Starting phenix.real_space_refine on Fri Aug 7 22:20:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10pp_75376/08_2026/10pp_75376.cif Found real_map, /net/cci-nas-00/data/ceres_data/10pp_75376/08_2026/10pp_75376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10pp_75376/08_2026/10pp_75376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10pp_75376/08_2026/10pp_75376.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10pp_75376/08_2026/10pp_75376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10pp_75376/08_2026/10pp_75376.map" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 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 176 5.16 5 C 14432 2.51 5 N 4356 2.21 5 O 4686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23650 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2150 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 2, 'TRANS': 281} Chain: "B" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2150 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 2, 'TRANS': 281} Chain: "C" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2150 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 2, 'TRANS': 281} Chain: "D" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2150 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 2, 'TRANS': 281} Chain: "E" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2150 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 2, 'TRANS': 281} Chain: "F" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2150 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 2, 'TRANS': 281} Chain: "G" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2150 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 2, 'TRANS': 281} Chain: "H" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2150 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 2, 'TRANS': 281} Chain: "I" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2150 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 2, 'TRANS': 281} Chain: "J" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2150 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 2, 'TRANS': 281} Chain: "K" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2150 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 2, 'TRANS': 281} Time building chain proxies: 5.71, per 1000 atoms: 0.24 Number of scatterers: 23650 At special positions: 0 Unit cell: (148.452, 146.316, 199.716, 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 176 16.00 O 4686 8.00 N 4356 7.00 C 14432 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: 2.04 Conformation dependent library (CDL) restraints added in 1.5 seconds 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5720 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 13 sheets defined 71.0% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.953A pdb=" N MET A 10 " --> pdb=" O ASN A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 98 Processing helix chain 'A' and resid 103 through 127 removed outlier: 3.526A pdb=" N ARG A 107 " --> pdb=" O SER A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 245 Processing helix chain 'A' and resid 249 through 276 removed outlier: 3.908A pdb=" N VAL A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASP A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 removed outlier: 4.039A pdb=" N LEU A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 284 " --> pdb=" O VAL A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 284' Processing helix chain 'B' and resid 6 through 33 Processing helix chain 'B' and resid 42 through 98 Processing helix chain 'B' and resid 103 through 127 Processing helix chain 'B' and resid 129 through 133 Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 191 through 246 Processing helix chain 'B' and resid 248 through 274 Processing helix chain 'B' and resid 278 through 284 removed outlier: 3.789A pdb=" N LEU B 283 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B 284 " --> pdb=" O VAL B 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 33 removed outlier: 4.027A pdb=" N PHE C 11 " --> pdb=" O MET C 7 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA C 12 " --> pdb=" O SER C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 98 Processing helix chain 'C' and resid 106 through 127 removed outlier: 4.373A pdb=" N ILE C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 245 removed outlier: 3.519A pdb=" N ASN C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 275 removed outlier: 4.063A pdb=" N ASP C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 283 removed outlier: 3.959A pdb=" N ARG C 282 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 283' Processing helix chain 'D' and resid 6 through 33 removed outlier: 3.735A pdb=" N MET D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 98 Processing helix chain 'D' and resid 103 through 127 Processing helix chain 'D' and resid 177 through 181 Processing helix chain 'D' and resid 191 through 245 removed outlier: 4.078A pdb=" N ASN D 196 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 276 Processing helix chain 'E' and resid 6 through 33 Processing helix chain 'E' and resid 42 through 98 removed outlier: 4.276A pdb=" N VAL E 48 " --> pdb=" O SER E 44 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS E 51 " --> pdb=" O ALA E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 127 Processing helix chain 'E' and resid 177 through 181 removed outlier: 3.503A pdb=" N GLY E 181 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 245 removed outlier: 4.072A pdb=" N MET E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY E 200 " --> pdb=" O ASN E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 276 removed outlier: 3.836A pdb=" N ALA E 268 " --> pdb=" O GLN E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 283 removed outlier: 4.007A pdb=" N ARG E 282 " --> pdb=" O GLN E 278 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU E 283 " --> pdb=" O ALA E 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 278 through 283' Processing helix chain 'F' and resid 6 through 33 Processing helix chain 'F' and resid 42 through 98 removed outlier: 3.610A pdb=" N MET F 52 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 127 Processing helix chain 'F' and resid 191 through 245 removed outlier: 3.552A pdb=" N ALA F 195 " --> pdb=" O SER F 191 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN F 196 " --> pdb=" O VAL F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 282 removed outlier: 3.735A pdb=" N GLU F 252 " --> pdb=" O ASP F 248 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN F 276 " --> pdb=" O GLN F 272 " (cutoff:3.500A) Proline residue: F 277 - end of helix Processing helix chain 'G' and resid 7 through 33 removed outlier: 4.282A pdb=" N PHE G 11 " --> pdb=" O MET G 7 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLN G 13 " --> pdb=" O ALA G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 98 removed outlier: 4.070A pdb=" N LYS G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 127 Processing helix chain 'G' and resid 191 through 245 removed outlier: 3.866A pdb=" N ASN G 196 " --> pdb=" O VAL G 192 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET G 197 " --> pdb=" O ASP G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 274 Processing helix chain 'G' and resid 275 through 282 removed outlier: 3.599A pdb=" N ALA G 279 " --> pdb=" O GLN G 276 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL G 280 " --> pdb=" O PRO G 277 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG G 282 " --> pdb=" O ALA G 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 33 removed outlier: 3.612A pdb=" N ALA H 33 " --> pdb=" O LYS H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 98 Processing helix chain 'H' and resid 103 through 127 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'H' and resid 177 through 181 Processing helix chain 'H' and resid 191 through 245 removed outlier: 3.912A pdb=" N ASN H 196 " --> pdb=" O VAL H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 284 Proline residue: H 277 - end of helix removed outlier: 3.911A pdb=" N VAL H 280 " --> pdb=" O GLN H 276 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG H 282 " --> pdb=" O GLN H 278 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU H 283 " --> pdb=" O ALA H 279 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU H 284 " --> pdb=" O VAL H 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 33 removed outlier: 3.852A pdb=" N MET I 10 " --> pdb=" O ASN I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 98 removed outlier: 3.806A pdb=" N GLU I 82 " --> pdb=" O GLY I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 128 Processing helix chain 'I' and resid 191 through 245 removed outlier: 3.654A pdb=" N ASN I 196 " --> pdb=" O VAL I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 276 removed outlier: 4.136A pdb=" N ASP I 255 " --> pdb=" O LYS I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 277 through 283 removed outlier: 3.711A pdb=" N VAL I 281 " --> pdb=" O GLN I 278 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU I 283 " --> pdb=" O VAL I 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 32 Processing helix chain 'J' and resid 42 through 98 removed outlier: 4.785A pdb=" N GLU J 82 " --> pdb=" O GLY J 78 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR J 83 " --> pdb=" O TYR J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 128 Processing helix chain 'J' and resid 191 through 245 Processing helix chain 'J' and resid 249 through 276 Processing helix chain 'J' and resid 277 through 283 removed outlier: 3.555A pdb=" N ARG J 282 " --> pdb=" O ALA J 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 33 removed outlier: 3.793A pdb=" N ARG K 14 " --> pdb=" O MET K 10 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN K 15 " --> pdb=" O PHE K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 99 removed outlier: 4.066A pdb=" N ASN K 99 " --> pdb=" O ILE K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 127 Processing helix chain 'K' and resid 177 through 181 Processing helix chain 'K' and resid 193 through 245 removed outlier: 4.375A pdb=" N MET K 197 " --> pdb=" O ASP K 193 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 276 removed outlier: 3.638A pdb=" N ASP K 255 " --> pdb=" O LYS K 251 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN K 272 " --> pdb=" O ALA K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 278 through 284 removed outlier: 3.783A pdb=" N ARG K 282 " --> pdb=" O GLN K 278 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU K 283 " --> pdb=" O ALA K 279 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 152 removed outlier: 3.596A pdb=" N MET A 149 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AA3, first strand: chain 'D' and resid 129 through 130 Processing sheet with id=AA4, first strand: chain 'D' and resid 149 through 152 removed outlier: 3.981A pdb=" N MET D 149 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE D 163 " --> pdb=" O MET D 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 149 through 152 removed outlier: 3.961A pdb=" N MET E 149 " --> pdb=" O ILE E 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 129 through 130 removed outlier: 3.571A pdb=" N MET G 133 " --> pdb=" O PHE G 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 149 through 152 removed outlier: 3.703A pdb=" N MET G 149 " --> pdb=" O ILE G 163 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE G 163 " --> pdb=" O MET G 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 149 through 152 removed outlier: 3.891A pdb=" N MET H 149 " --> pdb=" O ILE H 163 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE H 163 " --> pdb=" O MET H 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 129 through 130 removed outlier: 3.521A pdb=" N MET I 133 " --> pdb=" O PHE I 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 149 through 152 Processing sheet with id=AB2, first strand: chain 'J' and resid 129 through 130 removed outlier: 3.653A pdb=" N MET J 133 " --> pdb=" O PHE J 130 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 149 through 152 removed outlier: 3.526A pdb=" N MET J 149 " --> pdb=" O ILE J 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 128 through 130 removed outlier: 4.598A pdb=" N ALA K 128 " --> pdb=" O ILE K 135 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE K 135 " --> pdb=" O ALA K 128 " (cutoff:3.500A) 1908 hydrogen bonds defined for protein. 5646 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.58 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8548 1.34 - 1.46: 4261 1.46 - 1.58: 10665 1.58 - 1.70: 0 1.70 - 1.82: 352 Bond restraints: 23826 Sorted by residual: bond pdb=" C GLN G 276 " pdb=" N PRO G 277 " ideal model delta sigma weight residual 1.334 1.358 -0.024 8.40e-03 1.42e+04 8.19e+00 bond pdb=" C GLN E 276 " pdb=" N PRO E 277 " ideal model delta sigma weight residual 1.334 1.358 -0.024 8.40e-03 1.42e+04 8.15e+00 bond pdb=" C GLN B 276 " pdb=" N PRO B 277 " ideal model delta sigma weight residual 1.336 1.357 -0.021 9.80e-03 1.04e+04 4.48e+00 bond pdb=" CB GLN E 159 " pdb=" CG GLN E 159 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.27e+00 bond pdb=" C VAL E 153 " pdb=" N GLY E 154 " ideal model delta sigma weight residual 1.334 1.317 0.017 1.19e-02 7.06e+03 2.14e+00 ... (remaining 23821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 31393 2.01 - 4.02: 575 4.02 - 6.03: 30 6.03 - 8.04: 20 8.04 - 10.05: 3 Bond angle restraints: 32021 Sorted by residual: angle pdb=" N GLN F 276 " pdb=" CA GLN F 276 " pdb=" C GLN F 276 " ideal model delta sigma weight residual 109.81 119.86 -10.05 2.21e+00 2.05e-01 2.07e+01 angle pdb=" N ASN C 37 " pdb=" CA ASN C 37 " pdb=" C ASN C 37 " ideal model delta sigma weight residual 114.62 109.77 4.85 1.14e+00 7.69e-01 1.81e+01 angle pdb=" C ASP I 248 " pdb=" N MET I 249 " pdb=" CA MET I 249 " ideal model delta sigma weight residual 121.54 128.52 -6.98 1.91e+00 2.74e-01 1.34e+01 angle pdb=" N VAL F 281 " pdb=" CA VAL F 281 " pdb=" C VAL F 281 " ideal model delta sigma weight residual 112.80 108.80 4.00 1.15e+00 7.56e-01 1.21e+01 angle pdb=" C ASN K 6 " pdb=" N MET K 7 " pdb=" CA MET K 7 " ideal model delta sigma weight residual 121.54 128.15 -6.61 1.91e+00 2.74e-01 1.20e+01 ... (remaining 32016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 13221 17.94 - 35.88: 1064 35.88 - 53.82: 346 53.82 - 71.75: 81 71.75 - 89.69: 28 Dihedral angle restraints: 14740 sinusoidal: 5841 harmonic: 8899 Sorted by residual: dihedral pdb=" CA LEU K 136 " pdb=" C LEU K 136 " pdb=" N THR K 137 " pdb=" CA THR K 137 " ideal model delta harmonic sigma weight residual 180.00 156.55 23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ASN J 6 " pdb=" C ASN J 6 " pdb=" N MET J 7 " pdb=" CA MET J 7 " ideal model delta harmonic sigma weight residual -180.00 -158.25 -21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA ASN I 6 " pdb=" C ASN I 6 " pdb=" N MET I 7 " pdb=" CA MET I 7 " ideal model delta harmonic sigma weight residual 180.00 -159.23 -20.77 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 14737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2634 0.044 - 0.087: 762 0.087 - 0.131: 187 0.131 - 0.174: 33 0.174 - 0.218: 3 Chirality restraints: 3619 Sorted by residual: chirality pdb=" CA GLN F 276 " pdb=" N GLN F 276 " pdb=" C GLN F 276 " pdb=" CB GLN F 276 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE F 176 " pdb=" CA ILE F 176 " pdb=" CG1 ILE F 176 " pdb=" CG2 ILE F 176 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CB ILE A 187 " pdb=" CA ILE A 187 " pdb=" CG1 ILE A 187 " pdb=" CG2 ILE A 187 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.10e-01 ... (remaining 3616 not shown) Planarity restraints: 4334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET I 249 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C MET I 249 " -0.033 2.00e-02 2.50e+03 pdb=" O MET I 249 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA I 250 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 255 " 0.010 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C ASP H 255 " -0.033 2.00e-02 2.50e+03 pdb=" O ASP H 255 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR H 256 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN K 6 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C ASN K 6 " -0.032 2.00e-02 2.50e+03 pdb=" O ASN K 6 " 0.012 2.00e-02 2.50e+03 pdb=" N MET K 7 " 0.011 2.00e-02 2.50e+03 ... (remaining 4331 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5444 2.78 - 3.31: 24390 3.31 - 3.84: 39898 3.84 - 4.37: 42765 4.37 - 4.90: 72454 Nonbonded interactions: 184951 Sorted by model distance: nonbonded pdb=" N ASP A 106 " pdb=" OD1 ASP A 106 " model vdw 2.255 3.120 nonbonded pdb=" O ARG E 139 " pdb=" OG1 THR E 146 " model vdw 2.255 3.040 nonbonded pdb=" O THR A 137 " pdb=" OG1 THR A 137 " model vdw 2.271 3.040 nonbonded pdb=" O LEU H 80 " pdb=" OG1 THR H 84 " model vdw 2.313 3.040 nonbonded pdb=" OG SER G 144 " pdb=" N VAL G 145 " model vdw 2.320 3.120 ... (remaining 184946 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.200 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: 0.030 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 23.210 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 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 : 0.004 0.045 23826 Z= 0.225 Angle : 0.667 10.053 32021 Z= 0.398 Chirality : 0.044 0.218 3619 Planarity : 0.004 0.041 4334 Dihedral : 15.538 89.693 9020 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.16 % Favored : 97.81 % Rotamer: Outliers : 7.33 % Allowed : 11.92 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.14), residues: 3102 helix: 1.23 (0.10), residues: 2135 sheet: 0.07 (0.52), residues: 100 loop : -1.58 (0.19), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 245 TYR 0.013 0.001 TYR I 79 PHE 0.019 0.002 PHE G 72 HIS 0.008 0.001 HIS J 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.22 (23826) covalent geometry : angle 0.66659 / 0.40 (32021) hydrogen bonds : bond 0.10698 / 7.26 ( 1908) hydrogen bonds : angle 4.52183 / 3.28 ( 5646) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 769 time to evaluate : 0.923 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: 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: 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: A 1 MET cc_start: 0.5000 (pmm) cc_final: 0.1937 (mmp) REVERT: A 10 MET cc_start: 0.8402 (mtp) cc_final: 0.8134 (mtt) REVERT: A 57 ARG cc_start: 0.1071 (ttt180) cc_final: 0.0643 (ttt180) REVERT: A 127 HIS cc_start: 0.7142 (OUTLIER) cc_final: 0.6437 (m90) REVERT: A 131 ASN cc_start: 0.7024 (t0) cc_final: 0.6703 (t0) REVERT: A 189 MET cc_start: 0.9243 (OUTLIER) cc_final: 0.8696 (mmm) REVERT: A 197 MET cc_start: 0.8895 (mtm) cc_final: 0.8572 (mmp) REVERT: A 209 ILE cc_start: 0.9702 (OUTLIER) cc_final: 0.9483 (tt) REVERT: A 225 MET cc_start: 0.9324 (mmm) cc_final: 0.9052 (mmp) REVERT: A 242 SER cc_start: 0.8162 (m) cc_final: 0.7679 (t) REVERT: B 19 ASN cc_start: 0.9365 (m-40) cc_final: 0.9012 (m110) REVERT: B 21 LEU cc_start: 0.9667 (tp) cc_final: 0.9118 (tt) REVERT: B 26 ASN cc_start: 0.9170 (OUTLIER) cc_final: 0.8884 (t0) REVERT: B 29 LYS cc_start: 0.9531 (mttm) cc_final: 0.9111 (mtmm) REVERT: B 36 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7928 (pt) REVERT: B 65 ASN cc_start: 0.8420 (m-40) cc_final: 0.8186 (t0) REVERT: B 106 ASP cc_start: 0.8389 (m-30) cc_final: 0.8020 (t70) REVERT: B 163 ILE cc_start: 0.9319 (pt) cc_final: 0.9101 (mt) REVERT: B 207 LYS cc_start: 0.9412 (pptt) cc_final: 0.8923 (pttt) REVERT: B 219 TYR cc_start: 0.9026 (m-10) cc_final: 0.8712 (m-80) REVERT: B 223 PHE cc_start: 0.9115 (m-10) cc_final: 0.8891 (m-10) REVERT: C 29 LYS cc_start: 0.9162 (tppt) cc_final: 0.8809 (mmmm) REVERT: C 50 GLU cc_start: 0.9387 (OUTLIER) cc_final: 0.8854 (mm-30) REVERT: C 108 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8428 (pmm) REVERT: C 130 PHE cc_start: 0.8498 (t80) cc_final: 0.8091 (t80) REVERT: C 187 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8689 (mm) REVERT: C 189 MET cc_start: 0.8967 (mpp) cc_final: 0.8687 (mpp) REVERT: C 197 MET cc_start: 0.8965 (mtp) cc_final: 0.8751 (mtp) REVERT: C 219 TYR cc_start: 0.9405 (m-10) cc_final: 0.8717 (m-80) REVERT: C 237 MET cc_start: 0.9183 (mmm) cc_final: 0.8672 (mmm) REVERT: C 249 MET cc_start: 0.7395 (mpp) cc_final: 0.7116 (mmm) REVERT: C 272 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8387 (mm-40) REVERT: D 1 MET cc_start: 0.3327 (tpt) cc_final: 0.2331 (tpt) REVERT: D 10 MET cc_start: 0.9554 (mtm) cc_final: 0.9189 (mtt) REVERT: D 19 ASN cc_start: 0.9440 (m-40) cc_final: 0.8905 (t0) REVERT: D 106 ASP cc_start: 0.9112 (m-30) cc_final: 0.8907 (t70) REVERT: D 157 MET cc_start: 0.3498 (mmt) cc_final: 0.3019 (mmt) REVERT: D 224 GLU cc_start: 0.9585 (tt0) cc_final: 0.9309 (pt0) REVERT: D 237 MET cc_start: 0.9542 (mmm) cc_final: 0.8933 (mmm) REVERT: D 255 ASP cc_start: 0.9055 (t0) cc_final: 0.8741 (t0) REVERT: D 260 GLN cc_start: 0.9596 (mt0) cc_final: 0.9259 (mt0) REVERT: E 11 PHE cc_start: 0.8674 (t80) cc_final: 0.8468 (t80) REVERT: E 15 GLN cc_start: 0.9157 (mm-40) cc_final: 0.8790 (mm110) REVERT: E 19 ASN cc_start: 0.9051 (m-40) cc_final: 0.8785 (m-40) REVERT: E 66 ILE cc_start: 0.9661 (mt) cc_final: 0.9336 (tp) REVERT: E 206 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9133 (pp) REVERT: E 207 LYS cc_start: 0.9434 (mmtt) cc_final: 0.9131 (mmmm) REVERT: E 225 MET cc_start: 0.9222 (mmt) cc_final: 0.8987 (mmm) REVERT: E 230 ILE cc_start: 0.9526 (tp) cc_final: 0.9102 (pt) REVERT: E 256 TYR cc_start: 0.8787 (t80) cc_final: 0.8246 (t80) REVERT: F 28 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: F 29 LYS cc_start: 0.8981 (mttp) cc_final: 0.8502 (mmmt) REVERT: F 49 SER cc_start: 0.9323 (m) cc_final: 0.9005 (p) REVERT: F 50 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8750 (mm-30) REVERT: F 64 GLN cc_start: 0.9472 (mm-40) cc_final: 0.9140 (tm-30) REVERT: F 173 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8732 (mm) REVERT: F 251 LYS cc_start: 0.9346 (mmtt) cc_final: 0.8788 (mmmm) REVERT: F 252 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8376 (tp30) REVERT: F 269 MET cc_start: 0.4830 (mtt) cc_final: 0.4603 (ttt) REVERT: F 282 ARG cc_start: 0.9150 (tmt170) cc_final: 0.8813 (ptm-80) REVERT: G 1 MET cc_start: 0.4702 (OUTLIER) cc_final: 0.4461 (ptt) REVERT: G 11 PHE cc_start: 0.7405 (p90) cc_final: 0.6963 (p90) REVERT: G 52 MET cc_start: 0.9257 (mtp) cc_final: 0.8970 (mmm) REVERT: G 102 TYR cc_start: 0.8949 (m-80) cc_final: 0.8472 (m-80) REVERT: G 272 GLN cc_start: 0.8983 (mt0) cc_final: 0.8560 (mt0) REVERT: H 228 ASP cc_start: 0.9145 (t0) cc_final: 0.8937 (t0) REVERT: H 249 MET cc_start: 0.6037 (mmt) cc_final: 0.5778 (mmp) REVERT: H 259 ASN cc_start: 0.8423 (m110) cc_final: 0.8213 (t0) REVERT: I 11 PHE cc_start: 0.9269 (t80) cc_final: 0.9002 (t80) REVERT: I 14 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8775 (ttt180) REVERT: I 29 LYS cc_start: 0.9450 (mttt) cc_final: 0.8964 (mttm) REVERT: I 113 GLU cc_start: 0.8858 (tt0) cc_final: 0.8632 (tm-30) REVERT: I 117 LEU cc_start: 0.9541 (mt) cc_final: 0.9335 (tp) REVERT: I 133 MET cc_start: 0.5309 (mmt) cc_final: 0.5080 (mmt) REVERT: I 249 MET cc_start: 0.9285 (mtp) cc_final: 0.8651 (mmt) REVERT: I 269 MET cc_start: 0.8966 (mmp) cc_final: 0.8700 (tpp) REVERT: J 11 PHE cc_start: 0.8994 (t80) cc_final: 0.8365 (t80) REVERT: J 25 LYS cc_start: 0.9572 (tptm) cc_final: 0.8816 (tppt) REVERT: J 29 LYS cc_start: 0.9009 (pttp) cc_final: 0.8792 (pttp) REVERT: J 30 LEU cc_start: 0.9562 (tp) cc_final: 0.9256 (tp) REVERT: J 52 MET cc_start: 0.9076 (mmt) cc_final: 0.8829 (mmm) REVERT: J 55 GLN cc_start: 0.9549 (tt0) cc_final: 0.9281 (pt0) REVERT: J 85 ASP cc_start: 0.8483 (t0) cc_final: 0.8087 (t70) REVERT: J 106 ASP cc_start: 0.8624 (m-30) cc_final: 0.8195 (m-30) REVERT: J 110 ILE cc_start: 0.9421 (mm) cc_final: 0.9128 (mm) REVERT: J 113 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7973 (mt-10) REVERT: J 237 MET cc_start: 0.9490 (mmm) cc_final: 0.9210 (mmm) REVERT: J 249 MET cc_start: 0.7749 (mmt) cc_final: 0.7516 (mpp) REVERT: J 269 MET cc_start: 0.8920 (mmm) cc_final: 0.8590 (mmm) REVERT: J 272 GLN cc_start: 0.8830 (mt0) cc_final: 0.8535 (pt0) REVERT: K 5 HIS cc_start: 0.7436 (p90) cc_final: 0.6821 (p-80) REVERT: K 10 MET cc_start: 0.9067 (mtt) cc_final: 0.8756 (mtm) REVERT: K 91 ARG cc_start: 0.8964 (mtp85) cc_final: 0.8492 (ttt180) REVERT: K 102 TYR cc_start: 0.8623 (m-80) cc_final: 0.8414 (m-80) REVERT: K 173 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8970 (mt) REVERT: K 207 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9084 (tptt) REVERT: K 242 SER cc_start: 0.8993 (m) cc_final: 0.8672 (t) REVERT: K 243 ARG cc_start: 0.9056 (mmt180) cc_final: 0.8368 (ttt180) outliers start: 179 outliers final: 36 residues processed: 895 average time/residue: 0.1614 time to fit residues: 223.5744 Evaluate side-chains 553 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 501 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 127 HIS Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain H residue 157 MET Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 264 GLN Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain J residue 255 ASP Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 74 GLN Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 207 LYS Chi-restraints excluded: chain K residue 215 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN B 274 ASN D 26 ASN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN E 208 GLN E 259 ASN E 260 GLN ** F 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 ASN G 68 ASN ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 HIS H 55 GLN H 109 GLN ** H 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 26 ASN ** I 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 HIS J 34 GLN J 159 GLN ** K 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.058983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.052514 restraints weight = 161836.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.053689 restraints weight = 99569.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.054528 restraints weight = 68644.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.055141 restraints weight = 50857.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.055606 restraints weight = 39907.666| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23826 Z= 0.182 Angle : 0.628 11.676 32021 Z= 0.349 Chirality : 0.039 0.256 3619 Planarity : 0.003 0.042 4334 Dihedral : 7.090 60.803 3472 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.00 % Favored : 97.97 % Rotamer: Outliers : 4.95 % Allowed : 18.63 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.15), residues: 3102 helix: 2.20 (0.11), residues: 2178 sheet: 0.34 (0.53), residues: 110 loop : -1.28 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 222 TYR 0.027 0.002 TYR E 219 PHE 0.017 0.002 PHE C 130 HIS 0.009 0.002 HIS J 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (23826) covalent geometry : angle 0.62796 / 0.35 (32021) hydrogen bonds : bond 0.05034 / 3.44 ( 1908) hydrogen bonds : angle 3.98575 / 2.91 ( 5646) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 504 time to evaluate : 0.804 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5261 (pmm) cc_final: 0.1772 (mmp) REVERT: A 127 HIS cc_start: 0.7258 (OUTLIER) cc_final: 0.6500 (m90) REVERT: A 131 ASN cc_start: 0.7358 (t0) cc_final: 0.7019 (t0) REVERT: A 197 MET cc_start: 0.9071 (mtm) cc_final: 0.8667 (mmp) REVERT: A 260 GLN cc_start: 0.9155 (mt0) cc_final: 0.8897 (mt0) REVERT: B 10 MET cc_start: 0.9331 (mtt) cc_final: 0.9037 (mtt) REVERT: B 21 LEU cc_start: 0.9666 (tp) cc_final: 0.9315 (tt) REVERT: B 26 ASN cc_start: 0.9171 (OUTLIER) cc_final: 0.8627 (t0) REVERT: B 29 LYS cc_start: 0.9524 (mttm) cc_final: 0.9068 (mtmm) REVERT: B 65 ASN cc_start: 0.8672 (m-40) cc_final: 0.8358 (t0) REVERT: B 106 ASP cc_start: 0.8668 (m-30) cc_final: 0.8243 (t70) REVERT: B 163 ILE cc_start: 0.9511 (pt) cc_final: 0.9073 (mt) REVERT: B 270 LEU cc_start: 0.9661 (tt) cc_final: 0.9428 (pp) REVERT: C 10 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8464 (mpp) REVERT: C 29 LYS cc_start: 0.9311 (tppt) cc_final: 0.8758 (mmmm) REVERT: C 32 SER cc_start: 0.9344 (t) cc_final: 0.9040 (p) REVERT: C 50 GLU cc_start: 0.9306 (OUTLIER) cc_final: 0.8841 (mm-30) REVERT: C 161 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7559 (tp30) REVERT: C 187 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8621 (mt) REVERT: C 223 PHE cc_start: 0.8908 (m-10) cc_final: 0.8553 (m-10) REVERT: C 225 MET cc_start: 0.9190 (mmm) cc_final: 0.8340 (mmm) REVERT: C 249 MET cc_start: 0.7088 (mpp) cc_final: 0.6484 (mmm) REVERT: C 270 LEU cc_start: 0.9493 (tt) cc_final: 0.9225 (pp) REVERT: D 1 MET cc_start: 0.4177 (tpt) cc_final: 0.3975 (tpt) REVERT: D 19 ASN cc_start: 0.9140 (m-40) cc_final: 0.8865 (t0) REVERT: D 51 LYS cc_start: 0.6225 (OUTLIER) cc_final: 0.5622 (pttt) REVERT: D 102 TYR cc_start: 0.8492 (m-10) cc_final: 0.8047 (m-10) REVERT: D 157 MET cc_start: 0.4653 (mmt) cc_final: 0.4075 (mmt) REVERT: D 237 MET cc_start: 0.9397 (mmm) cc_final: 0.9176 (mmm) REVERT: D 255 ASP cc_start: 0.8805 (t0) cc_final: 0.8546 (t0) REVERT: E 11 PHE cc_start: 0.9022 (t80) cc_final: 0.8491 (t80) REVERT: E 15 GLN cc_start: 0.9320 (mm-40) cc_final: 0.9039 (mm110) REVERT: E 102 TYR cc_start: 0.8619 (m-10) cc_final: 0.8366 (m-10) REVERT: E 206 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9344 (pp) REVERT: E 207 LYS cc_start: 0.9590 (mmtt) cc_final: 0.9211 (mmmm) REVERT: E 225 MET cc_start: 0.9253 (mmt) cc_final: 0.9020 (mmm) REVERT: E 230 ILE cc_start: 0.9630 (OUTLIER) cc_final: 0.9215 (pt) REVERT: F 49 SER cc_start: 0.9481 (m) cc_final: 0.8896 (p) REVERT: F 50 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8830 (mm-30) REVERT: F 113 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7390 (mt-10) REVERT: F 168 MET cc_start: 0.9344 (mmm) cc_final: 0.8957 (mmm) REVERT: F 197 MET cc_start: 0.8942 (ptp) cc_final: 0.8664 (ptp) REVERT: F 282 ARG cc_start: 0.9106 (tmt170) cc_final: 0.8870 (ptm-80) REVERT: G 10 MET cc_start: 0.8381 (mtt) cc_final: 0.8146 (mtt) REVERT: G 27 ILE cc_start: 0.8573 (pt) cc_final: 0.8333 (mt) REVERT: G 52 MET cc_start: 0.9287 (mtp) cc_final: 0.8958 (mmm) REVERT: G 108 MET cc_start: 0.8871 (mtt) cc_final: 0.8599 (mtm) REVERT: G 149 MET cc_start: 0.7602 (tpt) cc_final: 0.7371 (tpt) REVERT: G 189 MET cc_start: 0.8748 (mmm) cc_final: 0.8440 (mmm) REVERT: G 225 MET cc_start: 0.9348 (mmm) cc_final: 0.8597 (mmm) REVERT: G 253 ILE cc_start: 0.9229 (tt) cc_final: 0.9019 (tp) REVERT: G 269 MET cc_start: 0.8957 (mmm) cc_final: 0.8605 (mmm) REVERT: H 197 MET cc_start: 0.9273 (mtp) cc_final: 0.8991 (mtp) REVERT: H 228 ASP cc_start: 0.9578 (t0) cc_final: 0.9338 (t0) REVERT: H 259 ASN cc_start: 0.8842 (OUTLIER) cc_final: 0.8282 (t0) REVERT: I 11 PHE cc_start: 0.9367 (t80) cc_final: 0.8842 (t80) REVERT: I 14 ARG cc_start: 0.9235 (OUTLIER) cc_final: 0.8846 (ttt180) REVERT: I 113 GLU cc_start: 0.9005 (tt0) cc_final: 0.8615 (tm-30) REVERT: I 269 MET cc_start: 0.9265 (mmp) cc_final: 0.8936 (mmm) REVERT: J 11 PHE cc_start: 0.9074 (t80) cc_final: 0.8609 (t80) REVERT: J 25 LYS cc_start: 0.9431 (tptm) cc_final: 0.8835 (tppt) REVERT: J 29 LYS cc_start: 0.9186 (pttp) cc_final: 0.8874 (pttp) REVERT: J 52 MET cc_start: 0.9190 (mmt) cc_final: 0.8938 (mmm) REVERT: J 55 GLN cc_start: 0.9620 (tt0) cc_final: 0.9208 (pt0) REVERT: J 85 ASP cc_start: 0.8953 (t0) cc_final: 0.8752 (t0) REVERT: J 93 LEU cc_start: 0.9406 (tp) cc_final: 0.9206 (tp) REVERT: J 113 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8155 (mt-10) REVERT: J 165 ILE cc_start: 0.9602 (OUTLIER) cc_final: 0.9308 (tt) REVERT: J 168 MET cc_start: 0.8709 (mmm) cc_final: 0.8508 (mmm) REVERT: J 237 MET cc_start: 0.9515 (mmm) cc_final: 0.9170 (mmm) REVERT: J 249 MET cc_start: 0.8173 (mmt) cc_final: 0.7757 (mpp) REVERT: K 7 MET cc_start: 0.7118 (mmm) cc_final: 0.6801 (mmm) REVERT: K 25 LYS cc_start: 0.9468 (ptpp) cc_final: 0.9255 (mtmm) REVERT: K 52 MET cc_start: 0.9134 (mmp) cc_final: 0.8790 (mtp) REVERT: K 237 MET cc_start: 0.9427 (mmm) cc_final: 0.9177 (mmm) REVERT: K 242 SER cc_start: 0.9003 (m) cc_final: 0.8736 (t) REVERT: K 243 ARG cc_start: 0.9259 (mmt180) cc_final: 0.8480 (ttt180) REVERT: K 255 ASP cc_start: 0.8589 (t0) cc_final: 0.8326 (t0) outliers start: 121 outliers final: 59 residues processed: 586 average time/residue: 0.1511 time to fit residues: 137.5686 Evaluate side-chains 506 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 435 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 127 HIS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 259 ASN Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 157 MET Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 259 ASN Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 264 GLN Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain J residue 5 HIS Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain J residue 157 MET Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 255 ASP Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 215 ASP Chi-restraints excluded: chain K residue 280 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 78 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 255 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 256 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 270 optimal weight: 0.2980 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN C 64 GLN D 26 ASN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN ** E 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 HIS ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 GLN ** F 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 152 HIS ** H 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 GLN ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN ** J 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 4 ASN K 212 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.058630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.052297 restraints weight = 164140.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.053481 restraints weight = 100477.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.054341 restraints weight = 68858.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.054966 restraints weight = 50604.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.055434 restraints weight = 39345.244| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23826 Z= 0.153 Angle : 0.600 10.538 32021 Z= 0.326 Chirality : 0.039 0.205 3619 Planarity : 0.003 0.031 4334 Dihedral : 5.955 59.901 3414 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.16 % Favored : 97.81 % Rotamer: Outliers : 4.91 % Allowed : 18.80 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.15), residues: 3102 helix: 2.51 (0.11), residues: 2178 sheet: 0.47 (0.55), residues: 110 loop : -1.07 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 160 TYR 0.019 0.001 TYR E 219 PHE 0.027 0.002 PHE C 11 HIS 0.010 0.001 HIS J 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (23826) covalent geometry : angle 0.60043 / 0.33 (32021) hydrogen bonds : bond 0.04719 / 3.23 ( 1908) hydrogen bonds : angle 3.85064 / 2.81 ( 5646) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 460 time to evaluate : 0.897 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: 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: A 1 MET cc_start: 0.5423 (pmm) cc_final: 0.1753 (mmt) REVERT: A 131 ASN cc_start: 0.7219 (t0) cc_final: 0.6875 (t0) REVERT: A 189 MET cc_start: 0.9033 (mmm) cc_final: 0.8633 (mmm) REVERT: A 197 MET cc_start: 0.9089 (mtm) cc_final: 0.8718 (mmp) REVERT: B 10 MET cc_start: 0.9302 (mtt) cc_final: 0.8963 (mtt) REVERT: B 21 LEU cc_start: 0.9641 (tp) cc_final: 0.9408 (tp) REVERT: B 25 LYS cc_start: 0.9431 (pttp) cc_final: 0.9141 (pttm) REVERT: B 26 ASN cc_start: 0.9028 (OUTLIER) cc_final: 0.6607 (t0) REVERT: B 29 LYS cc_start: 0.9473 (mttm) cc_final: 0.8991 (mtmm) REVERT: B 102 TYR cc_start: 0.8468 (m-10) cc_final: 0.8204 (m-10) REVERT: B 106 ASP cc_start: 0.8678 (m-30) cc_final: 0.8229 (t0) REVERT: B 163 ILE cc_start: 0.9579 (pt) cc_final: 0.9232 (mt) REVERT: B 255 ASP cc_start: 0.8654 (m-30) cc_final: 0.8201 (t70) REVERT: C 10 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8358 (mpp) REVERT: C 15 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8647 (mp10) REVERT: C 32 SER cc_start: 0.9333 (t) cc_final: 0.9018 (p) REVERT: C 50 GLU cc_start: 0.9325 (OUTLIER) cc_final: 0.8872 (mm-30) REVERT: C 85 ASP cc_start: 0.8913 (m-30) cc_final: 0.8528 (p0) REVERT: C 197 MET cc_start: 0.9318 (OUTLIER) cc_final: 0.9039 (mpp) REVERT: C 223 PHE cc_start: 0.8914 (m-10) cc_final: 0.8536 (m-10) REVERT: C 225 MET cc_start: 0.9127 (mmm) cc_final: 0.8821 (mmm) REVERT: C 237 MET cc_start: 0.9170 (mmm) cc_final: 0.8895 (mmm) REVERT: C 249 MET cc_start: 0.7132 (mpp) cc_final: 0.6609 (mmm) REVERT: C 270 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9204 (pp) REVERT: C 272 GLN cc_start: 0.8934 (mm-40) cc_final: 0.8523 (mm-40) REVERT: D 1 MET cc_start: 0.4243 (tpt) cc_final: 0.2881 (tpt) REVERT: D 10 MET cc_start: 0.9080 (mtt) cc_final: 0.8842 (mpp) REVERT: D 51 LYS cc_start: 0.6151 (OUTLIER) cc_final: 0.5579 (pttt) REVERT: D 157 MET cc_start: 0.5056 (mmt) cc_final: 0.4347 (mmt) REVERT: E 11 PHE cc_start: 0.8951 (t80) cc_final: 0.8506 (t80) REVERT: E 15 GLN cc_start: 0.9303 (mm-40) cc_final: 0.9036 (mm110) REVERT: E 102 TYR cc_start: 0.8574 (m-10) cc_final: 0.8320 (m-10) REVERT: E 108 MET cc_start: 0.9001 (mmm) cc_final: 0.8664 (mmm) REVERT: E 206 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9360 (pp) REVERT: E 207 LYS cc_start: 0.9574 (mmtt) cc_final: 0.9182 (mmmm) REVERT: E 223 PHE cc_start: 0.9055 (m-80) cc_final: 0.8346 (m-80) REVERT: E 230 ILE cc_start: 0.9681 (OUTLIER) cc_final: 0.9328 (tp) REVERT: E 269 MET cc_start: 0.9127 (mmp) cc_final: 0.8455 (tpp) REVERT: F 7 MET cc_start: 0.8548 (mmm) cc_final: 0.8114 (mmm) REVERT: F 10 MET cc_start: 0.9136 (mpp) cc_final: 0.8874 (mpp) REVERT: F 49 SER cc_start: 0.9247 (m) cc_final: 0.8889 (p) REVERT: F 50 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8788 (mm-30) REVERT: F 113 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7392 (mt-10) REVERT: F 165 ILE cc_start: 0.9669 (OUTLIER) cc_final: 0.9353 (mm) REVERT: F 168 MET cc_start: 0.9376 (mmm) cc_final: 0.9079 (mmm) REVERT: F 197 MET cc_start: 0.8975 (ptp) cc_final: 0.8718 (ptp) REVERT: F 282 ARG cc_start: 0.9098 (tmt170) cc_final: 0.8861 (ptm-80) REVERT: G 1 MET cc_start: 0.2812 (ptt) cc_final: 0.2598 (ptt) REVERT: G 11 PHE cc_start: 0.7712 (p90) cc_final: 0.7286 (p90) REVERT: G 52 MET cc_start: 0.9222 (mtp) cc_final: 0.8987 (mmm) REVERT: G 108 MET cc_start: 0.8923 (mtt) cc_final: 0.8628 (mtm) REVERT: G 189 MET cc_start: 0.8814 (mmm) cc_final: 0.8534 (mmm) REVERT: G 225 MET cc_start: 0.9411 (mmm) cc_final: 0.8678 (mmm) REVERT: G 253 ILE cc_start: 0.9235 (tt) cc_final: 0.9023 (tp) REVERT: H 197 MET cc_start: 0.9216 (mtp) cc_final: 0.8843 (mpp) REVERT: H 223 PHE cc_start: 0.9234 (m-80) cc_final: 0.8751 (m-80) REVERT: H 228 ASP cc_start: 0.9585 (t0) cc_final: 0.9332 (t0) REVERT: H 259 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.8402 (t0) REVERT: I 11 PHE cc_start: 0.9221 (t80) cc_final: 0.8913 (t80) REVERT: I 14 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8769 (ttt180) REVERT: I 29 LYS cc_start: 0.9384 (mttt) cc_final: 0.9123 (mttm) REVERT: I 108 MET cc_start: 0.9197 (mmm) cc_final: 0.8922 (mmp) REVERT: I 113 GLU cc_start: 0.8968 (tt0) cc_final: 0.8564 (tm-30) REVERT: I 225 MET cc_start: 0.8900 (ttm) cc_final: 0.8538 (mmm) REVERT: I 269 MET cc_start: 0.9329 (mmp) cc_final: 0.8902 (mmm) REVERT: J 11 PHE cc_start: 0.9067 (t80) cc_final: 0.8659 (t80) REVERT: J 25 LYS cc_start: 0.9536 (tptm) cc_final: 0.9119 (mmmt) REVERT: J 52 MET cc_start: 0.9151 (mmt) cc_final: 0.8889 (mmm) REVERT: J 55 GLN cc_start: 0.9618 (tt0) cc_final: 0.9153 (pt0) REVERT: J 85 ASP cc_start: 0.8997 (t0) cc_final: 0.8413 (t0) REVERT: J 152 HIS cc_start: 0.2263 (OUTLIER) cc_final: 0.1188 (m90) REVERT: J 168 MET cc_start: 0.8816 (mmm) cc_final: 0.8520 (mmm) REVERT: J 237 MET cc_start: 0.9522 (mmm) cc_final: 0.9152 (mmm) REVERT: J 249 MET cc_start: 0.8165 (mmt) cc_final: 0.7718 (mpp) REVERT: J 269 MET cc_start: 0.9054 (mmm) cc_final: 0.8387 (mmm) REVERT: J 272 GLN cc_start: 0.8774 (mt0) cc_final: 0.8264 (pt0) REVERT: K 52 MET cc_start: 0.8893 (mmp) cc_final: 0.8572 (mtm) REVERT: K 93 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9349 (mm) REVERT: K 242 SER cc_start: 0.9017 (m) cc_final: 0.8760 (t) REVERT: K 243 ARG cc_start: 0.9279 (mmt180) cc_final: 0.8462 (ttt180) REVERT: K 255 ASP cc_start: 0.8515 (t0) cc_final: 0.8139 (t0) outliers start: 120 outliers final: 64 residues processed: 547 average time/residue: 0.1549 time to fit residues: 132.2538 Evaluate side-chains 491 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 413 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 89 ARG Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 157 MET Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain H residue 259 ASN Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 260 GLN Chi-restraints excluded: chain I residue 264 GLN Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain J residue 157 MET Chi-restraints excluded: chain J residue 255 ASP Chi-restraints excluded: chain J residue 259 ASN Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 215 ASP Chi-restraints excluded: chain K residue 258 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 303 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 233 optimal weight: 0.0470 chunk 129 optimal weight: 10.0000 chunk 221 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 220 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 296 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 306 optimal weight: 4.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN B 264 GLN ** C 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN E 26 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 ASN E 260 GLN ** F 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 GLN ** G 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 26 ASN ** I 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 259 ASN J 5 HIS J 131 ASN J 236 ASN J 259 ASN ** J 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.058715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.052427 restraints weight = 164485.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.053588 restraints weight = 101791.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.054443 restraints weight = 70388.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.055058 restraints weight = 52077.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.055511 restraints weight = 40588.879| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23826 Z= 0.142 Angle : 0.598 11.267 32021 Z= 0.323 Chirality : 0.038 0.212 3619 Planarity : 0.003 0.030 4334 Dihedral : 5.689 58.768 3406 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.29 % Favored : 97.68 % Rotamer: Outliers : 4.55 % Allowed : 19.37 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.15), residues: 3102 helix: 2.63 (0.11), residues: 2178 sheet: 0.60 (0.54), residues: 110 loop : -0.99 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 35 TYR 0.016 0.001 TYR E 219 PHE 0.017 0.001 PHE D 72 HIS 0.006 0.001 HIS A 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (23826) covalent geometry : angle 0.59804 / 0.32 (32021) hydrogen bonds : bond 0.04552 / 3.11 ( 1908) hydrogen bonds : angle 3.79242 / 2.78 ( 5646) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 441 time to evaluate : 0.832 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: 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: A 1 MET cc_start: 0.5534 (pmm) cc_final: 0.1881 (mmt) REVERT: A 187 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8634 (mm) REVERT: A 189 MET cc_start: 0.9077 (mmm) cc_final: 0.8768 (mmm) REVERT: A 197 MET cc_start: 0.9058 (mtm) cc_final: 0.8725 (mmp) REVERT: A 249 MET cc_start: 0.8133 (mpp) cc_final: 0.7857 (mmt) REVERT: A 270 LEU cc_start: 0.9742 (tp) cc_final: 0.9379 (pp) REVERT: A 272 GLN cc_start: 0.9498 (mm-40) cc_final: 0.9013 (mm-40) REVERT: B 10 MET cc_start: 0.9288 (mtt) cc_final: 0.8804 (mtm) REVERT: B 21 LEU cc_start: 0.9657 (tp) cc_final: 0.9441 (tp) REVERT: B 25 LYS cc_start: 0.9438 (pttp) cc_final: 0.9188 (pttm) REVERT: B 26 ASN cc_start: 0.9018 (OUTLIER) cc_final: 0.8493 (t0) REVERT: B 29 LYS cc_start: 0.9442 (mttm) cc_final: 0.8967 (mttm) REVERT: B 102 TYR cc_start: 0.8499 (m-10) cc_final: 0.8188 (m-10) REVERT: B 106 ASP cc_start: 0.8596 (m-30) cc_final: 0.8156 (t0) REVERT: B 219 TYR cc_start: 0.9297 (m-10) cc_final: 0.8615 (m-10) REVERT: B 223 PHE cc_start: 0.9200 (m-80) cc_final: 0.8328 (m-80) REVERT: C 15 GLN cc_start: 0.9217 (OUTLIER) cc_final: 0.8832 (mm110) REVERT: C 32 SER cc_start: 0.9308 (t) cc_final: 0.9002 (p) REVERT: C 108 MET cc_start: 0.9104 (pmm) cc_final: 0.8619 (pmm) REVERT: C 197 MET cc_start: 0.9343 (OUTLIER) cc_final: 0.9029 (mpp) REVERT: C 223 PHE cc_start: 0.8904 (m-10) cc_final: 0.8448 (m-10) REVERT: C 249 MET cc_start: 0.7146 (mpp) cc_final: 0.6647 (mmm) REVERT: C 270 LEU cc_start: 0.9516 (tt) cc_final: 0.9266 (pp) REVERT: C 272 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8446 (mm-40) REVERT: D 1 MET cc_start: 0.4387 (tpt) cc_final: 0.3101 (tpt) REVERT: D 10 MET cc_start: 0.9034 (mtt) cc_final: 0.8826 (mpp) REVERT: D 29 LYS cc_start: 0.9579 (mttm) cc_final: 0.9319 (mtmm) REVERT: D 51 LYS cc_start: 0.6157 (OUTLIER) cc_final: 0.5612 (pttt) REVERT: D 157 MET cc_start: 0.4956 (mmt) cc_final: 0.4194 (mmt) REVERT: E 10 MET cc_start: 0.9168 (mpp) cc_final: 0.8918 (mpp) REVERT: E 11 PHE cc_start: 0.8915 (t80) cc_final: 0.8600 (t80) REVERT: E 102 TYR cc_start: 0.8570 (m-10) cc_final: 0.8352 (m-10) REVERT: E 108 MET cc_start: 0.8985 (mmm) cc_final: 0.8770 (mmm) REVERT: E 206 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9372 (pp) REVERT: E 207 LYS cc_start: 0.9530 (mmtt) cc_final: 0.9191 (mmmm) REVERT: E 230 ILE cc_start: 0.9695 (tp) cc_final: 0.9369 (tp) REVERT: E 269 MET cc_start: 0.8953 (mmp) cc_final: 0.8307 (mmp) REVERT: F 10 MET cc_start: 0.9042 (mpp) cc_final: 0.8809 (mpp) REVERT: F 49 SER cc_start: 0.9249 (m) cc_final: 0.8869 (p) REVERT: F 50 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8810 (mm-30) REVERT: F 113 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7393 (mt-10) REVERT: F 197 MET cc_start: 0.8976 (ptp) cc_final: 0.8701 (ptp) REVERT: F 282 ARG cc_start: 0.9126 (tmt170) cc_final: 0.8868 (ptm-80) REVERT: G 1 MET cc_start: 0.2929 (ptt) cc_final: 0.2560 (ptt) REVERT: G 11 PHE cc_start: 0.7798 (p90) cc_final: 0.7403 (p90) REVERT: G 20 GLU cc_start: 0.9209 (pp20) cc_final: 0.8878 (pp20) REVERT: G 52 MET cc_start: 0.9153 (mtp) cc_final: 0.8948 (mmm) REVERT: G 82 GLU cc_start: 0.6763 (tt0) cc_final: 0.6452 (tp30) REVERT: G 189 MET cc_start: 0.8850 (mmm) cc_final: 0.8544 (mmm) REVERT: G 225 MET cc_start: 0.9429 (mmm) cc_final: 0.8600 (mmm) REVERT: H 25 LYS cc_start: 0.9697 (mmmt) cc_final: 0.9207 (mtmm) REVERT: H 197 MET cc_start: 0.9234 (mtp) cc_final: 0.8953 (mpp) REVERT: H 228 ASP cc_start: 0.9602 (t0) cc_final: 0.9323 (t0) REVERT: H 255 ASP cc_start: 0.9114 (p0) cc_final: 0.8791 (p0) REVERT: H 259 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.8567 (m110) REVERT: I 11 PHE cc_start: 0.9224 (t80) cc_final: 0.8912 (t80) REVERT: I 14 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8779 (ttt180) REVERT: I 108 MET cc_start: 0.9303 (mmm) cc_final: 0.8959 (mmp) REVERT: I 113 GLU cc_start: 0.8953 (tt0) cc_final: 0.8573 (tm-30) REVERT: I 225 MET cc_start: 0.8948 (ttm) cc_final: 0.8614 (mmm) REVERT: I 269 MET cc_start: 0.9239 (mmp) cc_final: 0.8832 (mmp) REVERT: I 272 GLN cc_start: 0.8855 (mp10) cc_final: 0.8403 (mp10) REVERT: J 11 PHE cc_start: 0.9059 (t80) cc_final: 0.8687 (t80) REVERT: J 29 LYS cc_start: 0.9221 (pttp) cc_final: 0.8853 (pttp) REVERT: J 52 MET cc_start: 0.9170 (mmt) cc_final: 0.8692 (mtp) REVERT: J 55 GLN cc_start: 0.9625 (tt0) cc_final: 0.9137 (pt0) REVERT: J 85 ASP cc_start: 0.8997 (t0) cc_final: 0.8509 (t0) REVERT: J 152 HIS cc_start: 0.2365 (OUTLIER) cc_final: 0.1412 (m90) REVERT: J 225 MET cc_start: 0.8995 (mmp) cc_final: 0.8332 (mmm) REVERT: J 237 MET cc_start: 0.9478 (mmm) cc_final: 0.8974 (mmm) REVERT: J 249 MET cc_start: 0.8275 (mmt) cc_final: 0.7820 (mpp) REVERT: K 7 MET cc_start: 0.7647 (mmm) cc_final: 0.7351 (mmm) REVERT: K 52 MET cc_start: 0.8743 (mmp) cc_final: 0.8527 (mtm) REVERT: K 93 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9383 (mm) REVERT: K 189 MET cc_start: 0.8612 (mmm) cc_final: 0.8290 (mmm) REVERT: K 242 SER cc_start: 0.9025 (m) cc_final: 0.8763 (t) REVERT: K 243 ARG cc_start: 0.9297 (mmt180) cc_final: 0.8502 (ttt180) REVERT: K 255 ASP cc_start: 0.8580 (t0) cc_final: 0.8170 (t0) outliers start: 111 outliers final: 65 residues processed: 519 average time/residue: 0.1546 time to fit residues: 125.2795 Evaluate side-chains 490 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 415 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 89 ARG Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 259 ASN Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 157 MET Chi-restraints excluded: chain H residue 259 ASN Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 264 GLN Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain J residue 5 HIS Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain J residue 157 MET Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 255 ASP Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 74 GLN Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 215 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 303 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 276 optimal weight: 20.0000 chunk 284 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 306 optimal weight: 0.4980 chunk 60 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 264 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 chunk 152 optimal weight: 1.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN ** C 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 236 ASN ** J 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.058686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.052429 restraints weight = 164473.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.053612 restraints weight = 100958.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.054463 restraints weight = 69317.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.055084 restraints weight = 51037.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.055554 restraints weight = 39690.645| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23826 Z= 0.136 Angle : 0.614 12.269 32021 Z= 0.323 Chirality : 0.039 0.261 3619 Planarity : 0.002 0.022 4334 Dihedral : 5.446 59.071 3401 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.16 % Favored : 97.81 % Rotamer: Outliers : 4.14 % Allowed : 20.15 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.15), residues: 3102 helix: 2.67 (0.11), residues: 2178 sheet: 0.69 (0.53), residues: 110 loop : -0.96 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 222 TYR 0.016 0.001 TYR E 219 PHE 0.040 0.001 PHE C 11 HIS 0.009 0.001 HIS J 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (23826) covalent geometry : angle 0.61386 / 0.32 (32021) hydrogen bonds : bond 0.04482 / 3.07 ( 1908) hydrogen bonds : angle 3.77387 / 2.76 ( 5646) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 429 time to evaluate : 0.827 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: 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: A 1 MET cc_start: 0.5165 (pmm) cc_final: 0.1706 (mmp) REVERT: A 187 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8653 (mm) REVERT: A 189 MET cc_start: 0.9152 (mmm) cc_final: 0.8832 (mmm) REVERT: A 197 MET cc_start: 0.9030 (mtm) cc_final: 0.8710 (mmp) REVERT: A 224 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8636 (pt0) REVERT: A 270 LEU cc_start: 0.9738 (tp) cc_final: 0.9376 (pp) REVERT: A 272 GLN cc_start: 0.9516 (mm-40) cc_final: 0.9141 (mm-40) REVERT: B 21 LEU cc_start: 0.9654 (tp) cc_final: 0.9294 (tt) REVERT: B 25 LYS cc_start: 0.9397 (pttp) cc_final: 0.9111 (pttp) REVERT: B 26 ASN cc_start: 0.9019 (OUTLIER) cc_final: 0.6862 (t0) REVERT: B 29 LYS cc_start: 0.9464 (mttm) cc_final: 0.8963 (mtmm) REVERT: B 102 TYR cc_start: 0.8510 (m-10) cc_final: 0.8137 (m-10) REVERT: B 106 ASP cc_start: 0.8620 (m-30) cc_final: 0.8184 (t0) REVERT: B 219 TYR cc_start: 0.9309 (m-10) cc_final: 0.8577 (m-10) REVERT: B 223 PHE cc_start: 0.9201 (m-80) cc_final: 0.8350 (m-80) REVERT: B 237 MET cc_start: 0.8805 (mmt) cc_final: 0.8548 (mmt) REVERT: B 255 ASP cc_start: 0.8595 (m-30) cc_final: 0.8130 (t70) REVERT: B 270 LEU cc_start: 0.9656 (tt) cc_final: 0.9375 (pp) REVERT: B 276 GLN cc_start: 0.7985 (tp-100) cc_final: 0.7720 (tp-100) REVERT: C 15 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8799 (mm110) REVERT: C 26 ASN cc_start: 0.8977 (OUTLIER) cc_final: 0.8775 (t0) REVERT: C 32 SER cc_start: 0.9317 (t) cc_final: 0.9005 (p) REVERT: C 89 ARG cc_start: 0.9489 (OUTLIER) cc_final: 0.9258 (tpm170) REVERT: C 149 MET cc_start: 0.8302 (pmm) cc_final: 0.8039 (pmm) REVERT: C 161 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7487 (tp30) REVERT: C 197 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.9039 (mpp) REVERT: C 207 LYS cc_start: 0.9422 (ptmt) cc_final: 0.9108 (pttp) REVERT: C 223 PHE cc_start: 0.8866 (m-10) cc_final: 0.8413 (m-10) REVERT: C 225 MET cc_start: 0.9049 (mmm) cc_final: 0.8760 (mmm) REVERT: C 235 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8678 (pp20) REVERT: C 249 MET cc_start: 0.7070 (mpp) cc_final: 0.6619 (mmm) REVERT: C 270 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9237 (pp) REVERT: C 272 GLN cc_start: 0.9018 (mm-40) cc_final: 0.8456 (mm-40) REVERT: D 1 MET cc_start: 0.4260 (tpt) cc_final: 0.2998 (tpt) REVERT: D 7 MET cc_start: 0.8263 (mmm) cc_final: 0.7904 (mmp) REVERT: D 51 LYS cc_start: 0.6224 (OUTLIER) cc_final: 0.5708 (pttt) REVERT: D 157 MET cc_start: 0.4980 (mmt) cc_final: 0.4160 (mmt) REVERT: E 10 MET cc_start: 0.9073 (mpp) cc_final: 0.8872 (mpp) REVERT: E 108 MET cc_start: 0.9125 (mmm) cc_final: 0.8910 (mmm) REVERT: E 206 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9370 (pp) REVERT: E 207 LYS cc_start: 0.9519 (mmtt) cc_final: 0.9178 (mmmm) REVERT: E 230 ILE cc_start: 0.9729 (tp) cc_final: 0.9413 (tp) REVERT: E 269 MET cc_start: 0.8965 (mmp) cc_final: 0.8605 (mmp) REVERT: F 10 MET cc_start: 0.8994 (mpp) cc_final: 0.8729 (mpp) REVERT: F 49 SER cc_start: 0.9240 (m) cc_final: 0.8951 (p) REVERT: F 50 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8831 (mm-30) REVERT: F 113 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7413 (mt-10) REVERT: F 168 MET cc_start: 0.9232 (mmm) cc_final: 0.8788 (mmp) REVERT: F 197 MET cc_start: 0.8983 (ptp) cc_final: 0.8710 (ptp) REVERT: G 1 MET cc_start: 0.2696 (ptt) cc_final: 0.2394 (ptt) REVERT: G 11 PHE cc_start: 0.7818 (p90) cc_final: 0.7381 (p90) REVERT: G 82 GLU cc_start: 0.6964 (tt0) cc_final: 0.6682 (tp30) REVERT: G 189 MET cc_start: 0.8879 (mmm) cc_final: 0.8578 (mmm) REVERT: G 225 MET cc_start: 0.9448 (mmm) cc_final: 0.8603 (mmm) REVERT: H 15 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8970 (mm-40) REVERT: H 25 LYS cc_start: 0.9718 (mmmt) cc_final: 0.9149 (mtmm) REVERT: H 197 MET cc_start: 0.9249 (mtp) cc_final: 0.8941 (mpp) REVERT: H 228 ASP cc_start: 0.9602 (t0) cc_final: 0.9325 (t0) REVERT: H 259 ASN cc_start: 0.8968 (OUTLIER) cc_final: 0.8595 (m110) REVERT: I 11 PHE cc_start: 0.9237 (t80) cc_final: 0.8942 (t80) REVERT: I 14 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8754 (ttt180) REVERT: I 108 MET cc_start: 0.9318 (mmm) cc_final: 0.8881 (mmp) REVERT: I 113 GLU cc_start: 0.8990 (tt0) cc_final: 0.8611 (tm-30) REVERT: I 225 MET cc_start: 0.8967 (ttm) cc_final: 0.8637 (mmm) REVERT: I 249 MET cc_start: 0.9205 (mtp) cc_final: 0.8449 (mmt) REVERT: J 11 PHE cc_start: 0.9053 (t80) cc_final: 0.8797 (t80) REVERT: J 25 LYS cc_start: 0.9530 (tppt) cc_final: 0.9200 (tppt) REVERT: J 29 LYS cc_start: 0.9222 (pttp) cc_final: 0.8849 (pttp) REVERT: J 52 MET cc_start: 0.9141 (mmt) cc_final: 0.8691 (mtp) REVERT: J 55 GLN cc_start: 0.9611 (tt0) cc_final: 0.9141 (pt0) REVERT: J 85 ASP cc_start: 0.8981 (t0) cc_final: 0.8499 (t0) REVERT: J 152 HIS cc_start: 0.1934 (OUTLIER) cc_final: 0.1099 (m90) REVERT: J 236 ASN cc_start: 0.9167 (OUTLIER) cc_final: 0.8640 (t0) REVERT: J 237 MET cc_start: 0.9438 (mmm) cc_final: 0.8953 (mmm) REVERT: J 249 MET cc_start: 0.8269 (mmt) cc_final: 0.7719 (mpp) REVERT: J 269 MET cc_start: 0.9055 (mmm) cc_final: 0.8812 (mmm) REVERT: K 1 MET cc_start: 0.5277 (OUTLIER) cc_final: 0.4375 (pp-130) REVERT: K 7 MET cc_start: 0.7668 (mmm) cc_final: 0.7262 (mmm) REVERT: K 52 MET cc_start: 0.8633 (mmp) cc_final: 0.8414 (mtm) REVERT: K 74 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8479 (mt0) REVERT: K 93 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9416 (mm) REVERT: K 243 ARG cc_start: 0.9302 (mmt180) cc_final: 0.8548 (ttt180) REVERT: K 255 ASP cc_start: 0.8539 (t0) cc_final: 0.8082 (t0) outliers start: 101 outliers final: 62 residues processed: 503 average time/residue: 0.1626 time to fit residues: 127.6862 Evaluate side-chains 489 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 409 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 89 ARG Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 149 MET Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 157 MET Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain H residue 259 ASN Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 264 GLN Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain J residue 5 HIS Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain J residue 157 MET Chi-restraints excluded: chain J residue 236 ASN Chi-restraints excluded: chain J residue 255 ASP Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 74 GLN Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 215 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 28 optimal weight: 20.0000 chunk 178 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 281 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 HIS ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 HIS ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 HIS ** J 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.058033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.051928 restraints weight = 168387.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.053087 restraints weight = 103252.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.053927 restraints weight = 70683.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.054531 restraints weight = 51913.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.054989 restraints weight = 40289.617| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23826 Z= 0.173 Angle : 0.643 11.781 32021 Z= 0.345 Chirality : 0.039 0.199 3619 Planarity : 0.003 0.064 4334 Dihedral : 5.430 59.733 3399 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.45 % Favored : 97.52 % Rotamer: Outliers : 4.26 % Allowed : 20.52 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.15), residues: 3102 helix: 2.58 (0.11), residues: 2178 sheet: 0.63 (0.52), residues: 110 loop : -0.93 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 53 TYR 0.014 0.001 TYR E 102 PHE 0.028 0.002 PHE D 72 HIS 0.005 0.001 HIS A 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (23826) covalent geometry : angle 0.64321 / 0.35 (32021) hydrogen bonds : bond 0.04591 / 3.15 ( 1908) hydrogen bonds : angle 3.93531 / 2.89 ( 5646) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 416 time to evaluate : 1.007 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5171 (pmm) cc_final: 0.1236 (mmp) REVERT: A 10 MET cc_start: 0.8965 (mmm) cc_final: 0.8594 (mpp) REVERT: A 187 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8452 (mm) REVERT: A 189 MET cc_start: 0.9056 (mmm) cc_final: 0.8683 (mmm) REVERT: A 197 MET cc_start: 0.9016 (mtm) cc_final: 0.8715 (mmp) REVERT: A 224 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8544 (mt-10) REVERT: B 10 MET cc_start: 0.9186 (mtt) cc_final: 0.8804 (mtt) REVERT: B 21 LEU cc_start: 0.9654 (tp) cc_final: 0.9324 (tt) REVERT: B 25 LYS cc_start: 0.9397 (pttp) cc_final: 0.9084 (pttp) REVERT: B 26 ASN cc_start: 0.8989 (OUTLIER) cc_final: 0.8367 (t0) REVERT: B 29 LYS cc_start: 0.9450 (mttm) cc_final: 0.8959 (mtmm) REVERT: B 102 TYR cc_start: 0.8570 (m-10) cc_final: 0.8127 (m-10) REVERT: B 106 ASP cc_start: 0.8592 (m-30) cc_final: 0.8163 (t0) REVERT: B 152 HIS cc_start: 0.0947 (OUTLIER) cc_final: -0.0237 (m90) REVERT: B 223 PHE cc_start: 0.9196 (m-80) cc_final: 0.8333 (m-80) REVERT: B 242 SER cc_start: 0.8750 (OUTLIER) cc_final: 0.8412 (p) REVERT: C 11 PHE cc_start: 0.8444 (t80) cc_final: 0.7745 (m-10) REVERT: C 15 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8964 (mm-40) REVERT: C 89 ARG cc_start: 0.9459 (OUTLIER) cc_final: 0.9195 (tpm170) REVERT: C 161 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7597 (tp30) REVERT: C 207 LYS cc_start: 0.9443 (ptmt) cc_final: 0.9132 (pttp) REVERT: C 223 PHE cc_start: 0.8913 (m-10) cc_final: 0.8476 (m-10) REVERT: C 249 MET cc_start: 0.6868 (mpp) cc_final: 0.6344 (mmm) REVERT: C 270 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9264 (pp) REVERT: C 272 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8497 (mm-40) REVERT: D 1 MET cc_start: 0.4246 (tpt) cc_final: 0.3206 (tpt) REVERT: D 26 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.7513 (t0) REVERT: D 51 LYS cc_start: 0.6253 (OUTLIER) cc_final: 0.5706 (pttt) REVERT: D 85 ASP cc_start: 0.9199 (t0) cc_final: 0.8833 (p0) REVERT: D 157 MET cc_start: 0.5247 (mmt) cc_final: 0.4344 (mmt) REVERT: D 255 ASP cc_start: 0.8877 (t0) cc_final: 0.8370 (t70) REVERT: E 10 MET cc_start: 0.9127 (mpp) cc_final: 0.8890 (mpp) REVERT: E 52 MET cc_start: 0.9329 (mmm) cc_final: 0.8938 (mmm) REVERT: E 206 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9236 (pp) REVERT: E 207 LYS cc_start: 0.9559 (mmtt) cc_final: 0.9091 (mmmm) REVERT: E 223 PHE cc_start: 0.8984 (m-80) cc_final: 0.8763 (m-80) REVERT: E 230 ILE cc_start: 0.9735 (tp) cc_final: 0.9439 (tp) REVERT: E 256 TYR cc_start: 0.8659 (t80) cc_final: 0.8446 (t80) REVERT: E 269 MET cc_start: 0.8911 (mmp) cc_final: 0.8647 (mmm) REVERT: F 10 MET cc_start: 0.9022 (mpp) cc_final: 0.8728 (mpp) REVERT: F 49 SER cc_start: 0.9255 (m) cc_final: 0.8976 (p) REVERT: F 50 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8872 (mm-30) REVERT: F 113 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7502 (mt-10) REVERT: F 168 MET cc_start: 0.9284 (mmm) cc_final: 0.8886 (mmm) REVERT: F 197 MET cc_start: 0.9016 (ptp) cc_final: 0.8756 (ptp) REVERT: G 1 MET cc_start: 0.2546 (ptt) cc_final: 0.2279 (ptt) REVERT: G 11 PHE cc_start: 0.7889 (p90) cc_final: 0.7533 (p90) REVERT: G 82 GLU cc_start: 0.6794 (tt0) cc_final: 0.6515 (tp30) REVERT: G 108 MET cc_start: 0.8957 (ptp) cc_final: 0.8720 (mpp) REVERT: G 197 MET cc_start: 0.9259 (mtp) cc_final: 0.8891 (mpp) REVERT: G 225 MET cc_start: 0.9437 (mmm) cc_final: 0.8559 (mmm) REVERT: H 25 LYS cc_start: 0.9713 (mmmt) cc_final: 0.9146 (mtmm) REVERT: H 197 MET cc_start: 0.9221 (mtp) cc_final: 0.8916 (mpp) REVERT: H 223 PHE cc_start: 0.9221 (m-10) cc_final: 0.8813 (m-80) REVERT: H 228 ASP cc_start: 0.9588 (t0) cc_final: 0.9331 (t0) REVERT: H 259 ASN cc_start: 0.9032 (OUTLIER) cc_final: 0.8759 (m110) REVERT: I 11 PHE cc_start: 0.9261 (t80) cc_final: 0.8977 (t80) REVERT: I 14 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8748 (ttt180) REVERT: I 108 MET cc_start: 0.9312 (mmm) cc_final: 0.8850 (mmp) REVERT: I 225 MET cc_start: 0.8982 (ttm) cc_final: 0.8630 (mmm) REVERT: I 255 ASP cc_start: 0.8672 (t0) cc_final: 0.8457 (t0) REVERT: J 11 PHE cc_start: 0.9078 (t80) cc_final: 0.8732 (t80) REVERT: J 25 LYS cc_start: 0.9534 (tppt) cc_final: 0.9158 (tppt) REVERT: J 29 LYS cc_start: 0.9264 (pttp) cc_final: 0.8853 (pttp) REVERT: J 52 MET cc_start: 0.9146 (mmt) cc_final: 0.8735 (mtp) REVERT: J 55 GLN cc_start: 0.9620 (tt0) cc_final: 0.9139 (pt0) REVERT: J 85 ASP cc_start: 0.8950 (t0) cc_final: 0.8487 (t0) REVERT: J 96 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8591 (tm-30) REVERT: J 102 TYR cc_start: 0.8638 (m-10) cc_final: 0.8281 (m-10) REVERT: J 152 HIS cc_start: 0.2214 (OUTLIER) cc_final: 0.1314 (m90) REVERT: J 237 MET cc_start: 0.9437 (mmm) cc_final: 0.8966 (mmm) REVERT: J 249 MET cc_start: 0.8303 (mmt) cc_final: 0.7778 (mpp) REVERT: J 272 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8392 (mp10) REVERT: K 7 MET cc_start: 0.7405 (mmm) cc_final: 0.6961 (mmm) REVERT: K 93 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9349 (mm) REVERT: K 243 ARG cc_start: 0.9304 (mmt180) cc_final: 0.8562 (ttt180) REVERT: K 255 ASP cc_start: 0.8519 (t0) cc_final: 0.8135 (t0) outliers start: 104 outliers final: 70 residues processed: 492 average time/residue: 0.1568 time to fit residues: 121.4527 Evaluate side-chains 488 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 401 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 89 ARG Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 149 MET Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 157 MET Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain H residue 259 ASN Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain J residue 5 HIS Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain J residue 157 MET Chi-restraints excluded: chain J residue 255 ASP Chi-restraints excluded: chain J residue 272 GLN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 215 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 297 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 258 optimal weight: 6.9990 chunk 274 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 ASN ** F 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 GLN ** H 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 HIS J 236 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.058425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.052420 restraints weight = 166696.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.053576 restraints weight = 101971.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.054409 restraints weight = 69645.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.055004 restraints weight = 51014.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.055462 restraints weight = 39485.202| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23826 Z= 0.161 Angle : 0.659 11.590 32021 Z= 0.346 Chirality : 0.039 0.204 3619 Planarity : 0.003 0.049 4334 Dihedral : 5.310 59.848 3394 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.35 % Favored : 97.61 % Rotamer: Outliers : 4.26 % Allowed : 21.29 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.15), residues: 3102 helix: 2.58 (0.11), residues: 2178 sheet: 0.60 (0.52), residues: 110 loop : -0.93 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 53 TYR 0.012 0.001 TYR E 219 PHE 0.024 0.002 PHE C 11 HIS 0.008 0.001 HIS J 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (23826) covalent geometry : angle 0.65924 / 0.35 (32021) hydrogen bonds : bond 0.04568 / 3.15 ( 1908) hydrogen bonds : angle 3.91356 / 2.87 ( 5646) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 415 time to evaluate : 0.843 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5144 (pmm) cc_final: 0.1084 (mmt) REVERT: A 187 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8222 (mm) REVERT: A 189 MET cc_start: 0.9096 (mmm) cc_final: 0.8812 (mpp) REVERT: A 197 MET cc_start: 0.9003 (mtm) cc_final: 0.8715 (mmp) REVERT: A 224 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8578 (mt-10) REVERT: A 270 LEU cc_start: 0.9731 (tp) cc_final: 0.9387 (pp) REVERT: A 272 GLN cc_start: 0.9430 (mm-40) cc_final: 0.8977 (mm-40) REVERT: B 10 MET cc_start: 0.9221 (mtt) cc_final: 0.8791 (mtt) REVERT: B 21 LEU cc_start: 0.9657 (tp) cc_final: 0.9316 (tt) REVERT: B 25 LYS cc_start: 0.9409 (pttp) cc_final: 0.9088 (pttp) REVERT: B 26 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.6988 (t0) REVERT: B 29 LYS cc_start: 0.9434 (mttm) cc_final: 0.8943 (mtmm) REVERT: B 152 HIS cc_start: 0.0732 (OUTLIER) cc_final: -0.0486 (m90) REVERT: B 219 TYR cc_start: 0.9292 (m-10) cc_final: 0.8555 (m-10) REVERT: B 223 PHE cc_start: 0.9222 (m-80) cc_final: 0.8376 (m-80) REVERT: B 237 MET cc_start: 0.8704 (mmt) cc_final: 0.8376 (mmt) REVERT: B 242 SER cc_start: 0.8777 (OUTLIER) cc_final: 0.8433 (p) REVERT: B 255 ASP cc_start: 0.8609 (m-30) cc_final: 0.8194 (t70) REVERT: C 11 PHE cc_start: 0.8402 (t80) cc_final: 0.7840 (m-10) REVERT: C 15 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8946 (mp10) REVERT: C 85 ASP cc_start: 0.8836 (m-30) cc_final: 0.8436 (p0) REVERT: C 89 ARG cc_start: 0.9464 (OUTLIER) cc_final: 0.9239 (tpm170) REVERT: C 92 GLU cc_start: 0.7484 (mt-10) cc_final: 0.6623 (mt-10) REVERT: C 161 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7692 (tp30) REVERT: C 186 MET cc_start: 0.8530 (tpt) cc_final: 0.8319 (ttm) REVERT: C 197 MET cc_start: 0.9380 (mpp) cc_final: 0.9126 (mpp) REVERT: C 207 LYS cc_start: 0.9458 (ptmt) cc_final: 0.9130 (pttp) REVERT: C 223 PHE cc_start: 0.8934 (m-10) cc_final: 0.8492 (m-10) REVERT: C 225 MET cc_start: 0.9095 (mmm) cc_final: 0.8769 (mmm) REVERT: C 235 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8662 (pp20) REVERT: C 249 MET cc_start: 0.6966 (mpp) cc_final: 0.6494 (mmm) REVERT: C 270 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9287 (pp) REVERT: C 272 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8574 (mm-40) REVERT: D 1 MET cc_start: 0.4370 (tpt) cc_final: 0.3359 (tpt) REVERT: D 10 MET cc_start: 0.9253 (mpp) cc_final: 0.9016 (mpp) REVERT: D 26 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.7428 (t0) REVERT: D 51 LYS cc_start: 0.6418 (OUTLIER) cc_final: 0.5958 (pttt) REVERT: D 85 ASP cc_start: 0.9206 (t0) cc_final: 0.8809 (p0) REVERT: D 157 MET cc_start: 0.5218 (mmt) cc_final: 0.4272 (mmt) REVERT: D 197 MET cc_start: 0.8856 (mmm) cc_final: 0.8592 (mmm) REVERT: D 255 ASP cc_start: 0.8849 (t0) cc_final: 0.8382 (t70) REVERT: E 10 MET cc_start: 0.9166 (mpp) cc_final: 0.8951 (mtt) REVERT: E 108 MET cc_start: 0.8965 (mmm) cc_final: 0.8688 (mmm) REVERT: E 206 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9251 (pp) REVERT: E 207 LYS cc_start: 0.9565 (mmtt) cc_final: 0.9154 (mmmt) REVERT: E 223 PHE cc_start: 0.9063 (m-80) cc_final: 0.8786 (m-80) REVERT: E 230 ILE cc_start: 0.9759 (tp) cc_final: 0.9476 (tp) REVERT: E 269 MET cc_start: 0.8988 (mmp) cc_final: 0.8773 (mmm) REVERT: F 23 LEU cc_start: 0.9310 (tp) cc_final: 0.9043 (pp) REVERT: F 29 LYS cc_start: 0.9079 (ttmm) cc_final: 0.8583 (ttmt) REVERT: F 49 SER cc_start: 0.9256 (m) cc_final: 0.8986 (p) REVERT: F 50 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8889 (mm-30) REVERT: F 113 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7630 (mt-10) REVERT: F 197 MET cc_start: 0.9003 (ptp) cc_final: 0.8765 (ptp) REVERT: G 1 MET cc_start: 0.2333 (ptt) cc_final: 0.2076 (ptt) REVERT: G 11 PHE cc_start: 0.8005 (p90) cc_final: 0.7603 (p90) REVERT: G 82 GLU cc_start: 0.6993 (tt0) cc_final: 0.6699 (tp30) REVERT: G 168 MET cc_start: 0.8310 (mmm) cc_final: 0.8081 (mmm) REVERT: G 189 MET cc_start: 0.8949 (mmm) cc_final: 0.8577 (mmm) REVERT: G 197 MET cc_start: 0.9262 (mtp) cc_final: 0.8890 (mpp) REVERT: G 225 MET cc_start: 0.9460 (mmm) cc_final: 0.8560 (mmm) REVERT: G 237 MET cc_start: 0.9284 (mmt) cc_final: 0.8858 (tpp) REVERT: H 25 LYS cc_start: 0.9698 (mmmt) cc_final: 0.9142 (mtmm) REVERT: H 197 MET cc_start: 0.9245 (mtp) cc_final: 0.8953 (mpp) REVERT: H 228 ASP cc_start: 0.9601 (t0) cc_final: 0.9346 (t0) REVERT: H 259 ASN cc_start: 0.9112 (OUTLIER) cc_final: 0.8852 (m110) REVERT: I 11 PHE cc_start: 0.9238 (t80) cc_final: 0.8948 (t80) REVERT: I 14 ARG cc_start: 0.9220 (OUTLIER) cc_final: 0.8727 (ttt180) REVERT: I 52 MET cc_start: 0.9445 (mtp) cc_final: 0.8932 (mpp) REVERT: I 108 MET cc_start: 0.9119 (mmm) cc_final: 0.8718 (mmp) REVERT: I 149 MET cc_start: 0.8579 (tpp) cc_final: 0.8301 (tpp) REVERT: I 225 MET cc_start: 0.9010 (ttm) cc_final: 0.8658 (mmm) REVERT: I 237 MET cc_start: 0.9318 (tpp) cc_final: 0.9045 (tpt) REVERT: I 255 ASP cc_start: 0.8708 (t0) cc_final: 0.8488 (t0) REVERT: I 269 MET cc_start: 0.9359 (mmp) cc_final: 0.8997 (mmp) REVERT: J 11 PHE cc_start: 0.9076 (t80) cc_final: 0.8712 (t80) REVERT: J 25 LYS cc_start: 0.9543 (tppt) cc_final: 0.9138 (tppt) REVERT: J 29 LYS cc_start: 0.9311 (pttp) cc_final: 0.8912 (pttp) REVERT: J 52 MET cc_start: 0.9179 (mmt) cc_final: 0.8712 (mtp) REVERT: J 55 GLN cc_start: 0.9623 (tt0) cc_final: 0.9121 (pt0) REVERT: J 85 ASP cc_start: 0.8973 (t0) cc_final: 0.8498 (t0) REVERT: J 152 HIS cc_start: 0.2219 (OUTLIER) cc_final: 0.1305 (m90) REVERT: J 236 ASN cc_start: 0.9152 (OUTLIER) cc_final: 0.8700 (t0) REVERT: J 237 MET cc_start: 0.9406 (mmm) cc_final: 0.8938 (mmm) REVERT: J 249 MET cc_start: 0.8302 (mmt) cc_final: 0.7786 (mpp) REVERT: K 7 MET cc_start: 0.7422 (mmm) cc_final: 0.6996 (mmm) REVERT: K 52 MET cc_start: 0.9122 (mmp) cc_final: 0.8742 (mtp) REVERT: K 74 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8499 (mt0) REVERT: K 93 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9404 (mm) REVERT: K 255 ASP cc_start: 0.8477 (t0) cc_final: 0.8009 (t0) outliers start: 104 outliers final: 73 residues processed: 491 average time/residue: 0.1568 time to fit residues: 121.0480 Evaluate side-chains 484 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 394 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 89 ARG Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 259 ASN Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 149 MET Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain H residue 259 ASN Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain J residue 5 HIS Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain J residue 157 MET Chi-restraints excluded: chain J residue 236 ASN Chi-restraints excluded: chain J residue 255 ASP Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 74 GLN Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 215 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 39 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN ** C 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 GLN ** H 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 236 ASN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.058092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.052132 restraints weight = 166758.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.053280 restraints weight = 101835.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.054104 restraints weight = 69439.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.054702 restraints weight = 50835.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.055151 restraints weight = 39378.078| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23826 Z= 0.169 Angle : 0.681 12.443 32021 Z= 0.357 Chirality : 0.039 0.216 3619 Planarity : 0.003 0.043 4334 Dihedral : 5.240 59.400 3391 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.51 % Favored : 97.45 % Rotamer: Outliers : 4.22 % Allowed : 22.07 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.15), residues: 3102 helix: 2.48 (0.11), residues: 2189 sheet: 0.55 (0.51), residues: 110 loop : -0.97 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 53 TYR 0.018 0.001 TYR E 102 PHE 0.026 0.002 PHE D 72 HIS 0.013 0.001 HIS J 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (23826) covalent geometry : angle 0.68141 / 0.36 (32021) hydrogen bonds : bond 0.04585 / 3.15 ( 1908) hydrogen bonds : angle 3.94949 / 2.89 ( 5646) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 403 time to evaluate : 0.966 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: 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: A 1 MET cc_start: 0.5140 (pmm) cc_final: 0.1056 (mmt) REVERT: A 187 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8491 (mm) REVERT: A 189 MET cc_start: 0.9099 (mmm) cc_final: 0.8800 (mmm) REVERT: A 197 MET cc_start: 0.8990 (mtm) cc_final: 0.8716 (mmp) REVERT: A 224 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8536 (mt-10) REVERT: B 10 MET cc_start: 0.9239 (mtt) cc_final: 0.8822 (mtt) REVERT: B 21 LEU cc_start: 0.9642 (tp) cc_final: 0.9283 (tt) REVERT: B 25 LYS cc_start: 0.9393 (pttp) cc_final: 0.9067 (pttp) REVERT: B 26 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.7980 (t0) REVERT: B 29 LYS cc_start: 0.9456 (mttm) cc_final: 0.8964 (mtmm) REVERT: B 152 HIS cc_start: 0.0752 (OUTLIER) cc_final: -0.0399 (m90) REVERT: B 219 TYR cc_start: 0.9303 (m-10) cc_final: 0.8563 (m-10) REVERT: B 223 PHE cc_start: 0.9207 (m-80) cc_final: 0.8347 (m-80) REVERT: B 237 MET cc_start: 0.8939 (mmt) cc_final: 0.8670 (mmt) REVERT: B 242 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8462 (p) REVERT: B 255 ASP cc_start: 0.8591 (m-30) cc_final: 0.8364 (t0) REVERT: C 11 PHE cc_start: 0.8391 (t80) cc_final: 0.7959 (m-10) REVERT: C 89 ARG cc_start: 0.9458 (OUTLIER) cc_final: 0.9236 (tpm170) REVERT: C 92 GLU cc_start: 0.7437 (mt-10) cc_final: 0.6659 (mt-10) REVERT: C 161 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7641 (tp30) REVERT: C 197 MET cc_start: 0.9375 (mpp) cc_final: 0.9071 (mpp) REVERT: C 207 LYS cc_start: 0.9460 (ptmt) cc_final: 0.9153 (pttp) REVERT: C 223 PHE cc_start: 0.8886 (m-10) cc_final: 0.8471 (m-10) REVERT: C 249 MET cc_start: 0.6784 (mpp) cc_final: 0.6307 (mmm) REVERT: C 264 GLN cc_start: 0.9374 (mm-40) cc_final: 0.8954 (mp10) REVERT: C 270 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9289 (pp) REVERT: C 272 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8752 (mm-40) REVERT: D 1 MET cc_start: 0.4492 (tpt) cc_final: 0.3322 (tpt) REVERT: D 10 MET cc_start: 0.9246 (mpp) cc_final: 0.8863 (mpp) REVERT: D 26 ASN cc_start: 0.8720 (OUTLIER) cc_final: 0.7236 (t0) REVERT: D 51 LYS cc_start: 0.6430 (OUTLIER) cc_final: 0.5968 (pttt) REVERT: D 85 ASP cc_start: 0.9210 (t0) cc_final: 0.8800 (p0) REVERT: D 157 MET cc_start: 0.5187 (mmt) cc_final: 0.4214 (mmt) REVERT: D 207 LYS cc_start: 0.9480 (pttp) cc_final: 0.9262 (ptpp) REVERT: D 237 MET cc_start: 0.9494 (mmm) cc_final: 0.9272 (mmm) REVERT: D 255 ASP cc_start: 0.8837 (t0) cc_final: 0.8394 (t0) REVERT: E 10 MET cc_start: 0.9122 (mpp) cc_final: 0.8887 (mtt) REVERT: E 52 MET cc_start: 0.9289 (mmm) cc_final: 0.8930 (mmm) REVERT: E 108 MET cc_start: 0.8955 (mmm) cc_final: 0.8688 (mmm) REVERT: E 206 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9333 (pp) REVERT: E 207 LYS cc_start: 0.9577 (mmtt) cc_final: 0.9077 (mmmm) REVERT: E 223 PHE cc_start: 0.9056 (m-80) cc_final: 0.8766 (m-80) REVERT: E 230 ILE cc_start: 0.9766 (tp) cc_final: 0.9471 (tp) REVERT: F 49 SER cc_start: 0.9265 (m) cc_final: 0.8987 (p) REVERT: F 50 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8907 (mm-30) REVERT: F 168 MET cc_start: 0.9111 (mmm) cc_final: 0.8552 (mmp) REVERT: F 197 MET cc_start: 0.8965 (ptp) cc_final: 0.8695 (ptp) REVERT: G 1 MET cc_start: 0.2412 (ptt) cc_final: 0.2148 (ptt) REVERT: G 11 PHE cc_start: 0.8012 (p90) cc_final: 0.7599 (p90) REVERT: G 82 GLU cc_start: 0.6977 (tt0) cc_final: 0.6697 (tp30) REVERT: G 186 MET cc_start: 0.9390 (ttt) cc_final: 0.8844 (tmm) REVERT: G 189 MET cc_start: 0.8910 (mmm) cc_final: 0.8654 (mmm) REVERT: G 197 MET cc_start: 0.9267 (mtp) cc_final: 0.8914 (mpp) REVERT: G 211 LYS cc_start: 0.9645 (tmmt) cc_final: 0.9388 (ttmt) REVERT: G 225 MET cc_start: 0.9453 (mmm) cc_final: 0.8527 (mmm) REVERT: H 25 LYS cc_start: 0.9700 (mmmt) cc_final: 0.9156 (mtmm) REVERT: H 197 MET cc_start: 0.9233 (mtp) cc_final: 0.8941 (mpp) REVERT: H 228 ASP cc_start: 0.9597 (t0) cc_final: 0.9344 (t0) REVERT: H 237 MET cc_start: 0.8839 (tpt) cc_final: 0.8599 (tpt) REVERT: H 259 ASN cc_start: 0.9134 (OUTLIER) cc_final: 0.8913 (m110) REVERT: I 11 PHE cc_start: 0.9243 (t80) cc_final: 0.8940 (t80) REVERT: I 14 ARG cc_start: 0.9283 (OUTLIER) cc_final: 0.8693 (ttt180) REVERT: I 52 MET cc_start: 0.9439 (mtp) cc_final: 0.8921 (mpp) REVERT: I 108 MET cc_start: 0.9108 (mmm) cc_final: 0.8688 (mmp) REVERT: I 149 MET cc_start: 0.8522 (tpp) cc_final: 0.8292 (tpp) REVERT: I 225 MET cc_start: 0.8980 (ttm) cc_final: 0.8650 (mmm) REVERT: I 237 MET cc_start: 0.9274 (tpp) cc_final: 0.9046 (tpt) REVERT: I 255 ASP cc_start: 0.8685 (t0) cc_final: 0.8479 (t0) REVERT: J 11 PHE cc_start: 0.9061 (t80) cc_final: 0.8702 (t80) REVERT: J 25 LYS cc_start: 0.9536 (tppt) cc_final: 0.9080 (tppt) REVERT: J 29 LYS cc_start: 0.9319 (pttp) cc_final: 0.8873 (pttp) REVERT: J 52 MET cc_start: 0.9152 (mmt) cc_final: 0.8717 (mtp) REVERT: J 55 GLN cc_start: 0.9618 (tt0) cc_final: 0.9118 (pt0) REVERT: J 85 ASP cc_start: 0.8952 (t0) cc_final: 0.8491 (t0) REVERT: J 96 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8581 (tm-30) REVERT: J 102 TYR cc_start: 0.8641 (m-10) cc_final: 0.8224 (m-10) REVERT: J 152 HIS cc_start: 0.2130 (OUTLIER) cc_final: 0.1281 (m90) REVERT: J 237 MET cc_start: 0.9374 (mmm) cc_final: 0.8859 (mmm) REVERT: J 249 MET cc_start: 0.8310 (mmt) cc_final: 0.7816 (mpp) REVERT: K 7 MET cc_start: 0.7208 (mmm) cc_final: 0.6880 (mmm) REVERT: K 52 MET cc_start: 0.9085 (mmp) cc_final: 0.8650 (mtp) REVERT: K 93 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9370 (mm) REVERT: K 186 MET cc_start: 0.8056 (ptm) cc_final: 0.7792 (pmm) REVERT: K 189 MET cc_start: 0.8583 (mmm) cc_final: 0.8364 (mmm) REVERT: K 255 ASP cc_start: 0.8462 (t0) cc_final: 0.7955 (t0) outliers start: 103 outliers final: 71 residues processed: 479 average time/residue: 0.1497 time to fit residues: 113.2522 Evaluate side-chains 477 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 391 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 89 ARG Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 149 MET Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain H residue 253 ILE Chi-restraints excluded: chain H residue 259 ASN Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain J residue 5 HIS Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain J residue 157 MET Chi-restraints excluded: chain J residue 255 ASP Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 215 ASP Chi-restraints excluded: chain K residue 280 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 150 optimal weight: 7.9990 chunk 284 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 267 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 161 optimal weight: 20.0000 chunk 226 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 280 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 ASN ** F 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** H 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 HIS J 236 ASN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.057681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.051900 restraints weight = 171321.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.053028 restraints weight = 104704.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.053834 restraints weight = 71399.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.054419 restraints weight = 52199.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.054858 restraints weight = 40391.816| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23826 Z= 0.209 Angle : 0.732 13.236 32021 Z= 0.386 Chirality : 0.041 0.264 3619 Planarity : 0.003 0.043 4334 Dihedral : 5.328 58.564 3389 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.80 % Favored : 97.16 % Rotamer: Outliers : 4.26 % Allowed : 22.48 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.15), residues: 3102 helix: 2.30 (0.11), residues: 2189 sheet: 0.35 (0.51), residues: 110 loop : -1.09 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 53 TYR 0.023 0.002 TYR E 256 PHE 0.028 0.002 PHE E 11 HIS 0.006 0.001 HIS F 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.21 (23826) covalent geometry : angle 0.73200 / 0.39 (32021) hydrogen bonds : bond 0.04797 / 3.30 ( 1908) hydrogen bonds : angle 4.14117 / 3.04 ( 5646) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 390 time to evaluate : 0.927 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4658 (pmm) cc_final: 0.0679 (mmt) REVERT: A 187 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8445 (mm) REVERT: A 189 MET cc_start: 0.9136 (mmm) cc_final: 0.8851 (mmm) REVERT: A 197 MET cc_start: 0.8987 (mtm) cc_final: 0.8744 (mmp) REVERT: B 10 MET cc_start: 0.9235 (mtt) cc_final: 0.8805 (mtt) REVERT: B 21 LEU cc_start: 0.9638 (tp) cc_final: 0.9266 (tt) REVERT: B 25 LYS cc_start: 0.9388 (pttp) cc_final: 0.9036 (pttp) REVERT: B 26 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.7441 (t0) REVERT: B 29 LYS cc_start: 0.9487 (mttm) cc_final: 0.8982 (mtmm) REVERT: B 152 HIS cc_start: 0.1143 (OUTLIER) cc_final: 0.0242 (m90) REVERT: B 219 TYR cc_start: 0.9299 (m-10) cc_final: 0.8568 (m-10) REVERT: B 223 PHE cc_start: 0.9231 (m-80) cc_final: 0.8360 (m-80) REVERT: B 242 SER cc_start: 0.8849 (OUTLIER) cc_final: 0.8518 (p) REVERT: B 255 ASP cc_start: 0.8527 (m-30) cc_final: 0.8280 (t0) REVERT: C 15 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8726 (mp10) REVERT: C 89 ARG cc_start: 0.9440 (OUTLIER) cc_final: 0.9200 (tpm170) REVERT: C 92 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6443 (mt-10) REVERT: C 161 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7706 (tp30) REVERT: C 186 MET cc_start: 0.8235 (tpt) cc_final: 0.7979 (ptp) REVERT: C 197 MET cc_start: 0.9369 (mpp) cc_final: 0.9098 (mpp) REVERT: C 207 LYS cc_start: 0.9460 (ptmt) cc_final: 0.9148 (pttp) REVERT: C 223 PHE cc_start: 0.8935 (m-10) cc_final: 0.8521 (m-10) REVERT: C 249 MET cc_start: 0.6966 (mpp) cc_final: 0.6529 (mmm) REVERT: C 272 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8786 (mm-40) REVERT: D 1 MET cc_start: 0.4590 (tpt) cc_final: 0.4253 (tpt) REVERT: D 10 MET cc_start: 0.9264 (mpp) cc_final: 0.8858 (mpp) REVERT: D 26 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.7150 (t0) REVERT: D 51 LYS cc_start: 0.6442 (OUTLIER) cc_final: 0.5959 (pttt) REVERT: D 157 MET cc_start: 0.5280 (mmt) cc_final: 0.4260 (mmt) REVERT: D 197 MET cc_start: 0.8824 (mmm) cc_final: 0.8552 (mmm) REVERT: D 207 LYS cc_start: 0.9484 (pttp) cc_final: 0.9268 (ptpp) REVERT: D 237 MET cc_start: 0.9494 (mmm) cc_final: 0.9279 (mmm) REVERT: D 255 ASP cc_start: 0.8854 (t0) cc_final: 0.8374 (t0) REVERT: E 10 MET cc_start: 0.9150 (mpp) cc_final: 0.8856 (mtt) REVERT: E 108 MET cc_start: 0.8963 (mmm) cc_final: 0.8644 (mmm) REVERT: E 206 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9320 (pp) REVERT: E 207 LYS cc_start: 0.9594 (mmtt) cc_final: 0.9047 (mmmm) REVERT: E 223 PHE cc_start: 0.9046 (m-80) cc_final: 0.8703 (m-80) REVERT: E 230 ILE cc_start: 0.9783 (tp) cc_final: 0.9509 (tp) REVERT: F 168 MET cc_start: 0.9102 (mmm) cc_final: 0.8647 (mmm) REVERT: F 197 MET cc_start: 0.8897 (ptp) cc_final: 0.8670 (ptp) REVERT: G 11 PHE cc_start: 0.8056 (p90) cc_final: 0.7739 (p90) REVERT: G 82 GLU cc_start: 0.7143 (tt0) cc_final: 0.6786 (tp30) REVERT: G 168 MET cc_start: 0.8187 (mmm) cc_final: 0.7985 (mmm) REVERT: G 197 MET cc_start: 0.9282 (mtp) cc_final: 0.8927 (mpp) REVERT: G 211 LYS cc_start: 0.9660 (tmmt) cc_final: 0.9395 (ttmt) REVERT: G 225 MET cc_start: 0.9452 (mmm) cc_final: 0.8544 (mmm) REVERT: H 25 LYS cc_start: 0.9705 (mmmt) cc_final: 0.9415 (mmmt) REVERT: H 197 MET cc_start: 0.9207 (mtp) cc_final: 0.8924 (mpp) REVERT: H 228 ASP cc_start: 0.9572 (t0) cc_final: 0.9323 (t0) REVERT: H 237 MET cc_start: 0.8894 (tpt) cc_final: 0.8665 (tpt) REVERT: H 259 ASN cc_start: 0.9144 (OUTLIER) cc_final: 0.8913 (m110) REVERT: I 14 ARG cc_start: 0.9313 (OUTLIER) cc_final: 0.8651 (ttt180) REVERT: I 52 MET cc_start: 0.9418 (mtp) cc_final: 0.8958 (mpp) REVERT: I 108 MET cc_start: 0.9106 (mmm) cc_final: 0.8626 (mmp) REVERT: I 237 MET cc_start: 0.9246 (tpp) cc_final: 0.9029 (tpt) REVERT: I 255 ASP cc_start: 0.8711 (t0) cc_final: 0.8488 (t0) REVERT: J 25 LYS cc_start: 0.9533 (tppt) cc_final: 0.9054 (tppt) REVERT: J 29 LYS cc_start: 0.9341 (pttp) cc_final: 0.8876 (pttp) REVERT: J 52 MET cc_start: 0.9113 (mmt) cc_final: 0.8679 (mtp) REVERT: J 55 GLN cc_start: 0.9625 (tt0) cc_final: 0.9102 (pt0) REVERT: J 72 PHE cc_start: 0.9169 (t80) cc_final: 0.8755 (t80) REVERT: J 96 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8537 (tm-30) REVERT: J 102 TYR cc_start: 0.8704 (m-10) cc_final: 0.8254 (m-10) REVERT: J 152 HIS cc_start: 0.1971 (OUTLIER) cc_final: 0.0881 (m90) REVERT: J 225 MET cc_start: 0.8926 (mmp) cc_final: 0.8278 (mmm) REVERT: J 237 MET cc_start: 0.9390 (mmm) cc_final: 0.8912 (mmm) REVERT: J 249 MET cc_start: 0.8268 (mmt) cc_final: 0.7858 (pmm) REVERT: J 272 GLN cc_start: 0.8181 (mt0) cc_final: 0.7885 (pt0) REVERT: K 7 MET cc_start: 0.7300 (mmm) cc_final: 0.6888 (mmm) REVERT: K 52 MET cc_start: 0.9083 (mmp) cc_final: 0.8680 (mtp) REVERT: K 93 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9366 (mm) REVERT: K 186 MET cc_start: 0.7876 (ptm) cc_final: 0.7500 (pmm) REVERT: K 189 MET cc_start: 0.8590 (mmm) cc_final: 0.8320 (mmm) REVERT: K 255 ASP cc_start: 0.8519 (t0) cc_final: 0.8111 (t0) REVERT: K 256 TYR cc_start: 0.9176 (t80) cc_final: 0.8839 (t80) outliers start: 104 outliers final: 74 residues processed: 467 average time/residue: 0.1547 time to fit residues: 114.0011 Evaluate side-chains 467 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 378 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 89 ARG Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 259 ASN Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 149 MET Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain H residue 253 ILE Chi-restraints excluded: chain H residue 259 ASN Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain J residue 5 HIS Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain J residue 133 MET Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain J residue 157 MET Chi-restraints excluded: chain J residue 255 ASP Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 215 ASP Chi-restraints excluded: chain K residue 280 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 9 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 221 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 262 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 208 optimal weight: 7.9990 chunk 169 optimal weight: 7.9990 chunk 305 optimal weight: 4.9990 chunk 245 optimal weight: 10.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 GLN ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.058454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.052536 restraints weight = 166604.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.053693 restraints weight = 101179.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.054529 restraints weight = 68739.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.055126 restraints weight = 50159.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.055574 restraints weight = 38670.894| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23826 Z= 0.147 Angle : 0.721 12.745 32021 Z= 0.369 Chirality : 0.040 0.257 3619 Planarity : 0.003 0.037 4334 Dihedral : 5.230 56.651 3388 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.22 % Favored : 97.71 % Rotamer: Outliers : 3.52 % Allowed : 23.14 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.16), residues: 3102 helix: 2.41 (0.11), residues: 2189 sheet: 0.58 (0.53), residues: 110 loop : -1.10 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 53 TYR 0.021 0.001 TYR E 102 PHE 0.037 0.002 PHE C 11 HIS 0.012 0.001 HIS J 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (23826) covalent geometry : angle 0.72052 / 0.37 (32021) hydrogen bonds : bond 0.04642 / 3.19 ( 1908) hydrogen bonds : angle 3.97891 / 2.93 ( 5646) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 408 time to evaluate : 0.900 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4898 (pmm) cc_final: 0.0825 (mmt) REVERT: A 10 MET cc_start: 0.8968 (mmm) cc_final: 0.8524 (mpp) REVERT: A 11 PHE cc_start: 0.8658 (t80) cc_final: 0.8400 (t80) REVERT: A 15 GLN cc_start: 0.9405 (mm-40) cc_final: 0.8706 (mt0) REVERT: A 189 MET cc_start: 0.9136 (mmm) cc_final: 0.8871 (mmm) REVERT: A 197 MET cc_start: 0.8978 (mtm) cc_final: 0.8730 (mmp) REVERT: A 224 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8592 (mt-10) REVERT: A 282 ARG cc_start: 0.8916 (tpm170) cc_final: 0.8708 (tpm170) REVERT: B 10 MET cc_start: 0.9217 (mtt) cc_final: 0.8762 (mtt) REVERT: B 21 LEU cc_start: 0.9635 (tp) cc_final: 0.9247 (tt) REVERT: B 25 LYS cc_start: 0.9348 (pttp) cc_final: 0.8991 (pttp) REVERT: B 26 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.7384 (t0) REVERT: B 29 LYS cc_start: 0.9450 (mttm) cc_final: 0.8947 (mtmm) REVERT: B 152 HIS cc_start: 0.1108 (OUTLIER) cc_final: 0.0310 (m90) REVERT: B 219 TYR cc_start: 0.9298 (m-10) cc_final: 0.8565 (m-10) REVERT: B 223 PHE cc_start: 0.9208 (m-80) cc_final: 0.8346 (m-80) REVERT: B 237 MET cc_start: 0.8710 (mmt) cc_final: 0.8477 (mmt) REVERT: B 242 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8447 (p) REVERT: B 255 ASP cc_start: 0.8570 (m-30) cc_final: 0.8270 (t70) REVERT: C 11 PHE cc_start: 0.8385 (t80) cc_final: 0.7839 (m-10) REVERT: C 85 ASP cc_start: 0.8783 (m-30) cc_final: 0.8441 (p0) REVERT: C 161 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7650 (tp30) REVERT: C 197 MET cc_start: 0.9357 (mpp) cc_final: 0.9039 (mpp) REVERT: C 207 LYS cc_start: 0.9458 (ptmt) cc_final: 0.9152 (pttp) REVERT: C 223 PHE cc_start: 0.8909 (m-10) cc_final: 0.8549 (m-10) REVERT: C 235 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8647 (pp20) REVERT: C 249 MET cc_start: 0.6898 (mpp) cc_final: 0.6435 (mmm) REVERT: C 272 GLN cc_start: 0.9217 (mm-40) cc_final: 0.8774 (mm-40) REVERT: D 1 MET cc_start: 0.4524 (tpt) cc_final: 0.3395 (tpt) REVERT: D 10 MET cc_start: 0.9276 (mpp) cc_final: 0.8859 (mpp) REVERT: D 26 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.6974 (t0) REVERT: D 30 LEU cc_start: 0.9480 (mt) cc_final: 0.9220 (mt) REVERT: D 51 LYS cc_start: 0.6578 (OUTLIER) cc_final: 0.6137 (pttt) REVERT: D 64 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8434 (pt0) REVERT: D 85 ASP cc_start: 0.9142 (t0) cc_final: 0.8691 (p0) REVERT: D 157 MET cc_start: 0.5307 (mmt) cc_final: 0.4263 (mmt) REVERT: D 197 MET cc_start: 0.8821 (mmm) cc_final: 0.8545 (mmm) REVERT: D 207 LYS cc_start: 0.9487 (pttp) cc_final: 0.9257 (ptpp) REVERT: D 255 ASP cc_start: 0.8801 (t0) cc_final: 0.8328 (t0) REVERT: E 10 MET cc_start: 0.9132 (mpp) cc_final: 0.8858 (mtt) REVERT: E 108 MET cc_start: 0.8928 (mmm) cc_final: 0.8597 (mmm) REVERT: E 207 LYS cc_start: 0.9578 (mmtt) cc_final: 0.9340 (mmmt) REVERT: E 223 PHE cc_start: 0.9091 (m-80) cc_final: 0.8737 (m-80) REVERT: E 230 ILE cc_start: 0.9782 (tp) cc_final: 0.9513 (tp) REVERT: E 243 ARG cc_start: 0.8787 (tpp80) cc_final: 0.8208 (tpp80) REVERT: F 168 MET cc_start: 0.9072 (mmm) cc_final: 0.8543 (mmp) REVERT: F 197 MET cc_start: 0.8912 (ptp) cc_final: 0.8687 (ptp) REVERT: G 82 GLU cc_start: 0.6944 (tt0) cc_final: 0.6682 (tp30) REVERT: G 189 MET cc_start: 0.8767 (mmm) cc_final: 0.8428 (mmm) REVERT: G 197 MET cc_start: 0.9258 (mtp) cc_final: 0.8892 (mpp) REVERT: G 211 LYS cc_start: 0.9643 (tmmt) cc_final: 0.9366 (ttmt) REVERT: G 225 MET cc_start: 0.9455 (mmm) cc_final: 0.8533 (mmm) REVERT: G 255 ASP cc_start: 0.9245 (t0) cc_final: 0.8934 (t0) REVERT: H 25 LYS cc_start: 0.9675 (mmmt) cc_final: 0.9426 (mmmt) REVERT: H 95 ILE cc_start: 0.8933 (mm) cc_final: 0.8720 (pt) REVERT: H 197 MET cc_start: 0.9172 (mtp) cc_final: 0.8872 (mpp) REVERT: H 228 ASP cc_start: 0.9567 (t0) cc_final: 0.9298 (t0) REVERT: H 237 MET cc_start: 0.8864 (tpt) cc_final: 0.8597 (tpt) REVERT: I 11 PHE cc_start: 0.9207 (t80) cc_final: 0.8921 (t80) REVERT: I 14 ARG cc_start: 0.9258 (OUTLIER) cc_final: 0.8569 (ttt180) REVERT: I 52 MET cc_start: 0.9424 (mtp) cc_final: 0.8963 (mpp) REVERT: I 108 MET cc_start: 0.9110 (mmm) cc_final: 0.8636 (mmp) REVERT: I 237 MET cc_start: 0.9256 (tpp) cc_final: 0.9043 (tpt) REVERT: I 255 ASP cc_start: 0.8689 (t0) cc_final: 0.8476 (t0) REVERT: J 11 PHE cc_start: 0.8984 (t80) cc_final: 0.8658 (t80) REVERT: J 25 LYS cc_start: 0.9540 (tppt) cc_final: 0.9072 (tppt) REVERT: J 29 LYS cc_start: 0.9363 (pttp) cc_final: 0.8851 (pttp) REVERT: J 52 MET cc_start: 0.9108 (mmt) cc_final: 0.8649 (mtp) REVERT: J 55 GLN cc_start: 0.9603 (tt0) cc_final: 0.9150 (pt0) REVERT: J 72 PHE cc_start: 0.9083 (t80) cc_final: 0.8554 (t80) REVERT: J 96 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8453 (tm-30) REVERT: J 102 TYR cc_start: 0.8695 (m-10) cc_final: 0.8225 (m-10) REVERT: J 152 HIS cc_start: 0.2257 (OUTLIER) cc_final: 0.1487 (m90) REVERT: J 237 MET cc_start: 0.9369 (mmm) cc_final: 0.8848 (mmm) REVERT: J 249 MET cc_start: 0.8282 (mmt) cc_final: 0.7819 (pmm) REVERT: K 1 MET cc_start: 0.5266 (OUTLIER) cc_final: 0.4011 (ptt) REVERT: K 7 MET cc_start: 0.7220 (mmm) cc_final: 0.6873 (mmm) REVERT: K 52 MET cc_start: 0.9040 (mmp) cc_final: 0.8641 (mtp) REVERT: K 64 GLN cc_start: 0.9048 (pt0) cc_final: 0.8566 (pp30) REVERT: K 93 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9357 (mm) REVERT: K 186 MET cc_start: 0.7972 (ptm) cc_final: 0.7563 (pmm) REVERT: K 189 MET cc_start: 0.8535 (mmt) cc_final: 0.8273 (mmm) REVERT: K 255 ASP cc_start: 0.8451 (t0) cc_final: 0.7961 (t0) REVERT: K 256 TYR cc_start: 0.9189 (t80) cc_final: 0.8876 (t80) outliers start: 86 outliers final: 67 residues processed: 474 average time/residue: 0.1618 time to fit residues: 120.3232 Evaluate side-chains 470 residues out of total 2442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 391 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 149 MET Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain J residue 5 HIS Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain J residue 133 MET Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain J residue 157 MET Chi-restraints excluded: chain J residue 255 ASP Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 215 ASP Chi-restraints excluded: chain K residue 280 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 205 optimal weight: 9.9990 chunk 272 optimal weight: 0.9990 chunk 275 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 273 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 chunk 170 optimal weight: 0.0070 overall best weight: 3.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 ASN ** F 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.058635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.052700 restraints weight = 165221.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.053852 restraints weight = 100825.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.054683 restraints weight = 68686.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.055281 restraints weight = 50161.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.055733 restraints weight = 38703.931| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23826 Z= 0.148 Angle : 0.733 12.669 32021 Z= 0.376 Chirality : 0.040 0.260 3619 Planarity : 0.003 0.052 4334 Dihedral : 5.132 56.509 3388 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.48 % Favored : 97.49 % Rotamer: Outliers : 3.44 % Allowed : 23.71 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.16), residues: 3102 helix: 2.42 (0.11), residues: 2189 sheet: 0.61 (0.53), residues: 110 loop : -1.06 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 89 TYR 0.044 0.001 TYR E 256 PHE 0.034 0.002 PHE D 72 HIS 0.005 0.001 HIS A 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (23826) covalent geometry : angle 0.73336 / 0.38 (32021) hydrogen bonds : bond 0.04606 / 3.16 ( 1908) hydrogen bonds : angle 3.95629 / 2.91 ( 5646) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4299.18 seconds wall clock time: 75 minutes 4.91 seconds (4504.91 seconds total)