Starting phenix.real_space_refine on Thu Sep 26 08:10:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ti9_41282/09_2024/8ti9_41282.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ti9_41282/09_2024/8ti9_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ti9_41282/09_2024/8ti9_41282.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ti9_41282/09_2024/8ti9_41282.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ti9_41282/09_2024/8ti9_41282.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ti9_41282/09_2024/8ti9_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-5461/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: 8.43, per 1000 atoms: 0.67 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: 3.33 Conformation dependent library (CDL) restraints added in 1.6 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: 1.33 Creating SS restraints... Processing helix chain 'E' and resid 173 through 197 removed outlier: 3.599A pdb=" N ASN E 197 " --> pdb=" O VAL E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 213 removed outlier: 3.719A pdb=" N GLU E 213 " --> pdb=" O SER E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 223 removed outlier: 3.919A pdb=" N LEU E 218 " --> pdb=" O ASN E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 254 Processing helix chain 'E' and resid 255 through 258 removed outlier: 3.531A pdb=" N LYS E 258 " --> pdb=" O PRO E 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 255 through 258' Processing helix chain 'E' and resid 286 through 318 Processing helix chain 'E' and resid 336 through 340 removed outlier: 3.861A pdb=" N THR E 339 " --> pdb=" O MET E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 354 Processing helix chain 'E' and resid 363 through 379 Processing helix chain 'F' and resid 184 through 197 Processing helix chain 'F' and resid 203 through 214 removed outlier: 3.615A pdb=" N TRP F 207 " --> pdb=" O SER F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 220 Processing helix chain 'F' and resid 230 through 235 removed outlier: 3.997A pdb=" N VAL F 235 " --> pdb=" O GLU F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 306 removed outlier: 3.541A pdb=" N THR F 290 " --> pdb=" O HIS F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 317 Processing helix chain 'F' and resid 336 through 340 removed outlier: 3.525A pdb=" N THR F 339 " --> pdb=" O MET F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 356 removed outlier: 3.580A pdb=" N LEU F 356 " --> pdb=" O TYR F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 379 removed outlier: 3.728A pdb=" N VAL F 371 " --> pdb=" O LEU F 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 198 Processing helix chain 'G' and resid 203 through 214 removed outlier: 3.510A pdb=" N TRP G 207 " --> pdb=" O SER G 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN G 214 " --> pdb=" O VAL G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 220 removed outlier: 4.386A pdb=" N LEU G 218 " --> pdb=" O ASN G 214 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN G 220 " --> pdb=" O TRP G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 306 removed outlier: 3.542A pdb=" N THR G 290 " --> pdb=" O HIS G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 317 Processing helix chain 'G' and resid 336 through 340 removed outlier: 3.629A pdb=" N THR G 339 " --> pdb=" O MET G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 355 Processing helix chain 'G' and resid 363 through 379 Processing helix chain 'H' and resid 174 through 197 Processing helix chain 'H' and resid 203 through 213 removed outlier: 3.597A pdb=" N GLU H 213 " --> pdb=" O SER H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 222 removed outlier: 4.078A pdb=" N LEU H 218 " --> pdb=" O ASN H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 254 removed outlier: 3.535A pdb=" N PHE H 250 " --> pdb=" O LYS H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 318 Processing helix chain 'H' and resid 336 through 340 removed outlier: 3.575A pdb=" N THR H 339 " --> pdb=" O MET H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 354 Processing helix chain 'H' and resid 363 through 379 Processing helix chain 'A' and resid 174 through 197 removed outlier: 3.500A pdb=" N LEU A 181 " --> pdb=" O GLN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.593A pdb=" N GLU A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 222 removed outlier: 3.775A pdb=" N LEU A 218 " --> pdb=" O ASN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 254 Processing helix chain 'A' and resid 255 through 258 removed outlier: 3.610A pdb=" N LYS A 258 " --> pdb=" O PRO A 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 255 through 258' Processing helix chain 'A' and resid 286 through 318 Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.667A pdb=" N THR A 339 " --> pdb=" O MET A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 Processing helix chain 'A' and resid 363 through 379 Processing helix chain 'B' and resid 184 through 197 Processing helix chain 'B' and resid 203 through 214 removed outlier: 3.558A pdb=" N TRP B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 220 Processing helix chain 'B' and resid 286 through 306 Processing helix chain 'B' and resid 306 through 318 Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.549A pdb=" N THR B 339 " --> pdb=" O MET B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.639A pdb=" N GLU B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 379 removed outlier: 3.743A pdb=" N ARG B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 198 Processing helix chain 'C' and resid 203 through 214 removed outlier: 3.670A pdb=" N TRP C 207 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 214 " --> pdb=" O VAL C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'C' and resid 286 through 306 removed outlier: 3.523A pdb=" N THR C 290 " --> pdb=" O HIS C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 318 Processing helix chain 'C' and resid 336 through 340 Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 363 through 379 removed outlier: 3.882A pdb=" N VAL C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 197 Processing helix chain 'D' and resid 203 through 213 removed outlier: 3.624A pdb=" N GLU D 213 " --> pdb=" O SER D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 222 removed outlier: 3.855A pdb=" N LEU D 218 " --> pdb=" O ASN D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 254 removed outlier: 3.552A pdb=" N PHE D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 318 Processing helix chain 'D' and resid 336 through 340 removed outlier: 3.858A pdb=" N THR D 339 " --> pdb=" O MET D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 354 Processing helix chain 'D' and resid 363 through 379 Processing sheet with id=AA1, first strand: chain 'E' and resid 238 through 239 removed outlier: 7.010A pdb=" N THR E 226 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE E 263 " --> pdb=" O THR E 226 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU E 228 " --> pdb=" O ILE E 263 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE E 265 " --> pdb=" O LEU E 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 227 through 228 removed outlier: 7.135A pdb=" N CYS F 330 " --> pdb=" O THR F 360 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE F 362 " --> pdb=" O CYS F 330 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL F 332 " --> pdb=" O ILE F 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 227 through 228 removed outlier: 6.873A pdb=" N CYS G 330 " --> pdb=" O THR G 360 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE G 362 " --> pdb=" O CYS G 330 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL G 332 " --> pdb=" O ILE G 362 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 238 through 239 removed outlier: 6.402A pdb=" N LEU H 262 " --> pdb=" O VAL H 331 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE H 333 " --> pdb=" O LEU H 262 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ALA H 264 " --> pdb=" O ILE H 333 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 239 removed outlier: 3.542A pdb=" N VAL A 261 " --> pdb=" O THR A 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 227 through 228 removed outlier: 8.538A pdb=" N VAL B 331 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU B 262 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ILE B 333 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA B 264 " --> pdb=" O ILE B 333 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N CYS B 330 " --> pdb=" O THR B 360 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE B 362 " --> pdb=" O CYS B 330 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL B 332 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 227 through 228 removed outlier: 3.524A pdb=" N ILE C 263 " --> pdb=" O PHE C 250 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N CYS C 330 " --> pdb=" O THR C 360 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE C 362 " --> pdb=" O CYS C 330 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL C 332 " --> pdb=" O ILE C 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 238 through 239 697 hydrogen bonds defined for protein. 2004 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.45 Time building geometry restraints manager: 3.80 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: 0.00 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 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: 0.120 Process input model: 30.440 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.510 ------------------------------------------------------------------------------- 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= 0.140 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 *********************** 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 fitting. rotamer outliers: 18 poor density : 425 time to evaluate : 1.528 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: 0.2935 time to fit residues: 173.9686 Evaluate side-chains 227 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 219 time to evaluate : 1.519 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 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= 0.188 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 *********************** 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 fitting. rotamer outliers: 39 poor density : 259 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 317 GLN cc_start: 0.8236 (tp40) cc_final: 0.7713 (tm-30) REVERT: E 336 MET cc_start: 0.7051 (mtm) cc_final: 0.6632 (mtm) REVERT: F 320 LYS cc_start: 0.7434 (mptt) cc_final: 0.6968 (ttpt) REVERT: F 322 ASP cc_start: 0.8893 (m-30) cc_final: 0.8363 (m-30) REVERT: F 375 ILE cc_start: 0.9149 (mt) cc_final: 0.8837 (mt) REVERT: G 195 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8852 (mp0) REVERT: G 206 PHE cc_start: 0.7330 (t80) cc_final: 0.6892 (t80) REVERT: G 212 LYS cc_start: 0.7690 (tttt) cc_final: 0.7375 (ttmm) REVERT: G 232 GLU cc_start: 0.8477 (pp20) cc_final: 0.8265 (pp20) REVERT: G 259 ASP cc_start: 0.7488 (t0) cc_final: 0.7276 (p0) REVERT: G 277 GLU cc_start: 0.8346 (pt0) cc_final: 0.8119 (pt0) REVERT: G 372 LYS cc_start: 0.8840 (ptpt) cc_final: 0.8532 (pttm) REVERT: H 280 THR cc_start: 0.8269 (m) cc_final: 0.7985 (p) REVERT: H 304 GLN cc_start: 0.8001 (mt0) cc_final: 0.7699 (tm-30) REVERT: H 368 PHE cc_start: 0.8242 (m-80) cc_final: 0.7900 (m-80) REVERT: H 369 GLU cc_start: 0.8719 (tp30) cc_final: 0.8450 (tp30) REVERT: H 370 ARG cc_start: 0.6962 (tpt90) cc_final: 0.6740 (tpt90) REVERT: H 376 LYS cc_start: 0.9409 (tttt) cc_final: 0.9110 (pttp) REVERT: A 232 GLU cc_start: 0.6316 (mp0) cc_final: 0.6109 (mp0) REVERT: A 258 LYS cc_start: 0.6150 (mttt) cc_final: 0.5777 (tttt) REVERT: A 277 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7516 (mp0) REVERT: A 346 ARG cc_start: 0.7599 (mtt180) cc_final: 0.7224 (mtt-85) REVERT: B 312 TYR cc_start: 0.8292 (t80) cc_final: 0.7721 (t80) REVERT: B 336 MET cc_start: 0.8437 (mtm) cc_final: 0.8002 (mmm) REVERT: B 365 ASP cc_start: 0.7599 (p0) cc_final: 0.7304 (p0) REVERT: B 378 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8570 (mm) REVERT: C 192 SER cc_start: 0.9559 (t) cc_final: 0.9305 (p) REVERT: C 226 THR cc_start: 0.7989 (p) cc_final: 0.7749 (p) REVERT: C 308 GLN cc_start: 0.7644 (tt0) cc_final: 0.7418 (mm-40) REVERT: D 246 LYS cc_start: 0.8892 (mttt) cc_final: 0.8548 (mmmt) REVERT: D 256 PHE cc_start: 0.8215 (t80) cc_final: 0.7860 (p90) REVERT: D 259 ASP cc_start: 0.7103 (m-30) cc_final: 0.6278 (p0) REVERT: D 299 TYR cc_start: 0.8128 (t80) cc_final: 0.7755 (t80) REVERT: D 336 MET cc_start: 0.7815 (mtm) cc_final: 0.7524 (mtm) REVERT: D 365 ASP cc_start: 0.7742 (m-30) cc_final: 0.7403 (m-30) REVERT: D 376 LYS cc_start: 0.8692 (tttt) cc_final: 0.8171 (tmmt) outliers start: 39 outliers final: 23 residues processed: 289 average time/residue: 0.2619 time to fit residues: 106.6357 Evaluate side-chains 234 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 210 time to evaluate : 1.493 ------------------------------------------------------------------------------- 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 76 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 220 GLN E 347 HIS F 224 ASN F 347 HIS ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 ASN H 197 ASN H 201 ASN A 220 GLN ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 GLN D 186 ASN D 242 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 12736 Z= 0.466 Angle : 0.666 10.827 17314 Z= 0.352 Chirality : 0.049 0.189 2068 Planarity : 0.004 0.051 2146 Dihedral : 4.953 59.409 1666 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.51 % Allowed : 14.17 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.25 (0.22), residues: 1518 helix: 1.59 (0.17), residues: 844 sheet: -0.13 (0.45), residues: 148 loop : -0.02 (0.30), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 216 HIS 0.004 0.001 HIS G 286 PHE 0.021 0.002 PHE E 256 TYR 0.025 0.002 TYR B 283 ARG 0.004 0.001 ARG B 353 *********************** 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 285 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 221 time to evaluate : 1.468 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 317 GLN cc_start: 0.8398 (tp40) cc_final: 0.7695 (tm-30) REVERT: E 336 MET cc_start: 0.7164 (mtm) cc_final: 0.6814 (mtt) REVERT: F 312 TYR cc_start: 0.8670 (t80) cc_final: 0.8407 (t80) REVERT: F 375 ILE cc_start: 0.9083 (mt) cc_final: 0.8844 (mt) REVERT: G 195 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8790 (mp0) REVERT: G 197 ASN cc_start: 0.8522 (t0) cc_final: 0.8072 (t0) REVERT: G 206 PHE cc_start: 0.7448 (t80) cc_final: 0.7094 (t80) REVERT: G 212 LYS cc_start: 0.7616 (tttt) cc_final: 0.7320 (ttmm) REVERT: H 177 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7965 (tm-30) REVERT: H 198 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8398 (ptpt) REVERT: H 280 THR cc_start: 0.8348 (m) cc_final: 0.8032 (p) REVERT: H 304 GLN cc_start: 0.8173 (mt0) cc_final: 0.7691 (tm-30) REVERT: H 326 ILE cc_start: 0.6208 (mm) cc_final: 0.5964 (mm) REVERT: H 368 PHE cc_start: 0.8299 (m-80) cc_final: 0.7898 (m-80) REVERT: H 376 LYS cc_start: 0.9448 (tttt) cc_final: 0.9151 (pttp) REVERT: A 176 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8257 (p0) REVERT: A 177 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8397 (mm-40) REVERT: A 232 GLU cc_start: 0.6374 (mp0) cc_final: 0.6074 (mp0) REVERT: A 258 LYS cc_start: 0.6483 (mttt) cc_final: 0.5945 (tttt) REVERT: A 346 ARG cc_start: 0.7618 (mtt180) cc_final: 0.7225 (mtt-85) REVERT: B 317 GLN cc_start: 0.8421 (mp10) cc_final: 0.8197 (mp10) REVERT: B 378 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8536 (mm) REVERT: C 192 SER cc_start: 0.9564 (t) cc_final: 0.9312 (p) REVERT: C 204 GLU cc_start: 0.7804 (tt0) cc_final: 0.7591 (tt0) REVERT: C 226 THR cc_start: 0.8136 (p) cc_final: 0.7930 (p) REVERT: C 248 VAL cc_start: 0.8370 (OUTLIER) cc_final: 0.8126 (t) REVERT: C 308 GLN cc_start: 0.7754 (tt0) cc_final: 0.7545 (mm-40) REVERT: C 366 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8493 (mt-10) REVERT: D 188 LYS cc_start: 0.8507 (mmtm) cc_final: 0.8106 (mmmt) REVERT: D 204 GLU cc_start: 0.8151 (tt0) cc_final: 0.7366 (tm-30) REVERT: D 246 LYS cc_start: 0.8946 (mttt) cc_final: 0.8577 (mmmt) REVERT: D 256 PHE cc_start: 0.8346 (t80) cc_final: 0.8061 (p90) REVERT: D 259 ASP cc_start: 0.7316 (m-30) cc_final: 0.6415 (p0) REVERT: D 299 TYR cc_start: 0.8042 (t80) cc_final: 0.7823 (t80) REVERT: D 305 ARG cc_start: 0.7889 (tpp-160) cc_final: 0.7612 (tpt170) REVERT: D 336 MET cc_start: 0.7972 (mtm) cc_final: 0.7599 (mtm) REVERT: D 376 LYS cc_start: 0.8853 (tttt) cc_final: 0.8337 (tmmt) outliers start: 64 outliers final: 45 residues processed: 268 average time/residue: 0.2551 time to fit residues: 97.7699 Evaluate side-chains 245 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 196 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 194 TRP Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 337 PHE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 273 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 326 ILE Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain H residue 198 LYS 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 362 ILE Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 330 CYS 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 136 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 138 optimal weight: 4.9990 chunk 146 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 224 ASN G 197 ASN ** H 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 GLN A 220 GLN C 214 ASN D 186 ASN D 242 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12736 Z= 0.190 Angle : 0.526 9.382 17314 Z= 0.279 Chirality : 0.043 0.289 2068 Planarity : 0.003 0.054 2146 Dihedral : 4.661 58.188 1666 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.24 % Allowed : 15.73 % Favored : 81.03 % 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: 1.44 (0.22), residues: 1518 helix: 1.79 (0.18), residues: 844 sheet: -0.42 (0.39), residues: 184 loop : 0.18 (0.31), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 216 HIS 0.003 0.001 HIS A 347 PHE 0.021 0.001 PHE E 256 TYR 0.027 0.001 TYR C 283 ARG 0.003 0.000 ARG D 370 *********************** 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 270 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 224 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 306 GLU cc_start: 0.8532 (tp30) cc_final: 0.8239 (tp30) REVERT: E 317 GLN cc_start: 0.8362 (tp40) cc_final: 0.7650 (tm-30) REVERT: E 336 MET cc_start: 0.7053 (mtm) cc_final: 0.6699 (mtt) REVERT: F 312 TYR cc_start: 0.8560 (t80) cc_final: 0.8181 (t80) REVERT: F 316 ARG cc_start: 0.8198 (mtp85) cc_final: 0.7642 (mmp80) REVERT: G 197 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.8031 (t0) REVERT: G 206 PHE cc_start: 0.7341 (t80) cc_final: 0.6865 (t80) REVERT: G 212 LYS cc_start: 0.7489 (tttt) cc_final: 0.7181 (ttmm) REVERT: G 277 GLU cc_start: 0.8351 (pt0) cc_final: 0.8059 (pt0) REVERT: H 198 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8307 (ptpt) REVERT: H 280 THR cc_start: 0.8288 (m) cc_final: 0.7976 (p) REVERT: H 304 GLN cc_start: 0.8056 (mt0) cc_final: 0.7694 (tm-30) REVERT: H 306 GLU cc_start: 0.8415 (tp30) cc_final: 0.7917 (tp30) REVERT: H 326 ILE cc_start: 0.6143 (mm) cc_final: 0.5902 (mm) REVERT: H 368 PHE cc_start: 0.8208 (m-80) cc_final: 0.7861 (m-80) REVERT: H 376 LYS cc_start: 0.9440 (tttt) cc_final: 0.9148 (pttp) REVERT: A 177 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8401 (mm-40) REVERT: A 232 GLU cc_start: 0.6355 (mp0) cc_final: 0.6015 (mp0) REVERT: A 258 LYS cc_start: 0.6469 (mttt) cc_final: 0.5954 (tttt) REVERT: A 346 ARG cc_start: 0.7607 (mtt180) cc_final: 0.7255 (mtt-85) REVERT: B 317 GLN cc_start: 0.8478 (mp10) cc_final: 0.8243 (mp10) REVERT: B 336 MET cc_start: 0.8436 (mtm) cc_final: 0.8046 (mmm) REVERT: B 365 ASP cc_start: 0.7691 (p0) cc_final: 0.7445 (p0) REVERT: B 378 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8615 (mm) REVERT: C 192 SER cc_start: 0.9530 (t) cc_final: 0.9252 (p) REVERT: C 226 THR cc_start: 0.8062 (p) cc_final: 0.7843 (p) REVERT: D 188 LYS cc_start: 0.8482 (mmtm) cc_final: 0.8119 (mmmt) REVERT: D 246 LYS cc_start: 0.8879 (mttt) cc_final: 0.8532 (mmmt) REVERT: D 256 PHE cc_start: 0.8317 (t80) cc_final: 0.8086 (p90) REVERT: D 259 ASP cc_start: 0.7193 (m-30) cc_final: 0.6335 (p0) REVERT: D 299 TYR cc_start: 0.8031 (t80) cc_final: 0.7821 (t80) REVERT: D 305 ARG cc_start: 0.7867 (tpp-160) cc_final: 0.7625 (tpt170) REVERT: D 336 MET cc_start: 0.7643 (mtm) cc_final: 0.7385 (mtm) REVERT: D 376 LYS cc_start: 0.8810 (tttt) cc_final: 0.8292 (tmmt) outliers start: 46 outliers final: 28 residues processed: 255 average time/residue: 0.2477 time to fit residues: 91.7456 Evaluate side-chains 240 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 209 time to evaluate : 1.600 ------------------------------------------------------------------------------- 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 231 ASP Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 256 PHE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 375 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.0170 chunk 83 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 186 ASN H 197 ASN H 214 ASN A 220 GLN D 186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12736 Z= 0.179 Angle : 0.525 15.061 17314 Z= 0.272 Chirality : 0.043 0.250 2068 Planarity : 0.003 0.054 2146 Dihedral : 4.569 57.456 1666 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.03 % Allowed : 17.07 % Favored : 79.90 % 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: 1.57 (0.22), residues: 1518 helix: 1.88 (0.18), residues: 844 sheet: -0.34 (0.39), residues: 186 loop : 0.26 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP G 216 HIS 0.003 0.001 HIS A 347 PHE 0.021 0.001 PHE E 256 TYR 0.013 0.001 TYR G 312 ARG 0.002 0.000 ARG D 370 *********************** 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 265 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 222 time to evaluate : 1.530 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: 0.8381 (tp40) cc_final: 0.7657 (tm-30) REVERT: E 336 MET cc_start: 0.7036 (mtm) cc_final: 0.6620 (mtm) REVERT: F 312 TYR cc_start: 0.8566 (t80) cc_final: 0.8118 (t80) REVERT: F 316 ARG cc_start: 0.8231 (mtp85) cc_final: 0.7628 (mmp80) REVERT: F 322 ASP cc_start: 0.8968 (m-30) cc_final: 0.8364 (m-30) REVERT: G 197 ASN cc_start: 0.8298 (t0) cc_final: 0.7998 (t0) REVERT: G 212 LYS cc_start: 0.7461 (tttt) cc_final: 0.7116 (mtmm) REVERT: G 232 GLU cc_start: 0.8656 (pp20) cc_final: 0.8233 (pp20) REVERT: G 360 THR cc_start: 0.7849 (m) cc_final: 0.7614 (p) REVERT: G 372 LYS cc_start: 0.8852 (pttt) cc_final: 0.8630 (pttm) REVERT: H 198 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8318 (ptpt) REVERT: H 280 THR cc_start: 0.8327 (m) cc_final: 0.8007 (p) REVERT: H 304 GLN cc_start: 0.8056 (mt0) cc_final: 0.7673 (tm-30) REVERT: H 306 GLU cc_start: 0.8482 (tp30) cc_final: 0.7960 (tp30) REVERT: H 326 ILE cc_start: 0.6102 (mm) cc_final: 0.5867 (mm) REVERT: H 368 PHE cc_start: 0.8201 (m-80) cc_final: 0.7883 (m-80) REVERT: H 376 LYS cc_start: 0.9434 (tttt) cc_final: 0.9182 (pttp) REVERT: A 176 ASP cc_start: 0.8841 (p0) cc_final: 0.8337 (p0) REVERT: A 177 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8524 (mm-40) REVERT: A 232 GLU cc_start: 0.6349 (mp0) cc_final: 0.5983 (mp0) REVERT: A 258 LYS cc_start: 0.6430 (mttt) cc_final: 0.5931 (tttt) REVERT: A 277 GLU cc_start: 0.7620 (mp0) cc_final: 0.7385 (mp0) REVERT: A 346 ARG cc_start: 0.7618 (mtt180) cc_final: 0.7269 (mtt-85) REVERT: B 317 GLN cc_start: 0.8517 (mp10) cc_final: 0.8266 (mp10) REVERT: B 378 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8637 (mm) REVERT: C 188 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.9065 (mttt) REVERT: C 192 SER cc_start: 0.9531 (t) cc_final: 0.9249 (p) REVERT: C 226 THR cc_start: 0.8057 (p) cc_final: 0.7830 (p) REVERT: D 188 LYS cc_start: 0.8494 (mmtm) cc_final: 0.8118 (mmmt) REVERT: D 231 ASP cc_start: 0.8958 (p0) cc_final: 0.8724 (p0) REVERT: D 246 LYS cc_start: 0.8880 (mttt) cc_final: 0.8517 (mmmt) REVERT: D 256 PHE cc_start: 0.8304 (t80) cc_final: 0.8086 (p90) REVERT: D 259 ASP cc_start: 0.7158 (m-30) cc_final: 0.6320 (p0) REVERT: D 273 ILE cc_start: 0.8196 (pt) cc_final: 0.7974 (mm) REVERT: D 299 TYR cc_start: 0.8057 (t80) cc_final: 0.7817 (t80) REVERT: D 305 ARG cc_start: 0.7843 (tpp-160) cc_final: 0.7470 (tpt170) REVERT: D 336 MET cc_start: 0.7564 (mtm) cc_final: 0.7310 (mtm) REVERT: D 376 LYS cc_start: 0.8810 (tttt) cc_final: 0.8286 (tmmt) outliers start: 43 outliers final: 27 residues processed: 254 average time/residue: 0.2411 time to fit residues: 88.3305 Evaluate side-chains 236 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 206 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 194 TRP 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 G residue 326 ILE Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 256 PHE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain 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 330 CYS 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 49 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 230 ASN G 197 ASN ** G 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN D 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3295 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= 0.198 Angle : 0.529 12.206 17314 Z= 0.273 Chirality : 0.043 0.179 2068 Planarity : 0.003 0.054 2146 Dihedral : 4.564 57.154 1666 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.17 % Allowed : 17.07 % Favored : 79.76 % 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: 1.89 (0.18), residues: 840 sheet: -0.29 (0.39), residues: 186 loop : 0.29 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP G 216 HIS 0.003 0.001 HIS A 347 PHE 0.022 0.001 PHE E 256 TYR 0.013 0.001 TYR H 252 ARG 0.002 0.000 ARG F 353 *********************** 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 269 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 224 time to evaluate : 1.759 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 306 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8258 (tm-30) REVERT: E 317 GLN cc_start: 0.8398 (tp40) cc_final: 0.7677 (tm-30) REVERT: E 336 MET cc_start: 0.7006 (mtm) cc_final: 0.6581 (mtm) REVERT: F 312 TYR cc_start: 0.8564 (t80) cc_final: 0.8067 (t80) REVERT: F 316 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7695 (mmp80) REVERT: F 322 ASP cc_start: 0.8968 (m-30) cc_final: 0.8353 (m-30) REVERT: G 197 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.8140 (t0) REVERT: G 206 PHE cc_start: 0.7393 (t80) cc_final: 0.6862 (t80) REVERT: G 212 LYS cc_start: 0.7467 (tttt) cc_final: 0.7206 (mtmt) REVERT: G 360 THR cc_start: 0.7885 (m) cc_final: 0.7674 (p) REVERT: H 198 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8329 (ptpt) REVERT: H 280 THR cc_start: 0.8325 (m) cc_final: 0.8006 (p) REVERT: H 304 GLN cc_start: 0.8055 (mt0) cc_final: 0.7686 (tm-30) REVERT: H 306 GLU cc_start: 0.8504 (tp30) cc_final: 0.7981 (tp30) REVERT: H 326 ILE cc_start: 0.6149 (mm) cc_final: 0.5926 (mm) REVERT: H 368 PHE cc_start: 0.8198 (m-80) cc_final: 0.7880 (m-80) REVERT: H 376 LYS cc_start: 0.9451 (tttt) cc_final: 0.9194 (pttp) REVERT: A 176 ASP cc_start: 0.8839 (p0) cc_final: 0.8250 (p0) REVERT: A 177 GLN cc_start: 0.8926 (mm-40) cc_final: 0.8547 (mm-40) REVERT: A 232 GLU cc_start: 0.6373 (mp0) cc_final: 0.6020 (mp0) REVERT: A 258 LYS cc_start: 0.6408 (mttt) cc_final: 0.5926 (tttt) REVERT: A 277 GLU cc_start: 0.7697 (mp0) cc_final: 0.7380 (mp0) REVERT: A 346 ARG cc_start: 0.7629 (mtt180) cc_final: 0.7297 (mtt-85) REVERT: B 317 GLN cc_start: 0.8587 (mp10) cc_final: 0.8310 (mp10) REVERT: B 378 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8550 (mm) REVERT: C 188 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.9102 (mttt) REVERT: C 192 SER cc_start: 0.9533 (t) cc_final: 0.9275 (p) REVERT: C 226 THR cc_start: 0.8065 (p) cc_final: 0.7838 (p) REVERT: D 231 ASP cc_start: 0.8963 (p0) cc_final: 0.8727 (p0) REVERT: D 246 LYS cc_start: 0.8875 (mttt) cc_final: 0.8656 (mmmt) REVERT: D 256 PHE cc_start: 0.8316 (t80) cc_final: 0.8073 (p90) REVERT: D 259 ASP cc_start: 0.7175 (m-30) cc_final: 0.6334 (p0) REVERT: D 299 TYR cc_start: 0.8046 (t80) cc_final: 0.7800 (t80) REVERT: D 305 ARG cc_start: 0.7875 (tpp-160) cc_final: 0.7526 (tpt170) REVERT: D 336 MET cc_start: 0.7570 (mtm) cc_final: 0.7313 (mtm) REVERT: D 376 LYS cc_start: 0.8814 (tttt) cc_final: 0.8286 (tmmt) outliers start: 45 outliers final: 35 residues processed: 254 average time/residue: 0.2441 time to fit residues: 89.2851 Evaluate side-chains 247 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 208 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 194 TRP 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 E residue 362 ILE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 256 PHE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 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 330 CYS Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 337 PHE Chi-restraints excluded: chain D residue 338 ASP 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 141 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 220 GLN E 230 ASN ** G 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN C 208 GLN D 186 ASN D 314 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12736 Z= 0.226 Angle : 0.554 11.028 17314 Z= 0.285 Chirality : 0.044 0.297 2068 Planarity : 0.003 0.054 2146 Dihedral : 4.608 57.087 1666 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.46 % Allowed : 17.56 % Favored : 78.98 % 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: 1.57 (0.22), residues: 1518 helix: 1.87 (0.18), residues: 840 sheet: -0.26 (0.39), residues: 186 loop : 0.25 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP G 216 HIS 0.003 0.001 HIS H 286 PHE 0.023 0.001 PHE E 256 TYR 0.017 0.001 TYR B 283 ARG 0.002 0.000 ARG G 353 *********************** 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 270 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 221 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: symmetry clash REVERT: E 317 GLN cc_start: 0.8355 (tp40) cc_final: 0.7643 (tm-30) REVERT: E 336 MET cc_start: 0.6972 (mtm) cc_final: 0.6550 (mtm) REVERT: F 322 ASP cc_start: 0.8976 (m-30) cc_final: 0.8351 (m-30) REVERT: G 360 THR cc_start: 0.7897 (m) cc_final: 0.7672 (p) REVERT: H 198 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8285 (ptpt) REVERT: H 280 THR cc_start: 0.8327 (m) cc_final: 0.8005 (p) REVERT: H 304 GLN cc_start: 0.8022 (mt0) cc_final: 0.7675 (tm-30) REVERT: H 306 GLU cc_start: 0.8516 (tp30) cc_final: 0.8029 (tp30) REVERT: H 326 ILE cc_start: 0.6138 (mm) cc_final: 0.5921 (mm) REVERT: H 368 PHE cc_start: 0.8196 (m-80) cc_final: 0.7870 (m-80) REVERT: H 376 LYS cc_start: 0.9463 (tttt) cc_final: 0.9219 (pttp) REVERT: A 176 ASP cc_start: 0.8794 (p0) cc_final: 0.8158 (p0) REVERT: A 177 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8557 (mm-40) REVERT: A 232 GLU cc_start: 0.6374 (mp0) cc_final: 0.6005 (mp0) REVERT: A 258 LYS cc_start: 0.6535 (mttt) cc_final: 0.5992 (tttt) REVERT: A 277 GLU cc_start: 0.7661 (mp0) cc_final: 0.7371 (mp0) REVERT: A 346 ARG cc_start: 0.7673 (mtt180) cc_final: 0.7324 (mtt-85) REVERT: B 317 GLN cc_start: 0.8597 (mp10) cc_final: 0.8309 (mp10) REVERT: C 188 LYS cc_start: 0.9439 (OUTLIER) cc_final: 0.9091 (mttt) REVERT: C 192 SER cc_start: 0.9541 (t) cc_final: 0.9257 (p) REVERT: C 226 THR cc_start: 0.8048 (p) cc_final: 0.7806 (p) REVERT: D 246 LYS cc_start: 0.8866 (mttt) cc_final: 0.8624 (mmmt) REVERT: D 259 ASP cc_start: 0.7219 (m-30) cc_final: 0.6385 (p0) REVERT: D 299 TYR cc_start: 0.8075 (t80) cc_final: 0.7809 (t80) REVERT: D 305 ARG cc_start: 0.7857 (tpp-160) cc_final: 0.7537 (tpt170) REVERT: D 336 MET cc_start: 0.7593 (mtm) cc_final: 0.7369 (mtm) REVERT: D 376 LYS cc_start: 0.8823 (tttt) cc_final: 0.8287 (tmmt) outliers start: 49 outliers final: 35 residues processed: 257 average time/residue: 0.2401 time to fit residues: 89.0086 Evaluate side-chains 238 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 201 time to evaluate : 1.598 ------------------------------------------------------------------------------- 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 E residue 362 ILE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 326 ILE 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 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 284 SER Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 337 PHE Chi-restraints excluded: chain D residue 338 ASP 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 58 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 115 optimal weight: 0.3980 chunk 133 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 220 GLN E 230 ASN ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 GLN ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3543 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= 0.197 Angle : 0.563 11.085 17314 Z= 0.286 Chirality : 0.045 0.289 2068 Planarity : 0.003 0.054 2146 Dihedral : 4.579 56.724 1666 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.89 % Allowed : 18.97 % Favored : 78.14 % 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: 1.87 (0.18), residues: 840 sheet: -0.16 (0.39), residues: 186 loop : 0.26 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP G 216 HIS 0.003 0.001 HIS H 286 PHE 0.029 0.001 PHE E 256 TYR 0.019 0.001 TYR F 312 ARG 0.002 0.000 ARG D 370 *********************** 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 258 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 217 time to evaluate : 1.656 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: 0.8326 (tp40) cc_final: 0.7629 (tm-30) REVERT: E 336 MET cc_start: 0.6943 (mtm) cc_final: 0.6493 (mtm) REVERT: F 322 ASP cc_start: 0.8980 (m-30) cc_final: 0.8356 (m-30) REVERT: G 206 PHE cc_start: 0.7183 (t80) cc_final: 0.6789 (t80) REVERT: G 212 LYS cc_start: 0.7284 (tttt) cc_final: 0.7027 (mtmm) REVERT: H 198 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8292 (ptpp) REVERT: H 204 GLU cc_start: 0.7927 (tt0) cc_final: 0.7723 (tt0) REVERT: H 280 THR cc_start: 0.8357 (m) cc_final: 0.8036 (p) REVERT: H 304 GLN cc_start: 0.8054 (mt0) cc_final: 0.7683 (tm-30) REVERT: H 306 GLU cc_start: 0.8519 (tp30) cc_final: 0.8031 (tp30) REVERT: H 326 ILE cc_start: 0.6168 (mm) cc_final: 0.5962 (mm) REVERT: H 368 PHE cc_start: 0.8184 (m-80) cc_final: 0.7899 (m-80) REVERT: H 376 LYS cc_start: 0.9469 (tttt) cc_final: 0.9208 (pttp) REVERT: A 176 ASP cc_start: 0.8774 (p0) cc_final: 0.8130 (p0) REVERT: A 177 GLN cc_start: 0.8986 (mm-40) cc_final: 0.8665 (mm-40) REVERT: A 232 GLU cc_start: 0.6363 (mp0) cc_final: 0.6030 (mp0) REVERT: A 258 LYS cc_start: 0.6537 (mttt) cc_final: 0.5993 (tttt) REVERT: A 277 GLU cc_start: 0.7696 (mp0) cc_final: 0.7373 (mp0) REVERT: A 346 ARG cc_start: 0.7666 (mtt180) cc_final: 0.7318 (mtt-85) REVERT: B 317 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8329 (mp10) REVERT: C 188 LYS cc_start: 0.9434 (OUTLIER) cc_final: 0.9077 (mttt) REVERT: C 192 SER cc_start: 0.9541 (t) cc_final: 0.9276 (p) REVERT: C 226 THR cc_start: 0.8013 (p) cc_final: 0.7764 (p) REVERT: D 231 ASP cc_start: 0.8951 (p0) cc_final: 0.8722 (p0) REVERT: D 246 LYS cc_start: 0.8853 (mttt) cc_final: 0.8614 (mmmt) REVERT: D 259 ASP cc_start: 0.7171 (m-30) cc_final: 0.6395 (p0) REVERT: D 299 TYR cc_start: 0.8024 (t80) cc_final: 0.7745 (t80) REVERT: D 305 ARG cc_start: 0.7844 (tpp-160) cc_final: 0.7535 (tpt170) REVERT: D 350 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8445 (mm-30) REVERT: D 376 LYS cc_start: 0.8783 (tttt) cc_final: 0.8249 (tmmt) outliers start: 41 outliers final: 32 residues processed: 245 average time/residue: 0.2433 time to fit residues: 85.1586 Evaluate side-chains 240 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 205 time to evaluate : 1.486 ------------------------------------------------------------------------------- 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 E residue 362 ILE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 326 ILE 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 256 PHE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 317 GLN 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 248 VAL Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 331 VAL 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 128 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 140 optimal weight: 0.0060 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 144 optimal weight: 0.6980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 230 ASN ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 GLN ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12736 Z= 0.171 Angle : 0.568 15.274 17314 Z= 0.287 Chirality : 0.044 0.291 2068 Planarity : 0.003 0.054 2146 Dihedral : 4.526 56.124 1666 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.47 % Allowed : 19.39 % Favored : 78.14 % 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: 1.65 (0.22), residues: 1518 helix: 1.91 (0.18), residues: 840 sheet: -0.10 (0.40), residues: 186 loop : 0.30 (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 A 347 PHE 0.027 0.001 PHE E 256 TYR 0.013 0.001 TYR B 283 ARG 0.002 0.000 ARG D 370 *********************** 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 258 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 223 time to evaluate : 1.408 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: 0.8333 (tp40) cc_final: 0.7610 (tm-30) REVERT: E 336 MET cc_start: 0.6908 (mtm) cc_final: 0.6470 (mtm) REVERT: F 322 ASP cc_start: 0.8983 (m-30) cc_final: 0.8369 (m-30) REVERT: G 206 PHE cc_start: 0.7337 (t80) cc_final: 0.6935 (t80) REVERT: G 212 LYS cc_start: 0.7228 (tttt) cc_final: 0.6947 (mtmm) REVERT: H 189 LYS cc_start: 0.9139 (ptmm) cc_final: 0.8879 (pptt) REVERT: H 280 THR cc_start: 0.8335 (m) cc_final: 0.8015 (p) REVERT: H 304 GLN cc_start: 0.8044 (mt0) cc_final: 0.7695 (tm-30) REVERT: H 306 GLU cc_start: 0.8502 (tp30) cc_final: 0.8002 (tp30) REVERT: H 326 ILE cc_start: 0.6186 (mm) cc_final: 0.5985 (mm) REVERT: H 368 PHE cc_start: 0.8148 (m-80) cc_final: 0.7856 (m-80) REVERT: H 376 LYS cc_start: 0.9465 (tttt) cc_final: 0.9218 (pttp) REVERT: A 176 ASP cc_start: 0.8747 (p0) cc_final: 0.8108 (p0) REVERT: A 177 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8543 (mm-40) REVERT: A 232 GLU cc_start: 0.6358 (mp0) cc_final: 0.6011 (mp0) REVERT: A 258 LYS cc_start: 0.6608 (mttt) cc_final: 0.6060 (tttt) REVERT: A 277 GLU cc_start: 0.7624 (mp0) cc_final: 0.7344 (mp0) REVERT: A 279 ARG cc_start: 0.7375 (mmt-90) cc_final: 0.7143 (mtt-85) REVERT: A 346 ARG cc_start: 0.7665 (mtt180) cc_final: 0.7324 (mtt-85) REVERT: B 317 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8342 (mp10) REVERT: C 188 LYS cc_start: 0.9436 (OUTLIER) cc_final: 0.9074 (mttt) REVERT: C 192 SER cc_start: 0.9522 (t) cc_final: 0.9266 (p) REVERT: C 226 THR cc_start: 0.8010 (p) cc_final: 0.7759 (p) REVERT: C 366 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8785 (mt-10) REVERT: D 231 ASP cc_start: 0.8932 (p0) cc_final: 0.8700 (p0) REVERT: D 246 LYS cc_start: 0.8815 (mttt) cc_final: 0.8577 (mmmt) REVERT: D 259 ASP cc_start: 0.7143 (m-30) cc_final: 0.6462 (p0) REVERT: D 299 TYR cc_start: 0.8020 (t80) cc_final: 0.7744 (t80) REVERT: D 305 ARG cc_start: 0.7840 (tpp-160) cc_final: 0.7508 (tpt170) REVERT: D 306 GLU cc_start: 0.8715 (tp30) cc_final: 0.8491 (tp30) REVERT: D 350 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8435 (mm-30) REVERT: D 376 LYS cc_start: 0.8757 (tttt) cc_final: 0.8204 (tmmt) outliers start: 35 outliers final: 29 residues processed: 248 average time/residue: 0.2428 time to fit residues: 85.9182 Evaluate side-chains 234 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 203 time to evaluate : 1.378 ------------------------------------------------------------------------------- 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 E residue 362 ILE 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 261 VAL Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain H residue 256 PHE Chi-restraints excluded: chain 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 284 SER Chi-restraints excluded: chain B residue 317 GLN 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 330 CYS Chi-restraints excluded: chain D residue 331 VAL 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 88 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 139 optimal weight: 0.0470 chunk 120 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 128 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 230 ASN ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3698 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= 0.189 Angle : 0.568 14.127 17314 Z= 0.288 Chirality : 0.045 0.367 2068 Planarity : 0.003 0.053 2146 Dihedral : 4.529 56.108 1666 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.26 % Allowed : 19.75 % Favored : 78.00 % 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: 1.63 (0.22), residues: 1518 helix: 1.89 (0.18), residues: 840 sheet: -0.08 (0.39), residues: 186 loop : 0.27 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP G 216 HIS 0.003 0.001 HIS H 286 PHE 0.026 0.001 PHE E 256 TYR 0.029 0.001 TYR G 312 ARG 0.002 0.000 ARG D 370 ********************** 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 fitting. rotamer outliers: 32 poor density : 206 time to evaluate : 1.691 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: 0.8393 (tp40) cc_final: 0.7640 (tm-30) REVERT: E 336 MET cc_start: 0.6900 (mtm) cc_final: 0.6464 (mtm) REVERT: F 322 ASP cc_start: 0.8987 (m-30) cc_final: 0.8368 (m-30) REVERT: G 206 PHE cc_start: 0.7369 (t80) cc_final: 0.6968 (t80) REVERT: G 212 LYS cc_start: 0.7174 (tttt) cc_final: 0.6913 (mtmm) REVERT: H 189 LYS cc_start: 0.9105 (ptmm) cc_final: 0.8850 (pptt) REVERT: H 280 THR cc_start: 0.8321 (m) cc_final: 0.7998 (p) REVERT: H 304 GLN cc_start: 0.8040 (mt0) cc_final: 0.7682 (tm-30) REVERT: H 306 GLU cc_start: 0.8472 (tp30) cc_final: 0.7982 (tp30) REVERT: H 368 PHE cc_start: 0.8151 (m-80) cc_final: 0.7891 (m-80) REVERT: H 376 LYS cc_start: 0.9474 (tttt) cc_final: 0.9231 (pttp) REVERT: A 176 ASP cc_start: 0.8758 (p0) cc_final: 0.8231 (p0) REVERT: A 177 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8550 (mm-40) REVERT: A 232 GLU cc_start: 0.6350 (mp0) cc_final: 0.5993 (mp0) REVERT: A 258 LYS cc_start: 0.6558 (mttt) cc_final: 0.6010 (tttt) REVERT: A 277 GLU cc_start: 0.7620 (mp0) cc_final: 0.7336 (mp0) REVERT: A 346 ARG cc_start: 0.7668 (mtt180) cc_final: 0.7326 (mtt-85) REVERT: B 317 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8330 (mp10) REVERT: C 188 LYS cc_start: 0.9437 (OUTLIER) cc_final: 0.9088 (mttt) REVERT: C 192 SER cc_start: 0.9535 (t) cc_final: 0.9278 (p) REVERT: C 226 THR cc_start: 0.8024 (p) cc_final: 0.7775 (p) REVERT: C 366 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8777 (mt-10) REVERT: D 246 LYS cc_start: 0.8812 (mttt) cc_final: 0.8572 (mmmt) REVERT: D 259 ASP cc_start: 0.7168 (m-30) cc_final: 0.6523 (p0) REVERT: D 299 TYR cc_start: 0.8002 (t80) cc_final: 0.7721 (t80) REVERT: D 305 ARG cc_start: 0.7839 (tpp-160) cc_final: 0.7513 (tpt170) REVERT: D 306 GLU cc_start: 0.8716 (tp30) cc_final: 0.8506 (tp30) REVERT: D 350 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8436 (mm-30) REVERT: D 376 LYS cc_start: 0.8762 (tttt) cc_final: 0.8207 (tmmt) outliers start: 32 outliers final: 29 residues processed: 231 average time/residue: 0.2473 time to fit residues: 81.9111 Evaluate side-chains 231 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 200 time to evaluate : 1.601 ------------------------------------------------------------------------------- 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 E residue 362 ILE 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 261 VAL Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain H residue 256 PHE Chi-restraints excluded: chain 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 284 SER Chi-restraints excluded: chain B residue 317 GLN 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 248 VAL Chi-restraints excluded: chain D residue 330 CYS 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 36 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 120 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 230 ASN ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.106991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.090101 restraints weight = 28523.379| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 3.32 r_work: 0.3408 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3722 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= 0.199 Angle : 0.573 13.461 17314 Z= 0.292 Chirality : 0.045 0.374 2068 Planarity : 0.003 0.053 2146 Dihedral : 4.547 56.093 1666 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.47 % Allowed : 19.68 % Favored : 77.86 % 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: 1.62 (0.22), residues: 1518 helix: 1.88 (0.18), residues: 840 sheet: -0.10 (0.39), residues: 186 loop : 0.27 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP G 216 HIS 0.003 0.001 HIS H 286 PHE 0.026 0.001 PHE E 256 TYR 0.031 0.001 TYR F 312 ARG 0.002 0.000 ARG G 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2896.08 seconds wall clock time: 52 minutes 39.34 seconds (3159.34 seconds total)