to fit residues: 93.6594 Evaluate side-chains 238 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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 273 ILE Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain G residue 197 ASN 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 205 LYS Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 256 PHE Chi-restraints excluded: chain H residue 261 VAL 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 378 LEU 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 215 THR 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 82 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 4 optimal weight: 0.0670 chunk 33 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 197 ASN ** H 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 GLN ** C 208 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 = 0.107611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.090538 restraints weight = 28615.391| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 3.38 r_work: 0.3407 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3220 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= 0.118 Angle : 0.526 16.179 17314 Z= 0.272 Chirality : 0.043 0.271 2068 Planarity : 0.003 0.050 2146 Dihedral : 4.401 57.380 1666 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.82 % Allowed : 16.64 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.22), residues: 1518 helix: 2.07 (0.18), residues: 844 sheet: 0.02 (0.40), residues: 186 loop : 0.35 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP G 216 HIS 0.002 0.001 HIS A 347 PHE 0.022 0.001 PHE E 256 TYR 0.018 0.001 TYR B 278 ARG 0.002 0.000 ARG F 353 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 697) hydrogen bonds : angle 3.69942 ( 2004) covalent geometry : bond 0.00271 (12736) covalent geometry : angle 0.52570 (17314) *********************** 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 268 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 228 time to evaluate : 1.559 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: 0.8195 (tp40) cc_final: 0.7543 (tm-30) REVERT: E 336 MET cc_start: 0.6930 (mtm) cc_final: 0.6548 (mtm) REVERT: F 187 LEU cc_start: 0.8810 (mm) cc_final: 0.8583 (mm) REVERT: F 259 ASP cc_start: 0.7820 (t0) cc_final: 0.7587 (t70) REVERT: F 312 TYR cc_start: 0.8715 (t80) cc_final: 0.8493 (t80) REVERT: F 322 ASP cc_start: 0.8858 (m-30) cc_final: 0.8406 (m-30) REVERT: G 329 CYS cc_start: 0.8104 (m) cc_final: 0.6878 (p) REVERT: G 360 THR cc_start: 0.7885 (m) cc_final: 0.7673 (p) REVERT: H 198 LYS cc_start: 0.8750 (ptpp) cc_final: 0.8469 (ptpp) REVERT: H 280 THR cc_start: 0.8274 (m) cc_final: 0.7971 (p) REVERT: H 304 GLN cc_start: 0.8115 (mt0) cc_final: 0.7702 (tm-30) REVERT: H 306 GLU cc_start: 0.8551 (tp30) cc_final: 0.8014 (tp30) REVERT: H 326 ILE cc_start: 0.6223 (mm) cc_final: 0.6008 (mm) REVERT: H 336 MET cc_start: 0.7743 (tpp) cc_final: 0.7078 (mmm) REVERT: H 368 PHE cc_start: 0.8202 (m-80) cc_final: 0.7953 (m-80) REVERT: H 376 LYS cc_start: 0.9450 (tttt) cc_final: 0.9167 (pttp) REVERT: A 176 ASP cc_start: 0.8793 (p0) cc_final: 0.8295 (p0) REVERT: A 177 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8615 (mm-40) REVERT: A 232 GLU cc_start: 0.6379 (mp0) cc_final: 0.6137 (mp0) REVERT: A 258 LYS cc_start: 0.6559 (mttt) cc_final: 0.6058 (tttt) REVERT: A 279 ARG cc_start: 0.7355 (mmt-90) cc_final: 0.7108 (mtt-85) REVERT: A 346 ARG cc_start: 0.7691 (mtt180) cc_final: 0.7392 (mtt-85) REVERT: A 366 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6726 (mt-10) REVERT: B 378 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8532 (mm) REVERT: C 188 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.9215 (mttt) REVERT: C 192 SER cc_start: 0.9544 (t) cc_final: 0.9296 (p) REVERT: C 203 SER cc_start: 0.7543 (t) cc_final: 0.7322 (p) REVERT: C 226 THR cc_start: 0.7997 (p) cc_final: 0.7736 (p) REVERT: D 246 LYS cc_start: 0.8976 (mttt) cc_final: 0.8622 (mmmt) REVERT: D 256 PHE cc_start: 0.8477 (t80) cc_final: 0.7920 (p90) REVERT: D 259 ASP cc_start: 0.7183 (m-30) cc_final: 0.6317 (p0) REVERT: D 305 ARG cc_start: 0.7991 (tpp-160) cc_final: 0.7650 (tpt170) REVERT: D 376 LYS cc_start: 0.8810 (tttt) cc_final: 0.8224 (tmmt) outliers start: 40 outliers final: 30 residues processed: 256 average time/residue: 0.2469 time to fit residues: 90.9703 Evaluate side-chains 237 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 1.452 ------------------------------------------------------------------------------- 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 326 ILE 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 322 ASP Chi-restraints excluded: chain G residue 343 THR 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 277 GLU 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 97 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 45 optimal weight: 0.0170 chunk 48 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 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 = 0.3848 r_free = 0.3848 target = 0.107400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.090483 restraints weight = 28660.281| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.32 r_work: 0.3408 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3333 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= 0.123 Angle : 0.541 14.091 17314 Z= 0.279 Chirality : 0.043 0.269 2068 Planarity : 0.003 0.050 2146 Dihedral : 4.446 57.279 1666 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.10 % Allowed : 16.93 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.22), residues: 1518 helix: 1.99 (0.18), residues: 844 sheet: 0.04 (0.40), residues: 186 loop : 0.37 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP G 216 HIS 0.002 0.001 HIS H 286 PHE 0.023 0.001 PHE E 256 TYR 0.027 0.001 TYR B 278 ARG 0.013 0.000 ARG B 279 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 697) hydrogen bonds : angle 3.73851 ( 2004) covalent geometry : bond 0.00283 (12736) covalent geometry : angle 0.54077 (17314) *********************** 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 275 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 231 time to evaluate : 1.424 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: 0.8278 (tp40) cc_final: 0.7569 (tm-30) REVERT: E 336 MET cc_start: 0.6915 (mtm) cc_final: 0.6528 (mtm) REVERT: F 187 LEU cc_start: 0.8827 (mm) cc_final: 0.8615 (mm) REVERT: F 259 ASP cc_start: 0.7781 (t0) cc_final: 0.7569 (t70) REVERT: F 322 ASP cc_start: 0.8881 (m-30) cc_final: 0.8428 (m-30) REVERT: G 206 PHE cc_start: 0.7319 (t80) cc_final: 0.6958 (t80) REVERT: G 277 GLU cc_start: 0.8577 (pt0) cc_final: 0.8293 (pt0) REVERT: G 329 CYS cc_start: 0.7902 (m) cc_final: 0.6921 (p) REVERT: G 360 THR cc_start: 0.7893 (m) cc_final: 0.7685 (p) REVERT: H 198 LYS cc_start: 0.8761 (ptpp) cc_final: 0.8492 (ptpp) REVERT: H 280 THR cc_start: 0.8310 (m) cc_final: 0.8003 (p) REVERT: H 304 GLN cc_start: 0.8093 (mt0) cc_final: 0.7677 (tm-30) REVERT: H 306 GLU cc_start: 0.8577 (tp30) cc_final: 0.8036 (tp30) REVERT: H 326 ILE cc_start: 0.6200 (mm) cc_final: 0.5991 (mm) REVERT: H 336 MET cc_start: 0.7799 (tpp) cc_final: 0.7143 (mmm) REVERT: H 368 PHE cc_start: 0.8195 (m-80) cc_final: 0.7946 (m-80) REVERT: H 376 LYS cc_start: 0.9451 (tttt) cc_final: 0.9187 (pttp) REVERT: A 176 ASP cc_start: 0.8757 (p0) cc_final: 0.8244 (p0) REVERT: A 177 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8583 (mm-40) REVERT: A 232 GLU cc_start: 0.6385 (mp0) cc_final: 0.6108 (mp0) REVERT: A 258 LYS cc_start: 0.6560 (mttt) cc_final: 0.6058 (tttt) REVERT: A 279 ARG cc_start: 0.7354 (mmt-90) cc_final: 0.7108 (mtt-85) REVERT: A 346 ARG cc_start: 0.7710 (mtt180) cc_final: 0.7396 (mtt-85) REVERT: A 366 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6616 (mt-10) REVERT: B 278 TYR cc_start: 0.7841 (t80) cc_final: 0.7371 (t80) REVERT: C 188 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.9175 (mttt) REVERT: C 192 SER cc_start: 0.9548 (t) cc_final: 0.9285 (p) REVERT: C 226 THR cc_start: 0.7994 (p) cc_final: 0.7730 (p) REVERT: D 220 GLN cc_start: 0.8361 (tp40) cc_final: 0.8088 (tp40) REVERT: D 246 LYS cc_start: 0.8955 (mttt) cc_final: 0.8607 (mmmt) REVERT: D 256 PHE cc_start: 0.8481 (t80) cc_final: 0.8008 (p90) REVERT: D 259 ASP cc_start: 0.7173 (m-30) cc_final: 0.6312 (p0) REVERT: D 305 ARG cc_start: 0.7999 (tpp-160) cc_final: 0.7688 (tpt170) REVERT: D 376 LYS cc_start: 0.8796 (tttt) cc_final: 0.8204 (tmmt) outliers start: 44 outliers final: 33 residues processed: 260 average time/residue: 0.2463 time to fit residues: 91.7107 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 : 1.541 ------------------------------------------------------------------------------- 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 273 ILE 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 205 LYS Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 256 PHE Chi-restraints excluded: chain H residue 261 VAL Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 277 GLU 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 209 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 67 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.107015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.089955 restraints weight = 28760.650| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.33 r_work: 0.3401 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3430 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= 0.137 Angle : 0.572 12.175 17314 Z= 0.294 Chirality : 0.044 0.301 2068 Planarity : 0.003 0.047 2146 Dihedral : 4.492 57.295 1666 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.75 % Allowed : 17.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.22), residues: 1518 helix: 1.91 (0.18), residues: 844 sheet: 0.04 (0.40), residues: 186 loop : 0.36 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP G 216 HIS 0.002 0.001 HIS H 286 PHE 0.023 0.001 PHE E 256 TYR 0.022 0.001 TYR B 283 ARG 0.009 0.000 ARG B 279 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 697) hydrogen bonds : angle 3.82610 ( 2004) covalent geometry : bond 0.00320 (12736) covalent geometry : angle 0.57229 (17314) *********************** 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 254 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 215 time to evaluate : 1.493 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: E 246 LYS cc_start: 0.3607 (OUTLIER) cc_final: 0.3190 (tptt) REVERT: E 317 GLN cc_start: 0.8318 (tp40) cc_final: 0.7592 (tm-30) REVERT: E 336 MET cc_start: 0.6945 (mtm) cc_final: 0.6562 (mtm) REVERT: F 259 ASP cc_start: 0.7809 (t0) cc_final: 0.7566 (t70) REVERT: F 312 TYR cc_start: 0.8581 (t80) cc_final: 0.8377 (t80) REVERT: F 322 ASP cc_start: 0.8884 (m-30) cc_final: 0.8389 (m-30) REVERT: G 206 PHE cc_start: 0.7391 (t80) cc_final: 0.7057 (t80) REVERT: G 329 CYS cc_start: 0.7726 (m) cc_final: 0.6871 (p) REVERT: G 360 THR cc_start: 0.7897 (m) cc_final: 0.7683 (p) REVERT: H 280 THR cc_start: 0.8321 (m) cc_final: 0.7988 (p) REVERT: H 304 GLN cc_start: 0.8094 (mt0) cc_final: 0.7684 (tm-30) REVERT: H 306 GLU cc_start: 0.8576 (tp30) cc_final: 0.8065 (tp30) REVERT: H 326 ILE cc_start: 0.6205 (mm) cc_final: 0.6003 (mm) REVERT: H 368 PHE cc_start: 0.8201 (m-80) cc_final: 0.7931 (m-80) REVERT: H 376 LYS cc_start: 0.9449 (tttt) cc_final: 0.9191 (pttp) REVERT: A 177 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8616 (mm-40) REVERT: A 232 GLU cc_start: 0.6389 (mp0) cc_final: 0.6109 (mp0) REVERT: A 258 LYS cc_start: 0.6572 (mttt) cc_final: 0.6072 (tttt) REVERT: A 279 ARG cc_start: 0.7377 (mmt-90) cc_final: 0.7123 (mtt-85) REVERT: A 346 ARG cc_start: 0.7725 (mtt180) cc_final: 0.7416 (mtt-85) REVERT: A 366 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6762 (mt-10) REVERT: B 278 TYR cc_start: 0.7848 (t80) cc_final: 0.7567 (t80) REVERT: C 188 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9160 (mttt) REVERT: C 192 SER cc_start: 0.9551 (t) cc_final: 0.9309 (p) REVERT: C 226 THR cc_start: 0.8004 (p) cc_final: 0.7735 (p) REVERT: D 220 GLN cc_start: 0.8451 (tp40) cc_final: 0.8165 (tp40) REVERT: D 246 LYS cc_start: 0.8942 (mttt) cc_final: 0.8600 (mmmt) REVERT: D 256 PHE cc_start: 0.8465 (t80) cc_final: 0.8102 (p90) REVERT: D 259 ASP cc_start: 0.7178 (m-30) cc_final: 0.6368 (p0) REVERT: D 305 ARG cc_start: 0.7994 (tpp-160) cc_final: 0.7693 (tpt170) REVERT: D 376 LYS cc_start: 0.8807 (tttt) cc_final: 0.8208 (tmmt) outliers start: 39 outliers final: 33 residues processed: 244 average time/residue: 0.2475 time to fit residues: 86.8632 Evaluate side-chains 237 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 1.437 ------------------------------------------------------------------------------- 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 273 ILE 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 205 LYS Chi-restraints excluded: chain H residue 251 LEU 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 277 GLU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 191 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 68 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 41 optimal weight: 0.1980 chunk 148 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** ** H 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 ASN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.107754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.090802 restraints weight = 28680.313| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 3.33 r_work: 0.3419 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3520 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= 0.124 Angle : 0.587 15.855 17314 Z= 0.297 Chirality : 0.045 0.341 2068 Planarity : 0.003 0.048 2146 Dihedral : 4.488 56.881 1666 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.47 % Allowed : 18.34 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.22), residues: 1518 helix: 1.97 (0.18), residues: 844 sheet: 0.11 (0.40), residues: 186 loop : 0.37 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP G 216 HIS 0.002 0.001 HIS H 286 PHE 0.024 0.001 PHE E 256 TYR 0.021 0.001 TYR B 283 ARG 0.008 0.000 ARG B 279 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 697) hydrogen bonds : angle 3.77325 ( 2004) covalent geometry : bond 0.00286 (12736) covalent geometry : angle 0.58672 (17314) *********************** 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 250 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 215 time to evaluate : 1.447 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: E 246 LYS cc_start: 0.3870 (OUTLIER) cc_final: 0.3412 (tptt) REVERT: E 317 GLN cc_start: 0.8304 (tp40) cc_final: 0.7571 (tm-30) REVERT: E 336 MET cc_start: 0.6863 (mtm) cc_final: 0.6487 (mtm) REVERT: F 259 ASP cc_start: 0.7749 (t0) cc_final: 0.7547 (t70) REVERT: F 322 ASP cc_start: 0.8896 (m-30) cc_final: 0.8387 (m-30) REVERT: G 206 PHE cc_start: 0.7411 (t80) cc_final: 0.7054 (t80) REVERT: G 329 CYS cc_start: 0.8034 (m) cc_final: 0.6952 (p) REVERT: G 360 THR cc_start: 0.7874 (m) cc_final: 0.7674 (p) REVERT: H 198 LYS cc_start: 0.8762 (ptpp) cc_final: 0.8458 (ptpp) REVERT: H 280 THR cc_start: 0.8376 (m) cc_final: 0.8024 (p) REVERT: H 304 GLN cc_start: 0.8082 (mt0) cc_final: 0.7685 (tm-30) REVERT: H 306 GLU cc_start: 0.8572 (tp30) cc_final: 0.8060 (tp30) REVERT: H 368 PHE cc_start: 0.8214 (m-80) cc_final: 0.7944 (m-80) REVERT: H 376 LYS cc_start: 0.9445 (tttt) cc_final: 0.9181 (pttp) REVERT: A 176 ASP cc_start: 0.8765 (p0) cc_final: 0.8253 (p0) REVERT: A 177 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8593 (mm-40) REVERT: A 232 GLU cc_start: 0.6350 (mp0) cc_final: 0.6062 (mp0) REVERT: A 258 LYS cc_start: 0.6595 (mttt) cc_final: 0.6064 (tttt) REVERT: A 279 ARG cc_start: 0.7325 (mmt-90) cc_final: 0.7067 (mtt-85) REVERT: A 346 ARG cc_start: 0.7705 (mtt180) cc_final: 0.7402 (mtt-85) REVERT: A 366 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6746 (mt-10) REVERT: B 278 TYR cc_start: 0.7787 (t80) cc_final: 0.7555 (t80) REVERT: C 192 SER cc_start: 0.9555 (t) cc_final: 0.9287 (p) REVERT: C 226 THR cc_start: 0.7975 (p) cc_final: 0.7701 (p) REVERT: D 179 ASN cc_start: 0.8763 (m110) cc_final: 0.8553 (m-40) REVERT: D 186 ASN cc_start: 0.8602 (m-40) cc_final: 0.8366 (m110) REVERT: D 204 GLU cc_start: 0.8049 (tt0) cc_final: 0.7563 (tm-30) REVERT: D 220 GLN cc_start: 0.8428 (tp40) cc_final: 0.8169 (tp40) REVERT: D 246 LYS cc_start: 0.8889 (mttt) cc_final: 0.8555 (mmmt) REVERT: D 256 PHE cc_start: 0.8483 (t80) cc_final: 0.8090 (p90) REVERT: D 259 ASP cc_start: 0.7184 (m-30) cc_final: 0.6410 (p0) REVERT: D 273 ILE cc_start: 0.8133 (pt) cc_final: 0.7902 (mm) REVERT: D 350 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8234 (mm-30) REVERT: D 376 LYS cc_start: 0.8796 (tttt) cc_final: 0.8201 (tmmt) outliers start: 35 outliers final: 29 residues processed: 240 average time/residue: 0.2511 time to fit residues: 86.1271 Evaluate side-chains 236 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 1.474 ------------------------------------------------------------------------------- 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 273 ILE 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 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 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 191 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 284 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 126 optimal weight: 0.9980 chunk 143 optimal weight: 0.0980 chunk 76 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 101 optimal weight: 0.0670 chunk 147 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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** ** H 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.108246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.091302 restraints weight = 28401.343| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.32 r_work: 0.3426 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12736 Z= 0.119 Angle : 0.587 14.969 17314 Z= 0.298 Chirality : 0.045 0.368 2068 Planarity : 0.003 0.048 2146 Dihedral : 4.497 56.512 1666 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.19 % Allowed : 18.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.22), residues: 1518 helix: 2.03 (0.18), residues: 840 sheet: 0.15 (0.40), residues: 186 loop : 0.37 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP G 216 HIS 0.002 0.001 HIS H 286 PHE 0.024 0.001 PHE E 256 TYR 0.020 0.001 TYR B 283 ARG 0.007 0.000 ARG B 279 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 697) hydrogen bonds : angle 3.74529 ( 2004) covalent geometry : bond 0.00274 (12736) covalent geometry : angle 0.58717 (17314) ********************** 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: 31 poor density : 214 time to evaluate : 1.538 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: 0.3916 (OUTLIER) cc_final: 0.3465 (tptt) REVERT: E 317 GLN cc_start: 0.8294 (tp40) cc_final: 0.7574 (tm-30) REVERT: E 336 MET cc_start: 0.6862 (mtm) cc_final: 0.6488 (mtm) REVERT: F 322 ASP cc_start: 0.8870 (m-30) cc_final: 0.8357 (m-30) REVERT: G 329 CYS cc_start: 0.8048 (m) cc_final: 0.7084 (p) REVERT: G 360 THR cc_start: 0.7942 (m) cc_final: 0.7739 (p) REVERT: H 198 LYS cc_start: 0.8682 (ptpp) cc_final: 0.8367 (ptpp) REVERT: H 280 THR cc_start: 0.8350 (m) cc_final: 0.7996 (p) REVERT: H 304 GLN cc_start: 0.8079 (mt0) cc_final: 0.7688 (tm-30) REVERT: H 306 GLU cc_start: 0.8576 (tp30) cc_final: 0.8061 (tp30) REVERT: H 336 MET cc_start: 0.8084 (tpp) cc_final: 0.7523 (mmm) REVERT: H 368 PHE cc_start: 0.8168 (m-80) cc_final: 0.7913 (m-80) REVERT: H 376 LYS cc_start: 0.9434 (tttt) cc_final: 0.9176 (pttp) REVERT: A 176 ASP cc_start: 0.8760 (p0) cc_final: 0.8273 (p0) REVERT: A 177 GLN cc_start: 0.8988 (mm-40) cc_final: 0.8604 (mm-40) REVERT: A 232 GLU cc_start: 0.6326 (mp0) cc_final: 0.6032 (mp0) REVERT: A 258 LYS cc_start: 0.6678 (mttt) cc_final: 0.6122 (tttt) REVERT: A 279 ARG cc_start: 0.7349 (mmt-90) cc_final: 0.7097 (mtt-85) REVERT: A 346 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7388 (mtt-85) REVERT: C 192 SER cc_start: 0.9551 (t) cc_final: 0.9289 (p) REVERT: C 226 THR cc_start: 0.7970 (p) cc_final: 0.7695 (p) REVERT: C 277 GLU cc_start: 0.7951 (pt0) cc_final: 0.7742 (pt0) REVERT: D 220 GLN cc_start: 0.8399 (tp40) cc_final: 0.8175 (tp40) REVERT: D 246 LYS cc_start: 0.8873 (mttt) cc_final: 0.8613 (mmmt) REVERT: D 256 PHE cc_start: 0.8474 (t80) cc_final: 0.8086 (p90) REVERT: D 259 ASP cc_start: 0.7215 (m-30) cc_final: 0.6488 (p0) REVERT: D 273 ILE cc_start: 0.8142 (pt) cc_final: 0.7920 (mm) REVERT: D 350 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8218 (mm-30) REVERT: D 376 LYS cc_start: 0.8778 (tttt) cc_final: 0.8177 (tmmt) outliers start: 31 outliers final: 28 residues processed: 237 average time/residue: 0.2484 time to fit residues: 84.6208 Evaluate side-chains 233 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 1.386 ------------------------------------------------------------------------------- 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 343 THR Chi-restraints excluded: chain H residue 199 LEU 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 B residue 191 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 284 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 58 optimal weight: 8.9990 chunk 98 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** H 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN 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 = 0.107592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.090638 restraints weight = 28464.033| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.32 r_work: 0.3417 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12736 Z= 0.134 Angle : 0.594 14.481 17314 Z= 0.304 Chirality : 0.045 0.361 2068 Planarity : 0.003 0.048 2146 Dihedral : 4.509 56.538 1666 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.33 % Allowed : 18.55 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.22), residues: 1518 helix: 1.97 (0.18), residues: 840 sheet: 0.13 (0.40), residues: 186 loop : 0.35 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP G 216 HIS 0.003 0.001 HIS H 286 PHE 0.029 0.001 PHE E 256 TYR 0.022 0.001 TYR B 283 ARG 0.007 0.000 ARG B 279 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 697) hydrogen bonds : angle 3.83366 ( 2004) covalent geometry : bond 0.00312 (12736) covalent geometry : angle 0.59354 (17314) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6289.09 seconds wall clock time: 113 minutes 2.23 seconds (6782.23 seconds total)