Starting phenix.real_space_refine on Thu May 15 02:10:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ti9_41282/05_2025/8ti9_41282.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ti9_41282/05_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_41282/05_2025/8ti9_41282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ti9_41282/05_2025/8ti9_41282.map" model { file = "/net/cci-nas-00/data/ceres_data/8ti9_41282/05_2025/8ti9_41282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ti9_41282/05_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-5687/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: 8.72, per 1000 atoms: 0.70 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: 3.28 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: 4.31 Time building geometry restraints manager: 3.85 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: 0.02 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: 4.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.780 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 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 : 1.455 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: 0.2933 time to fit residues: 174.5252 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 : 1.493 ------------------------------------------------------------------------------- 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 = 0.107860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.090861 restraints weight = 27853.808| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.36 r_work: 0.3406 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2356 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= 0.128 Angle : 0.533 7.189 17314 Z= 0.282 Chirality : 0.044 0.218 2068 Planarity : 0.004 0.047 2146 Dihedral : 4.355 57.901 1670 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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: 2.05 (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 0.04133 ( 697) hydrogen bonds : angle 3.88024 ( 2004) covalent geometry : bond 0.00287 (12736) covalent geometry : angle 0.53283 (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 298 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 259 time to evaluate : 1.348 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: 0.8152 (tp40) cc_final: 0.7617 (tm-30) REVERT: E 336 MET cc_start: 0.6961 (mtm) cc_final: 0.6579 (mtm) REVERT: F 259 ASP cc_start: 0.7909 (t0) cc_final: 0.7694 (t70) REVERT: F 320 LYS cc_start: 0.7397 (mptt) cc_final: 0.6988 (ttpt) REVERT: F 322 ASP cc_start: 0.8797 (m-30) cc_final: 0.8312 (m-30) REVERT: F 375 ILE cc_start: 0.9200 (mt) cc_final: 0.8842 (mt) REVERT: G 195 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8884 (mp0) REVERT: G 206 PHE cc_start: 0.7399 (t80) cc_final: 0.6959 (t80) REVERT: G 212 LYS cc_start: 0.7693 (tttt) cc_final: 0.7369 (ttmm) REVERT: G 232 GLU cc_start: 0.8490 (pp20) cc_final: 0.8287 (pp20) REVERT: G 259 ASP cc_start: 0.7575 (t0) cc_final: 0.7304 (p0) REVERT: G 277 GLU cc_start: 0.8496 (pt0) cc_final: 0.8271 (pt0) REVERT: G 372 LYS cc_start: 0.8873 (ptpt) cc_final: 0.8558 (pttm) REVERT: H 280 THR cc_start: 0.8263 (m) cc_final: 0.7981 (p) REVERT: H 304 GLN cc_start: 0.7996 (mt0) cc_final: 0.7656 (tm-30) REVERT: H 368 PHE cc_start: 0.8253 (m-80) cc_final: 0.7943 (m-80) REVERT: H 369 GLU cc_start: 0.8726 (tp30) cc_final: 0.8466 (tp30) REVERT: H 370 ARG cc_start: 0.7098 (tpt90) cc_final: 0.6867 (tpt90) REVERT: H 376 LYS cc_start: 0.9432 (tttt) cc_final: 0.9103 (pttp) REVERT: A 258 LYS cc_start: 0.6197 (mttt) cc_final: 0.5811 (tttt) REVERT: A 277 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7683 (mp0) REVERT: A 346 ARG cc_start: 0.7633 (mtt180) cc_final: 0.7280 (mtt-85) REVERT: B 312 TYR cc_start: 0.8321 (t80) cc_final: 0.7769 (t80) REVERT: B 336 MET cc_start: 0.8455 (mtm) cc_final: 0.7956 (mmm) REVERT: B 365 ASP cc_start: 0.7593 (p0) cc_final: 0.7314 (p0) REVERT: B 378 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8600 (mm) REVERT: C 192 SER cc_start: 0.9591 (t) cc_final: 0.9331 (p) REVERT: C 226 THR cc_start: 0.7946 (p) cc_final: 0.7709 (p) REVERT: C 308 GLN cc_start: 0.7661 (tt0) cc_final: 0.7415 (mm-40) REVERT: C 354 LYS cc_start: 0.7906 (mmmt) cc_final: 0.7700 (mmtm) REVERT: D 246 LYS cc_start: 0.8946 (mttt) cc_final: 0.8587 (mmmt) REVERT: D 256 PHE cc_start: 0.8393 (t80) cc_final: 0.7910 (p90) REVERT: D 259 ASP cc_start: 0.7145 (m-30) cc_final: 0.6262 (p0) REVERT: D 299 TYR cc_start: 0.8159 (t80) cc_final: 0.7756 (t80) REVERT: D 336 MET cc_start: 0.7838 (mtm) cc_final: 0.7552 (mtm) REVERT: D 365 ASP cc_start: 0.7796 (m-30) cc_final: 0.7497 (m-30) REVERT: D 376 LYS cc_start: 0.8680 (tttt) cc_final: 0.8117 (tmmt) outliers start: 39 outliers final: 23 residues processed: 289 average time/residue: 0.2498 time to fit residues: 102.0910 Evaluate side-chains 235 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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: 0.9990 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 177 GLN E 220 GLN G 197 ASN ** H 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 ASN H 197 ASN H 201 ASN A 220 GLN D 186 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.106780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.089752 restraints weight = 28760.938| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.39 r_work: 0.3393 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12736 Z= 0.128 Angle : 0.513 10.964 17314 Z= 0.271 Chirality : 0.043 0.146 2068 Planarity : 0.003 0.050 2146 Dihedral : 4.379 57.751 1666 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.53 % Allowed : 13.82 % Favored : 82.65 % 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 (0.23), residues: 1518 helix: 2.09 (0.18), residues: 848 sheet: -0.10 (0.40), residues: 184 loop : 0.33 (0.32), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 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 0.005 0.000 ARG B 279 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 697) hydrogen bonds : angle 3.82186 ( 2004) covalent geometry : bond 0.00292 (12736) covalent geometry : angle 0.51270 (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 283 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 233 time to evaluate : 1.386 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: 0.9287 (mt) cc_final: 0.9083 (pp) REVERT: E 317 GLN cc_start: 0.8221 (tp40) cc_final: 0.7614 (tm-30) REVERT: E 336 MET cc_start: 0.6999 (mtm) cc_final: 0.6606 (mtm) REVERT: F 259 ASP cc_start: 0.7953 (t0) cc_final: 0.7663 (t70) REVERT: F 320 LYS cc_start: 0.7443 (mptt) cc_final: 0.7167 (ttpt) REVERT: F 322 ASP cc_start: 0.8807 (m-30) cc_final: 0.8327 (m-30) REVERT: F 375 ILE cc_start: 0.9122 (mt) cc_final: 0.8845 (mt) REVERT: G 197 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.7848 (t0) REVERT: G 206 PHE cc_start: 0.7440 (t80) cc_final: 0.6980 (t80) REVERT: G 212 LYS cc_start: 0.7498 (tttt) cc_final: 0.7188 (ttmm) REVERT: G 277 GLU cc_start: 0.8517 (pt0) cc_final: 0.8299 (pt0) REVERT: H 198 LYS cc_start: 0.8710 (ptpp) cc_final: 0.8323 (ptpt) REVERT: H 280 THR cc_start: 0.8251 (m) cc_final: 0.7968 (p) REVERT: H 304 GLN cc_start: 0.8104 (mt0) cc_final: 0.7725 (tm-30) REVERT: H 326 ILE cc_start: 0.6301 (mm) cc_final: 0.6011 (mt) REVERT: H 368 PHE cc_start: 0.8242 (m-80) cc_final: 0.7935 (m-80) REVERT: H 370 ARG cc_start: 0.7049 (tpt90) cc_final: 0.6840 (tpt90) REVERT: H 376 LYS cc_start: 0.9441 (tttt) cc_final: 0.9159 (pttp) REVERT: A 177 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8500 (mm-40) REVERT: A 258 LYS cc_start: 0.6479 (mttt) cc_final: 0.5983 (tttt) REVERT: A 277 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7732 (mp0) REVERT: A 346 ARG cc_start: 0.7695 (mtt180) cc_final: 0.7370 (mtt-85) REVERT: B 312 TYR cc_start: 0.8352 (t80) cc_final: 0.7946 (t80) REVERT: B 336 MET cc_start: 0.8463 (mtm) cc_final: 0.8018 (mmm) REVERT: B 365 ASP cc_start: 0.7675 (p0) cc_final: 0.7422 (p0) REVERT: B 378 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8558 (mm) REVERT: C 192 SER cc_start: 0.9557 (t) cc_final: 0.9304 (p) REVERT: C 226 THR cc_start: 0.7952 (p) cc_final: 0.7717 (p) REVERT: D 188 LYS cc_start: 0.8397 (mmtm) cc_final: 0.8017 (mmmt) REVERT: D 246 LYS cc_start: 0.8958 (mttt) cc_final: 0.8592 (mmmt) REVERT: D 256 PHE cc_start: 0.8446 (t80) cc_final: 0.7932 (p90) REVERT: D 259 ASP cc_start: 0.7208 (m-30) cc_final: 0.6313 (p0) REVERT: D 299 TYR cc_start: 0.8153 (t80) cc_final: 0.7688 (t80) REVERT: D 336 MET cc_start: 0.7821 (mtm) cc_final: 0.7598 (mtm) REVERT: D 365 ASP cc_start: 0.7788 (m-30) cc_final: 0.7485 (m-30) REVERT: D 376 LYS cc_start: 0.8724 (tttt) cc_final: 0.8169 (tmmt) outliers start: 50 outliers final: 28 residues processed: 269 average time/residue: 0.2569 time to fit residues: 98.7194 Evaluate side-chains 243 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 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 H residue 197 ASN 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 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 348 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 379 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 148 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 50 optimal weight: 0.0040 chunk 62 optimal weight: 0.8980 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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 186 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.107725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.090716 restraints weight = 28057.811| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.31 r_work: 0.3413 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12736 Z= 0.114 Angle : 0.508 9.021 17314 Z= 0.269 Chirality : 0.043 0.266 2068 Planarity : 0.003 0.051 2146 Dihedral : 4.394 57.405 1666 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.75 % Allowed : 15.02 % Favored : 82.23 % 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: 1.84 (0.23), residues: 1518 helix: 2.07 (0.18), residues: 846 sheet: -0.01 (0.40), residues: 186 loop : 0.32 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 216 HIS 0.003 0.001 HIS A 347 PHE 0.020 0.001 PHE E 256 TYR 0.020 0.001 TYR B 278 ARG 0.002 0.000 ARG B 279 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 697) hydrogen bonds : angle 3.77310 ( 2004) covalent geometry : bond 0.00254 (12736) covalent geometry : angle 0.50835 (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 264 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 1.553 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: 0.8237 (tp40) cc_final: 0.7600 (tm-30) REVERT: E 336 MET cc_start: 0.6953 (mtm) cc_final: 0.6554 (mtm) REVERT: F 259 ASP cc_start: 0.7844 (t0) cc_final: 0.7541 (t70) REVERT: F 320 LYS cc_start: 0.7475 (mptt) cc_final: 0.7221 (ttpt) REVERT: F 322 ASP cc_start: 0.8823 (m-30) cc_final: 0.8337 (m-30) REVERT: G 195 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8181 (mp0) REVERT: G 212 LYS cc_start: 0.7475 (tttt) cc_final: 0.7225 (mtmt) REVERT: G 360 THR cc_start: 0.7951 (m) cc_final: 0.7731 (p) REVERT: H 280 THR cc_start: 0.8239 (m) cc_final: 0.7954 (p) REVERT: H 304 GLN cc_start: 0.8072 (mt0) cc_final: 0.7695 (tm-30) REVERT: H 306 GLU cc_start: 0.8450 (tp30) cc_final: 0.7933 (tp30) REVERT: H 326 ILE cc_start: 0.6251 (mm) cc_final: 0.6032 (mm) REVERT: H 368 PHE cc_start: 0.8229 (m-80) cc_final: 0.7990 (m-80) REVERT: H 376 LYS cc_start: 0.9445 (tttt) cc_final: 0.9161 (pttp) REVERT: A 176 ASP cc_start: 0.8893 (p0) cc_final: 0.8447 (p0) REVERT: A 177 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8518 (mm-40) REVERT: A 258 LYS cc_start: 0.6518 (mttt) cc_final: 0.6028 (tttt) REVERT: A 277 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7721 (mp0) REVERT: A 346 ARG cc_start: 0.7692 (mtt180) cc_final: 0.7371 (mtt-85) REVERT: B 336 MET cc_start: 0.8460 (mtm) cc_final: 0.8114 (mmm) REVERT: B 365 ASP cc_start: 0.7742 (p0) cc_final: 0.7536 (p0) REVERT: B 378 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8638 (mm) REVERT: C 192 SER cc_start: 0.9551 (t) cc_final: 0.9279 (p) REVERT: C 203 SER cc_start: 0.7550 (t) cc_final: 0.7316 (p) REVERT: C 226 THR cc_start: 0.7941 (p) cc_final: 0.7695 (p) REVERT: D 188 LYS cc_start: 0.8433 (mmtm) cc_final: 0.8068 (mmmt) REVERT: D 246 LYS cc_start: 0.8933 (mttt) cc_final: 0.8575 (mmmt) REVERT: D 256 PHE cc_start: 0.8443 (t80) cc_final: 0.7918 (p90) REVERT: D 259 ASP cc_start: 0.7155 (m-30) cc_final: 0.6267 (p0) REVERT: D 305 ARG cc_start: 0.7913 (tpp-160) cc_final: 0.7663 (tpt170) REVERT: D 365 ASP cc_start: 0.7777 (m-30) cc_final: 0.7464 (m-30) REVERT: D 376 LYS cc_start: 0.8753 (tttt) cc_final: 0.8167 (tmmt) outliers start: 39 outliers final: 25 residues processed: 253 average time/residue: 0.2409 time to fit residues: 87.4837 Evaluate side-chains 229 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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: 0.8980 chunk 49 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 122 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 114 optimal weight: 0.0040 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN H 197 ASN A 220 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.107828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.090460 restraints weight = 28750.056| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.37 r_work: 0.3411 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12736 Z= 0.120 Angle : 0.516 10.812 17314 Z= 0.270 Chirality : 0.042 0.167 2068 Planarity : 0.003 0.050 2146 Dihedral : 4.413 57.273 1666 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.17 % Allowed : 15.44 % Favored : 81.38 % 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: 1.82 (0.22), residues: 1518 helix: 2.04 (0.18), residues: 844 sheet: -0.01 (0.40), residues: 186 loop : 0.35 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile 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 0.013 0.001 TYR F 312 ARG 0.003 0.000 ARG G 316 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 697) hydrogen bonds : angle 3.72733 ( 2004) covalent geometry : bond 0.00275 (12736) covalent geometry : angle 0.51646 (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 267 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 1.502 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: 0.8193 (tp40) cc_final: 0.7552 (tm-30) REVERT: E 336 MET cc_start: 0.6908 (mtm) cc_final: 0.6520 (mtm) REVERT: F 259 ASP cc_start: 0.7841 (t0) cc_final: 0.7523 (t70) REVERT: F 320 LYS cc_start: 0.7518 (mptt) cc_final: 0.7293 (ttpt) REVERT: F 322 ASP cc_start: 0.8854 (m-30) cc_final: 0.8354 (m-30) REVERT: G 212 LYS cc_start: 0.7394 (tttt) cc_final: 0.7178 (mtmt) REVERT: G 360 THR cc_start: 0.7933 (m) cc_final: 0.7694 (p) REVERT: H 198 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8298 (ptpt) REVERT: H 280 THR cc_start: 0.8266 (m) cc_final: 0.7956 (p) REVERT: H 304 GLN cc_start: 0.8074 (mt0) cc_final: 0.7678 (tm-30) REVERT: H 306 GLU cc_start: 0.8539 (tp30) cc_final: 0.8009 (tp30) REVERT: H 326 ILE cc_start: 0.6151 (mm) cc_final: 0.5936 (mm) REVERT: H 368 PHE cc_start: 0.8207 (m-80) cc_final: 0.7993 (m-80) REVERT: H 376 LYS cc_start: 0.9459 (tttt) cc_final: 0.9183 (pttp) REVERT: A 176 ASP cc_start: 0.8893 (p0) cc_final: 0.8416 (p0) REVERT: A 177 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8580 (mm-40) REVERT: A 258 LYS cc_start: 0.6531 (mttt) cc_final: 0.6025 (tttt) REVERT: A 346 ARG cc_start: 0.7673 (mtt180) cc_final: 0.7351 (mtt-85) REVERT: B 378 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8623 (mm) REVERT: C 188 LYS cc_start: 0.9437 (OUTLIER) cc_final: 0.9204 (mttt) REVERT: C 192 SER cc_start: 0.9560 (t) cc_final: 0.9302 (p) REVERT: C 203 SER cc_start: 0.7586 (t) cc_final: 0.7352 (p) REVERT: C 226 THR cc_start: 0.7970 (p) cc_final: 0.7717 (p) REVERT: D 188 LYS cc_start: 0.8460 (mmtm) cc_final: 0.8088 (mmmt) REVERT: D 246 LYS cc_start: 0.8943 (mttt) cc_final: 0.8595 (mmmt) REVERT: D 256 PHE cc_start: 0.8456 (t80) cc_final: 0.7924 (p90) REVERT: D 259 ASP cc_start: 0.7164 (m-30) cc_final: 0.6285 (p0) REVERT: D 305 ARG cc_start: 0.7944 (tpp-160) cc_final: 0.7732 (tpt170) REVERT: D 376 LYS cc_start: 0.8784 (tttt) cc_final: 0.8205 (tmmt) outliers start: 45 outliers final: 30 residues processed: 253 average time/residue: 0.2476 time to fit residues: 89.4269 Evaluate side-chains 235 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 329 CYS Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 205 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 82 optimal weight: 0.9980 chunk 144 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 145 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** 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 = 0.3849 r_free = 0.3849 target = 0.107370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.090376 restraints weight = 28688.251| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.34 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: 0.7703 moved from start: 0.3279 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= 0.128 Angle : 0.547 15.492 17314 Z= 0.278 Chirality : 0.043 0.278 2068 Planarity : 0.003 0.050 2146 Dihedral : 4.403 57.364 1666 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.17 % Allowed : 16.50 % Favored : 80.32 % 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: 1.81 (0.22), residues: 1518 helix: 2.01 (0.18), residues: 844 sheet: 0.03 (0.40), residues: 186 loop : 0.36 (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 H 286 PHE 0.022 0.001 PHE E 256 TYR 0.016 0.001 TYR B 278 ARG 0.003 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 697) hydrogen bonds : angle 3.75764 ( 2004) covalent geometry : bond 0.00293 (12736) covalent geometry : angle 0.54721 (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 265 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 220 time to evaluate : 1.334 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: 0.8203 (tp40) cc_final: 0.7548 (tm-30) REVERT: E 336 MET cc_start: 0.6943 (mtm) cc_final: 0.6561 (mtm) REVERT: F 187 LEU cc_start: 0.8800 (mm) cc_final: 0.8559 (mm) REVERT: F 259 ASP cc_start: 0.7802 (t0) cc_final: 0.7536 (t70) REVERT: F 322 ASP cc_start: 0.8873 (m-30) cc_final: 0.8380 (m-30) REVERT: G 212 LYS cc_start: 0.7395 (tttt) cc_final: 0.7188 (ttmm) REVERT: G 277 GLU cc_start: 0.8587 (pt0) cc_final: 0.8301 (pt0) REVERT: G 360 THR cc_start: 0.7887 (m) cc_final: 0.7670 (p) REVERT: H 198 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8309 (ptpt) REVERT: H 280 THR cc_start: 0.8276 (m) cc_final: 0.7970 (p) REVERT: H 304 GLN cc_start: 0.8106 (mt0) cc_final: 0.7684 (tm-30) REVERT: H 306 GLU cc_start: 0.8558 (tp30) cc_final: 0.8022 (tp30) REVERT: H 326 ILE cc_start: 0.6170 (mm) cc_final: 0.5956 (mm) REVERT: H 368 PHE cc_start: 0.8202 (m-80) cc_final: 0.7985 (m-80) REVERT: H 376 LYS cc_start: 0.9460 (tttt) cc_final: 0.9201 (pttp) REVERT: A 177 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8597 (mm-40) REVERT: A 258 LYS cc_start: 0.6542 (mttt) cc_final: 0.6041 (tttt) REVERT: A 346 ARG cc_start: 0.7687 (mtt180) cc_final: 0.7386 (mtt-85) REVERT: B 378 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8526 (mm) REVERT: C 188 LYS cc_start: 0.9437 (OUTLIER) cc_final: 0.9209 (mttt) REVERT: C 192 SER cc_start: 0.9542 (t) cc_final: 0.9289 (p) REVERT: C 203 SER cc_start: 0.7559 (t) cc_final: 0.7337 (p) REVERT: C 226 THR cc_start: 0.7987 (p) cc_final: 0.7721 (p) REVERT: D 246 LYS cc_start: 0.8984 (mttt) cc_final: 0.8627 (mmmt) REVERT: D 256 PHE cc_start: 0.8483 (t80) cc_final: 0.7927 (p90) REVERT: D 259 ASP cc_start: 0.7175 (m-30) cc_final: 0.6307 (p0) REVERT: D 376 LYS cc_start: 0.8782 (tttt) cc_final: 0.8187 (tmmt) outliers start: 45 outliers final: 33 residues processed: 249 average time/residue: 0.2389 time to fit residues: 85.6448 Evaluate side-chains 242 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 256 PHE Chi-restraints excluded: chain 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 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 215 THR Chi-restraints excluded: chain D residue 337 PHE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 375 ILE 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: 3.9990 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 45 optimal weight: 0.0570 chunk 48 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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** ** G 208 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.107827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.090919 restraints weight = 28570.705| |-----------------------------------------------------------------------------| r_work (start): 0.3545 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: 0.7689 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12736 Z= 0.118 Angle : 0.542 13.293 17314 Z= 0.277 Chirality : 0.043 0.269 2068 Planarity : 0.003 0.049 2146 Dihedral : 4.397 57.212 1666 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.03 % Allowed : 16.93 % Favored : 80.04 % 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: 1.82 (0.22), residues: 1518 helix: 2.02 (0.18), residues: 844 sheet: 0.06 (0.40), residues: 186 loop : 0.38 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP G 216 HIS 0.002 0.001 HIS H 286 PHE 0.023 0.001 PHE E 256 TYR 0.016 0.001 TYR F 312 ARG 0.002 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 697) hydrogen bonds : angle 3.70608 ( 2004) covalent geometry : bond 0.00271 (12736) covalent geometry : angle 0.54247 (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 271 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 228 time to evaluate : 1.848 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 317 GLN cc_start: 0.8293 (tp40) cc_final: 0.7587 (tm-30) REVERT: E 336 MET cc_start: 0.6894 (mtm) cc_final: 0.6510 (mtm) REVERT: F 259 ASP cc_start: 0.7746 (t0) cc_final: 0.7537 (t70) REVERT: F 322 ASP cc_start: 0.8860 (m-30) cc_final: 0.8403 (m-30) REVERT: G 212 LYS cc_start: 0.7229 (tttt) cc_final: 0.6992 (mtmm) REVERT: G 360 THR cc_start: 0.7956 (m) cc_final: 0.7731 (p) REVERT: H 198 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8291 (ptpt) REVERT: H 280 THR cc_start: 0.8293 (m) cc_final: 0.7984 (p) REVERT: H 304 GLN cc_start: 0.8106 (mt0) cc_final: 0.7686 (tm-30) REVERT: H 306 GLU cc_start: 0.8574 (tp30) cc_final: 0.8032 (tp30) REVERT: H 326 ILE cc_start: 0.6222 (mm) cc_final: 0.6014 (mm) REVERT: H 368 PHE cc_start: 0.8182 (m-80) cc_final: 0.7951 (m-80) REVERT: H 376 LYS cc_start: 0.9460 (tttt) cc_final: 0.9216 (pttp) REVERT: A 176 ASP cc_start: 0.8837 (p0) cc_final: 0.8387 (p0) REVERT: A 177 GLN cc_start: 0.9018 (mm-40) cc_final: 0.8655 (mm-40) REVERT: A 258 LYS cc_start: 0.6569 (mttt) cc_final: 0.6068 (tttt) REVERT: A 346 ARG cc_start: 0.7717 (mtt180) cc_final: 0.7404 (mtt-85) REVERT: C 188 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.9183 (mttt) REVERT: C 192 SER cc_start: 0.9540 (t) cc_final: 0.9275 (p) REVERT: C 226 THR cc_start: 0.7987 (p) cc_final: 0.7722 (p) REVERT: D 246 LYS cc_start: 0.8944 (mttt) cc_final: 0.8598 (mmmt) REVERT: D 256 PHE cc_start: 0.8470 (t80) cc_final: 0.7954 (p90) REVERT: D 259 ASP cc_start: 0.7163 (m-30) cc_final: 0.6311 (p0) REVERT: D 376 LYS cc_start: 0.8798 (tttt) cc_final: 0.8208 (tmmt) outliers start: 43 outliers final: 32 residues processed: 255 average time/residue: 0.2385 time to fit residues: 87.3961 Evaluate side-chains 235 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain 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 198 LYS Chi-restraints excluded: chain H residue 199 LEU 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 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: 4.9990 chunk 59 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** A 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 = 0.3841 r_free = 0.3841 target = 0.106801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.090030 restraints weight = 28702.875| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.31 r_work: 0.3402 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12736 Z= 0.142 Angle : 0.571 14.873 17314 Z= 0.295 Chirality : 0.044 0.177 2068 Planarity : 0.003 0.046 2146 Dihedral : 4.490 57.299 1666 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.75 % Allowed : 17.63 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.76 (0.22), residues: 1518 helix: 1.94 (0.18), residues: 844 sheet: 0.08 (0.40), residues: 186 loop : 0.37 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP G 216 HIS 0.002 0.001 HIS H 286 PHE 0.029 0.001 PHE G 206 TYR 0.024 0.001 TYR F 312 ARG 0.006 0.000 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 697) hydrogen bonds : angle 3.78404 ( 2004) covalent geometry : bond 0.00331 (12736) covalent geometry : angle 0.57123 (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 : 1.365 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: 0.3691 (OUTLIER) cc_final: 0.3303 (tptt) REVERT: E 317 GLN cc_start: 0.8315 (tp40) cc_final: 0.7595 (tm-30) REVERT: E 336 MET cc_start: 0.6921 (mtm) cc_final: 0.6545 (mtm) REVERT: F 259 ASP cc_start: 0.7815 (t0) cc_final: 0.7574 (t70) REVERT: F 322 ASP cc_start: 0.8865 (m-30) cc_final: 0.8364 (m-30) REVERT: G 212 LYS cc_start: 0.7165 (tttt) cc_final: 0.6938 (mtmm) REVERT: G 360 THR cc_start: 0.7901 (m) cc_final: 0.7673 (p) REVERT: H 198 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8277 (ptpp) REVERT: H 280 THR cc_start: 0.8256 (m) cc_final: 0.7949 (p) REVERT: H 304 GLN cc_start: 0.8139 (mt0) cc_final: 0.7717 (tm-30) REVERT: H 306 GLU cc_start: 0.8589 (tp30) cc_final: 0.8085 (tp30) REVERT: H 368 PHE cc_start: 0.8199 (m-80) cc_final: 0.7976 (m-80) REVERT: H 376 LYS cc_start: 0.9472 (tttt) cc_final: 0.9219 (pttp) REVERT: A 176 ASP cc_start: 0.8822 (p0) cc_final: 0.8573 (p0) REVERT: A 177 GLN cc_start: 0.9000 (mm-40) cc_final: 0.8688 (mm110) REVERT: A 258 LYS cc_start: 0.6624 (mttt) cc_final: 0.6106 (tttt) REVERT: A 346 ARG cc_start: 0.7726 (mtt180) cc_final: 0.7413 (mtt-85) REVERT: C 188 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9183 (mttt) REVERT: C 192 SER cc_start: 0.9550 (t) cc_final: 0.9310 (p) REVERT: C 226 THR cc_start: 0.8005 (p) cc_final: 0.7737 (p) REVERT: D 220 GLN cc_start: 0.8338 (tp40) cc_final: 0.8094 (tp40) REVERT: D 246 LYS cc_start: 0.8932 (mttt) cc_final: 0.8595 (mmmt) REVERT: D 256 PHE cc_start: 0.8441 (t80) cc_final: 0.8090 (p90) REVERT: D 259 ASP cc_start: 0.7223 (m-30) cc_final: 0.6414 (p0) REVERT: D 376 LYS cc_start: 0.8824 (tttt) cc_final: 0.8228 (tmmt) outliers start: 39 outliers final: 31 residues processed: 242 average time/residue: 0.2454 time to fit residues: 84.8295 Evaluate side-chains 237 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 246 LYS Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 199 LEU 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 329 CYS 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: 0.9980 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 118 optimal weight: 0.2980 chunk 119 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 97 optimal weight: 0.4980 chunk 89 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 186 ASN ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 ASN ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.107566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.090627 restraints weight = 28670.180| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.35 r_work: 0.3414 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3526 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= 0.131 Angle : 0.594 13.977 17314 Z= 0.304 Chirality : 0.044 0.344 2068 Planarity : 0.003 0.048 2146 Dihedral : 4.509 57.002 1666 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.40 % Allowed : 17.91 % Favored : 79.69 % 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: 1.75 (0.22), residues: 1518 helix: 1.93 (0.18), residues: 840 sheet: 0.10 (0.40), residues: 186 loop : 0.37 (0.31), residues: 492 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 0.031 0.001 PHE G 206 TYR 0.025 0.001 TYR F 312 ARG 0.010 0.000 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 697) hydrogen bonds : angle 3.80351 ( 2004) covalent geometry : bond 0.00301 (12736) covalent geometry : angle 0.59391 (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 249 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 1.480 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: 0.3842 (OUTLIER) cc_final: 0.3391 (tptt) REVERT: E 317 GLN cc_start: 0.8307 (tp40) cc_final: 0.7575 (tm-30) REVERT: E 336 MET cc_start: 0.6876 (mtm) cc_final: 0.6515 (mtm) REVERT: F 259 ASP cc_start: 0.7770 (t0) cc_final: 0.7554 (t70) REVERT: F 322 ASP cc_start: 0.8860 (m-30) cc_final: 0.8326 (m-30) REVERT: G 360 THR cc_start: 0.7902 (m) cc_final: 0.7685 (p) REVERT: H 189 LYS cc_start: 0.9114 (ptmm) cc_final: 0.8817 (pptt) REVERT: H 198 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8376 (ptpp) REVERT: H 280 THR cc_start: 0.8314 (m) cc_final: 0.7972 (p) REVERT: H 304 GLN cc_start: 0.8130 (mt0) cc_final: 0.7713 (tm-30) REVERT: H 306 GLU cc_start: 0.8582 (tp30) cc_final: 0.8078 (tp30) REVERT: H 368 PHE cc_start: 0.8173 (m-80) cc_final: 0.7962 (m-80) REVERT: H 376 LYS cc_start: 0.9477 (tttt) cc_final: 0.9220 (pttp) REVERT: A 232 GLU cc_start: 0.6386 (mp0) cc_final: 0.6107 (mp0) REVERT: A 258 LYS cc_start: 0.6672 (mttt) cc_final: 0.6122 (tttt) REVERT: A 346 ARG cc_start: 0.7721 (mtt180) cc_final: 0.7412 (mtt-85) REVERT: A 366 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6773 (mt-10) REVERT: C 192 SER cc_start: 0.9550 (t) cc_final: 0.9296 (p) REVERT: C 226 THR cc_start: 0.7983 (p) cc_final: 0.7710 (p) REVERT: D 220 GLN cc_start: 0.8368 (tp40) cc_final: 0.8152 (tp40) REVERT: D 246 LYS cc_start: 0.8879 (mttt) cc_final: 0.8545 (mmmt) REVERT: D 256 PHE cc_start: 0.8454 (t80) cc_final: 0.8074 (p90) REVERT: D 259 ASP cc_start: 0.7198 (m-30) cc_final: 0.6419 (p0) REVERT: D 376 LYS cc_start: 0.8817 (tttt) cc_final: 0.8218 (tmmt) outliers start: 34 outliers final: 29 residues processed: 240 average time/residue: 0.2655 time to fit residues: 91.3204 Evaluate side-chains 230 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 246 LYS Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 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 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: 1.9990 chunk 143 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 147 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.106221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.089347 restraints weight = 28676.173| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.28 r_work: 0.3397 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12736 Z= 0.164 Angle : 0.607 13.882 17314 Z= 0.315 Chirality : 0.046 0.373 2068 Planarity : 0.004 0.047 2146 Dihedral : 4.622 57.082 1666 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.33 % Allowed : 17.98 % Favored : 79.69 % 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: 1.59 (0.22), residues: 1518 helix: 1.80 (0.18), residues: 840 sheet: 0.02 (0.40), residues: 186 loop : 0.32 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP G 216 HIS 0.003 0.001 HIS H 286 PHE 0.024 0.002 PHE E 256 TYR 0.038 0.001 TYR F 312 ARG 0.006 0.000 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 697) hydrogen bonds : angle 3.92856 ( 2004) covalent geometry : bond 0.00382 (12736) covalent geometry : angle 0.60724 (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 238 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 1.597 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: 0.3942 (OUTLIER) cc_final: 0.3439 (tptt) REVERT: E 317 GLN cc_start: 0.8327 (tp40) cc_final: 0.7576 (tm-30) REVERT: E 336 MET cc_start: 0.6900 (mtm) cc_final: 0.6508 (mtm) REVERT: F 259 ASP cc_start: 0.7885 (t0) cc_final: 0.7567 (t70) REVERT: F 322 ASP cc_start: 0.8860 (m-30) cc_final: 0.8333 (m-30) REVERT: G 360 THR cc_start: 0.7778 (m) cc_final: 0.7546 (p) REVERT: H 189 LYS cc_start: 0.9176 (ptmm) cc_final: 0.8879 (pptt) REVERT: H 198 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8402 (ptpp) REVERT: H 280 THR cc_start: 0.8355 (m) cc_final: 0.8004 (p) REVERT: H 304 GLN cc_start: 0.8107 (mt0) cc_final: 0.7666 (tm-30) REVERT: H 306 GLU cc_start: 0.8579 (tp30) cc_final: 0.8069 (tp30) REVERT: H 368 PHE cc_start: 0.8158 (m-80) cc_final: 0.7929 (m-80) REVERT: H 376 LYS cc_start: 0.9488 (tttt) cc_final: 0.9220 (pttp) REVERT: A 232 GLU cc_start: 0.6370 (mp0) cc_final: 0.6094 (mp0) REVERT: A 258 LYS cc_start: 0.6725 (mttt) cc_final: 0.6140 (tttt) REVERT: A 346 ARG cc_start: 0.7710 (mtt180) cc_final: 0.7393 (mtt-85) REVERT: C 192 SER cc_start: 0.9577 (t) cc_final: 0.9331 (p) REVERT: C 226 THR cc_start: 0.7989 (p) cc_final: 0.7715 (p) REVERT: D 220 GLN cc_start: 0.8434 (tp40) cc_final: 0.8213 (tp40) REVERT: D 246 LYS cc_start: 0.8908 (mttt) cc_final: 0.8571 (mmmt) REVERT: D 256 PHE cc_start: 0.8524 (t80) cc_final: 0.8121 (p90) REVERT: D 259 ASP cc_start: 0.7302 (m-30) cc_final: 0.6479 (p0) REVERT: D 273 ILE cc_start: 0.8166 (pt) cc_final: 0.7945 (mm) REVERT: D 365 ASP cc_start: 0.7747 (m-30) cc_final: 0.7457 (m-30) REVERT: D 376 LYS cc_start: 0.8824 (tttt) cc_final: 0.8219 (tmmt) outliers start: 33 outliers final: 31 residues processed: 227 average time/residue: 0.2591 time to fit residues: 84.6982 Evaluate side-chains 224 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 246 LYS Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 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 199 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 213 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 87 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 62 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.107838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.090947 restraints weight = 28374.713| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.29 r_work: 0.3421 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12736 Z= 0.128 Angle : 0.596 13.270 17314 Z= 0.306 Chirality : 0.045 0.367 2068 Planarity : 0.003 0.048 2146 Dihedral : 4.551 56.455 1666 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.40 % Allowed : 17.91 % Favored : 79.69 % 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: 1.69 (0.22), residues: 1518 helix: 1.88 (0.18), residues: 840 sheet: 0.05 (0.40), residues: 186 loop : 0.36 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP G 216 HIS 0.002 0.001 HIS H 286 PHE 0.024 0.001 PHE E 256 TYR 0.036 0.001 TYR F 312 ARG 0.007 0.000 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 697) hydrogen bonds : angle 3.83144 ( 2004) covalent geometry : bond 0.00297 (12736) covalent geometry : angle 0.59646 (17314) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5746.47 seconds wall clock time: 101 minutes 20.05 seconds (6080.05 seconds total)