Starting phenix.real_space_refine on Thu Mar 5 12:04:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mxy_24076/03_2026/7mxy_24076_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mxy_24076/03_2026/7mxy_24076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mxy_24076/03_2026/7mxy_24076_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mxy_24076/03_2026/7mxy_24076_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mxy_24076/03_2026/7mxy_24076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mxy_24076/03_2026/7mxy_24076.map" } resolution = 2.18 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.432 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: 6 Type Number sf(0) Gaussians S 70 5.16 5 C 7416 2.51 5 N 1714 2.21 5 O 1911 1.98 5 F 25 1.80 5 H 11129 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22265 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 4457 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 4, 'TRANS': 278} Chain: "B" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 4433 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 3, 'TRANS': 277} Chain: "C" Number of atoms: 4400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 4400 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 3, 'TRANS': 275} Chain: "D" Number of atoms: 4446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4446 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 4, 'TRANS': 277} Chain: "E" Number of atoms: 4422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 4422 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 4, 'TRANS': 276} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.09, per 1000 atoms: 0.18 Number of scatterers: 22265 At special positions: 0 Unit cell: (87.74, 99.51, 98.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 70 16.00 F 25 9.00 O 1911 8.00 N 1714 7.00 C 7416 6.00 H 11129 1.00 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: 2.15 Conformation dependent library (CDL) restraints added in 591.2 milliseconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2592 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 1 sheets defined 85.3% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 21 through 38 removed outlier: 3.801A pdb=" N LYS A 35 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HIS A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 68 Processing helix chain 'A' and resid 70 through 78 removed outlier: 3.916A pdb=" N ILE A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 91 through 100 removed outlier: 4.231A pdb=" N MET A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 100 " --> pdb=" O CYS A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 118 removed outlier: 4.167A pdb=" N LEU A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 148 Processing helix chain 'A' and resid 164 through 178 Processing helix chain 'A' and resid 181 through 206 Processing helix chain 'A' and resid 209 through 227 removed outlier: 4.369A pdb=" N VAL A 216 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 244 Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 257 through 271 Processing helix chain 'A' and resid 274 through 291 removed outlier: 5.481A pdb=" N GLU A 283 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N HIS A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 36 removed outlier: 3.605A pdb=" N LYS B 35 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA B 36 " --> pdb=" O GLY B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 68 Processing helix chain 'B' and resid 70 through 78 removed outlier: 3.835A pdb=" N GLU B 75 " --> pdb=" O HIS B 71 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 90 Processing helix chain 'B' and resid 91 through 99 removed outlier: 4.222A pdb=" N MET B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 118 removed outlier: 3.821A pdb=" N LEU B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N THR B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 152 Processing helix chain 'B' and resid 164 through 179 Processing helix chain 'B' and resid 181 through 206 Processing helix chain 'B' and resid 208 through 227 removed outlier: 4.042A pdb=" N VAL B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 244 Processing helix chain 'B' and resid 249 through 271 removed outlier: 3.843A pdb=" N LYS B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Proline residue: B 260 - end of helix Processing helix chain 'B' and resid 273 through 291 removed outlier: 5.487A pdb=" N GLU B 283 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N HIS B 284 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 35 removed outlier: 3.602A pdb=" N LYS C 35 " --> pdb=" O TYR C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 68 Processing helix chain 'C' and resid 70 through 78 removed outlier: 3.820A pdb=" N ILE C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 91 through 101 removed outlier: 4.228A pdb=" N MET C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 118 removed outlier: 3.970A pdb=" N LEU C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 148 Processing helix chain 'C' and resid 148 through 153 removed outlier: 3.545A pdb=" N GLY C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 179 Processing helix chain 'C' and resid 181 through 206 Processing helix chain 'C' and resid 208 through 226 removed outlier: 3.951A pdb=" N VAL C 216 " --> pdb=" O TYR C 212 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 245 Processing helix chain 'C' and resid 249 through 255 Processing helix chain 'C' and resid 257 through 271 Processing helix chain 'C' and resid 273 through 289 removed outlier: 6.026A pdb=" N GLU C 283 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N HIS C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 36 removed outlier: 3.716A pdb=" N LYS D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA D 36 " --> pdb=" O GLY D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 68 Processing helix chain 'D' and resid 70 through 78 removed outlier: 3.664A pdb=" N ILE D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 90 Processing helix chain 'D' and resid 91 through 101 removed outlier: 4.244A pdb=" N MET D 95 " --> pdb=" O PRO D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 118 removed outlier: 3.971A pdb=" N LEU D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 148 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 164 through 179 removed outlier: 3.544A pdb=" N GLN D 168 " --> pdb=" O ASN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 206 Processing helix chain 'D' and resid 208 through 226 removed outlier: 3.871A pdb=" N VAL D 216 " --> pdb=" O TYR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 249 through 255 removed outlier: 3.721A pdb=" N TYR D 254 " --> pdb=" O VAL D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 271 Processing helix chain 'D' and resid 273 through 289 removed outlier: 5.953A pdb=" N GLU D 283 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N HIS D 284 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 36 removed outlier: 3.550A pdb=" N TYR E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS E 35 " --> pdb=" O TYR E 31 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA E 36 " --> pdb=" O GLY E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 68 Processing helix chain 'E' and resid 70 through 78 removed outlier: 3.590A pdb=" N GLU E 75 " --> pdb=" O HIS E 71 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 90 removed outlier: 3.942A pdb=" N VAL E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 100 removed outlier: 4.232A pdb=" N MET E 95 " --> pdb=" O PRO E 91 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR E 100 " --> pdb=" O CYS E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 118 removed outlier: 4.114A pdb=" N LEU E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N THR E 113 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 153 removed outlier: 4.267A pdb=" N LEU E 151 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 179 Processing helix chain 'E' and resid 181 through 206 Processing helix chain 'E' and resid 208 through 227 removed outlier: 4.090A pdb=" N VAL E 216 " --> pdb=" O TYR E 212 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY E 227 " --> pdb=" O PHE E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 244 Processing helix chain 'E' and resid 249 through 256 Processing helix chain 'E' and resid 257 through 271 Processing helix chain 'E' and resid 273 through 289 removed outlier: 5.628A pdb=" N GLU E 283 " --> pdb=" O PHE E 279 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N HIS E 284 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.678A pdb=" N VAL D 13 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N VAL B 13 " --> pdb=" O LYS C 16 " (cutoff:3.500A) 857 hydrogen bonds defined for protein. 2559 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: 5.07 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.00: 11089 1.00 - 1.20: 49 1.20 - 1.40: 4971 1.40 - 1.61: 6344 1.61 - 1.81: 100 Bond restraints: 22553 Sorted by residual: bond pdb=" SG CYS D 96 " pdb=" HG CYS D 96 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" SG CYS D 192 " pdb=" HG CYS D 192 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" ND2 ASN E 108 " pdb="HD21 ASN E 108 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" ND2 ASN E 108 " pdb="HD22 ASN E 108 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" ND2 ASN D 193 " pdb="HD21 ASN D 193 " ideal model delta sigma weight residual 0.860 0.977 -0.117 2.00e-02 2.50e+03 3.40e+01 ... (remaining 22548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 40014 1.89 - 3.78: 497 3.78 - 5.66: 65 5.66 - 7.55: 9 7.55 - 9.44: 6 Bond angle restraints: 40591 Sorted by residual: angle pdb=" N ILE D 194 " pdb=" CA ILE D 194 " pdb=" C ILE D 194 " ideal model delta sigma weight residual 110.62 102.71 7.91 1.02e+00 9.61e-01 6.01e+01 angle pdb=" N LEU E 262 " pdb=" CA LEU E 262 " pdb=" C LEU E 262 " ideal model delta sigma weight residual 111.28 106.27 5.01 1.09e+00 8.42e-01 2.12e+01 angle pdb=" N THR D 109 " pdb=" CA THR D 109 " pdb=" CB THR D 109 " ideal model delta sigma weight residual 110.32 116.71 -6.39 1.70e+00 3.46e-01 1.41e+01 angle pdb=" N GLY E 264 " pdb=" CA GLY E 264 " pdb=" C GLY E 264 " ideal model delta sigma weight residual 112.77 108.12 4.65 1.28e+00 6.10e-01 1.32e+01 angle pdb=" N PHE D 94 " pdb=" CA PHE D 94 " pdb=" C PHE D 94 " ideal model delta sigma weight residual 111.28 107.38 3.90 1.09e+00 8.42e-01 1.28e+01 ... (remaining 40586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 9308 18.00 - 36.00: 883 36.00 - 54.00: 370 54.00 - 71.99: 103 71.99 - 89.99: 12 Dihedral angle restraints: 10676 sinusoidal: 5398 harmonic: 5278 Sorted by residual: dihedral pdb=" CA PHE C 90 " pdb=" C PHE C 90 " pdb=" N PRO C 91 " pdb=" CA PRO C 91 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA VAL C 158 " pdb=" C VAL C 158 " pdb=" N HIS C 159 " pdb=" CA HIS C 159 " ideal model delta harmonic sigma weight residual 180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA VAL E 213 " pdb=" C VAL E 213 " pdb=" N PHE E 214 " pdb=" CA PHE E 214 " ideal model delta harmonic sigma weight residual -180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 10673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1665 0.078 - 0.155: 81 0.155 - 0.233: 6 0.233 - 0.311: 3 0.311 - 0.388: 2 Chirality restraints: 1757 Sorted by residual: chirality pdb=" CA ASN D 193 " pdb=" N ASN D 193 " pdb=" C ASN D 193 " pdb=" CB ASN D 193 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA THR E 261 " pdb=" N THR E 261 " pdb=" C THR E 261 " pdb=" CB THR E 261 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA THR D 109 " pdb=" N THR D 109 " pdb=" C THR D 109 " pdb=" CB THR D 109 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1754 not shown) Planarity restraints: 3269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 108 " 0.192 2.00e-02 2.50e+03 1.92e-01 5.51e+02 pdb=" CG ASN E 108 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN E 108 " -0.180 2.00e-02 2.50e+03 pdb=" ND2 ASN E 108 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN E 108 " -0.272 2.00e-02 2.50e+03 pdb="HD22 ASN E 108 " 0.278 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 193 " 0.180 2.00e-02 2.50e+03 1.79e-01 4.79e+02 pdb=" CG ASN D 193 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN D 193 " -0.169 2.00e-02 2.50e+03 pdb=" ND2 ASN D 193 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN D 193 " 0.261 2.00e-02 2.50e+03 pdb="HD22 ASN D 193 " -0.250 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 265 " -0.068 2.00e-02 2.50e+03 6.66e-02 6.65e+01 pdb=" CG ASN E 265 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN E 265 " 0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN E 265 " -0.007 2.00e-02 2.50e+03 pdb="HD21 ASN E 265 " 0.094 2.00e-02 2.50e+03 pdb="HD22 ASN E 265 " -0.094 2.00e-02 2.50e+03 ... (remaining 3266 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1845 2.21 - 2.81: 47808 2.81 - 3.40: 67237 3.40 - 4.00: 89789 4.00 - 4.60: 137785 Nonbonded interactions: 344464 Sorted by model distance: nonbonded pdb=" O ASN B 257 " pdb=" HG1 THR B 261 " model vdw 1.611 2.450 nonbonded pdb=" O THR C 106 " pdb=" HG1 THR C 109 " model vdw 1.628 2.450 nonbonded pdb=" OE1 GLU C 229 " pdb="HD21 ASN C 234 " model vdw 1.634 2.450 nonbonded pdb=" OD1 ASN B 157 " pdb="HD22 ASN B 164 " model vdw 1.638 2.450 nonbonded pdb=" O CYS C 96 " pdb=" HG1 THR C 100 " model vdw 1.659 2.450 ... (remaining 344459 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 289 or resid 1001)) selection = (chain 'B' and (resid 12 through 289 or resid 401)) selection = (chain 'C' and (resid 12 through 289 or resid 401)) selection = (chain 'D' and (resid 12 through 289 or resid 401)) selection = (chain 'E' and resid 12 through 401) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 21.620 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 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 : 0.006 0.090 11424 Z= 0.349 Angle : 0.655 8.012 15507 Z= 0.369 Chirality : 0.042 0.388 1757 Planarity : 0.004 0.042 1886 Dihedral : 18.004 89.992 3862 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.20 % Allowed : 30.88 % Favored : 65.92 % 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: 1.25 (0.22), residues: 1396 helix: 1.49 (0.16), residues: 1108 sheet: None (None), residues: 0 loop : -1.73 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 290 TYR 0.018 0.001 TYR B 228 PHE 0.019 0.001 PHE E 223 HIS 0.011 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00608 (11424) covalent geometry : angle 0.65548 (15507) hydrogen bonds : bond 0.09672 ( 857) hydrogen bonds : angle 5.15258 ( 2559) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 373 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8331 (t) REVERT: A 83 VAL cc_start: 0.7988 (t) cc_final: 0.7713 (t) REVERT: B 279 PHE cc_start: 0.7429 (m-80) cc_final: 0.6323 (t80) REVERT: C 258 LEU cc_start: 0.7748 (mt) cc_final: 0.7344 (mt) REVERT: D 261 THR cc_start: 0.7959 (m) cc_final: 0.7748 (m) REVERT: E 158 VAL cc_start: 0.7326 (t) cc_final: 0.7108 (m) REVERT: E 283 GLU cc_start: 0.5389 (OUTLIER) cc_final: 0.4410 (mt-10) outliers start: 37 outliers final: 27 residues processed: 405 average time/residue: 0.5650 time to fit residues: 268.3119 Evaluate side-chains 384 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 355 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 283 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN D 257 ASN D 284 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.252589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.244206 restraints weight = 33285.379| |-----------------------------------------------------------------------------| r_work (start): 0.4813 rms_B_bonded: 0.79 r_work: 0.4825 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.4769 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work (final): 0.4769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11424 Z= 0.153 Angle : 0.522 6.156 15507 Z= 0.294 Chirality : 0.037 0.157 1757 Planarity : 0.003 0.045 1886 Dihedral : 8.287 87.849 1596 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.89 % Allowed : 29.50 % Favored : 66.61 % 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: 1.47 (0.22), residues: 1396 helix: 1.66 (0.15), residues: 1121 sheet: None (None), residues: 0 loop : -1.90 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 27 TYR 0.014 0.001 TYR C 38 PHE 0.020 0.001 PHE E 223 HIS 0.011 0.001 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00328 (11424) covalent geometry : angle 0.52209 (15507) hydrogen bonds : bond 0.04034 ( 857) hydrogen bonds : angle 4.41222 ( 2559) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 361 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 VAL cc_start: 0.8781 (OUTLIER) cc_final: 0.8468 (t) REVERT: A 202 PHE cc_start: 0.7653 (m-10) cc_final: 0.7269 (m-10) REVERT: B 165 HIS cc_start: 0.7657 (OUTLIER) cc_final: 0.7355 (p90) REVERT: B 175 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.6123 (mt-10) REVERT: B 223 PHE cc_start: 0.7371 (OUTLIER) cc_final: 0.7164 (t80) REVERT: B 279 PHE cc_start: 0.7518 (m-80) cc_final: 0.6572 (t80) REVERT: C 23 GLU cc_start: 0.6833 (mp0) cc_final: 0.6592 (mp0) REVERT: E 173 ILE cc_start: 0.8358 (mm) cc_final: 0.7974 (mt) outliers start: 45 outliers final: 31 residues processed: 391 average time/residue: 0.5764 time to fit residues: 264.0503 Evaluate side-chains 387 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 352 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 283 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 136 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS B 193 ASN D 157 ASN D 257 ASN D 284 HIS E 180 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.249342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.240882 restraints weight = 33099.707| |-----------------------------------------------------------------------------| r_work (start): 0.4786 rms_B_bonded: 0.79 r_work: 0.4797 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.4739 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work (final): 0.4739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11424 Z= 0.216 Angle : 0.559 5.256 15507 Z= 0.320 Chirality : 0.039 0.171 1757 Planarity : 0.004 0.048 1886 Dihedral : 7.761 86.533 1581 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.71 % Allowed : 27.68 % Favored : 66.61 % 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: 1.16 (0.22), residues: 1396 helix: 1.45 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -2.11 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 74 TYR 0.016 0.002 TYR C 38 PHE 0.021 0.002 PHE E 223 HIS 0.012 0.002 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00470 (11424) covalent geometry : angle 0.55912 (15507) hydrogen bonds : bond 0.04504 ( 857) hydrogen bonds : angle 4.46267 ( 2559) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 352 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 VAL cc_start: 0.8814 (OUTLIER) cc_final: 0.8500 (t) REVERT: A 163 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7134 (mtpt) REVERT: A 247 LYS cc_start: 0.6393 (OUTLIER) cc_final: 0.6123 (mppt) REVERT: B 175 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.6193 (mt-10) REVERT: B 279 PHE cc_start: 0.7582 (m-80) cc_final: 0.6587 (t80) REVERT: C 23 GLU cc_start: 0.7035 (mp0) cc_final: 0.6739 (mp0) REVERT: C 86 TYR cc_start: 0.7943 (t80) cc_final: 0.7428 (t80) REVERT: D 104 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7472 (mp) REVERT: E 283 GLU cc_start: 0.5362 (OUTLIER) cc_final: 0.4517 (mt-10) outliers start: 66 outliers final: 36 residues processed: 386 average time/residue: 0.5931 time to fit residues: 267.0084 Evaluate side-chains 380 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 338 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 283 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 39 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN B 40 ASN B 159 HIS B 193 ASN B 245 ASN D 157 ASN D 284 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.247405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.238842 restraints weight = 33260.547| |-----------------------------------------------------------------------------| r_work (start): 0.4768 rms_B_bonded: 0.80 r_work: 0.4780 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.4721 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work (final): 0.4721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 11424 Z= 0.273 Angle : 0.602 5.617 15507 Z= 0.347 Chirality : 0.041 0.180 1757 Planarity : 0.004 0.057 1886 Dihedral : 7.658 83.199 1577 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 6.06 % Allowed : 27.85 % Favored : 66.09 % 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: 0.74 (0.22), residues: 1396 helix: 1.14 (0.15), residues: 1122 sheet: None (None), residues: 0 loop : -2.12 (0.32), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 290 TYR 0.020 0.002 TYR B 212 PHE 0.021 0.002 PHE E 223 HIS 0.013 0.002 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00600 (11424) covalent geometry : angle 0.60194 (15507) hydrogen bonds : bond 0.04888 ( 857) hydrogen bonds : angle 4.57620 ( 2559) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 352 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7696 (mmt) cc_final: 0.7415 (mmm) REVERT: A 95 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7225 (mpp) REVERT: A 122 LYS cc_start: 0.6239 (OUTLIER) cc_final: 0.5825 (mptt) REVERT: A 163 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.7074 (mtpt) REVERT: A 247 LYS cc_start: 0.6405 (OUTLIER) cc_final: 0.6143 (mppt) REVERT: B 175 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.6189 (mt-10) REVERT: B 223 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7168 (t80) REVERT: B 279 PHE cc_start: 0.7644 (m-80) cc_final: 0.6603 (t80) REVERT: C 23 GLU cc_start: 0.7166 (mp0) cc_final: 0.6903 (mp0) REVERT: C 86 TYR cc_start: 0.8030 (t80) cc_final: 0.7524 (t80) REVERT: D 104 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7532 (mp) REVERT: E 86 TYR cc_start: 0.7937 (t80) cc_final: 0.7416 (t80) REVERT: E 173 ILE cc_start: 0.8392 (mm) cc_final: 0.8005 (mt) REVERT: E 283 GLU cc_start: 0.5511 (OUTLIER) cc_final: 0.4378 (mm-30) outliers start: 70 outliers final: 43 residues processed: 389 average time/residue: 0.5868 time to fit residues: 266.6760 Evaluate side-chains 395 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 344 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 283 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 63 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 193 ASN B 245 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.248719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.240289 restraints weight = 33205.285| |-----------------------------------------------------------------------------| r_work (start): 0.4774 rms_B_bonded: 0.80 r_work: 0.4783 rms_B_bonded: 1.02 restraints_weight: 0.5000 r_work: 0.4724 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work (final): 0.4724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 11424 Z= 0.208 Angle : 0.551 5.319 15507 Z= 0.316 Chirality : 0.038 0.167 1757 Planarity : 0.004 0.042 1886 Dihedral : 7.446 80.076 1577 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 6.06 % Allowed : 27.94 % Favored : 66.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.95 (0.22), residues: 1396 helix: 1.31 (0.15), residues: 1124 sheet: None (None), residues: 0 loop : -2.17 (0.32), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 290 TYR 0.016 0.002 TYR D 236 PHE 0.021 0.002 PHE E 223 HIS 0.013 0.002 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00455 (11424) covalent geometry : angle 0.55112 (15507) hydrogen bonds : bond 0.04426 ( 857) hydrogen bonds : angle 4.45830 ( 2559) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 352 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7685 (mmt) cc_final: 0.7483 (mmm) REVERT: A 95 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7176 (mpp) REVERT: A 163 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7203 (mtpt) REVERT: A 245 ASN cc_start: 0.7525 (t0) cc_final: 0.7323 (t0) REVERT: A 247 LYS cc_start: 0.6399 (OUTLIER) cc_final: 0.6146 (mppt) REVERT: B 175 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.6122 (mt-10) REVERT: B 223 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7021 (t80) REVERT: B 279 PHE cc_start: 0.7633 (m-80) cc_final: 0.6587 (t80) REVERT: C 23 GLU cc_start: 0.7056 (mp0) cc_final: 0.6699 (mp0) REVERT: C 86 TYR cc_start: 0.8090 (t80) cc_final: 0.7497 (t80) REVERT: D 104 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7470 (mp) REVERT: E 86 TYR cc_start: 0.7956 (t80) cc_final: 0.7438 (t80) REVERT: E 283 GLU cc_start: 0.5311 (OUTLIER) cc_final: 0.4467 (mt-10) outliers start: 70 outliers final: 40 residues processed: 388 average time/residue: 0.5673 time to fit residues: 257.5554 Evaluate side-chains 389 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 342 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 283 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 62 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 11 optimal weight: 0.3980 chunk 8 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 overall best weight: 6.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS B 193 ASN B 245 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.247650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.239117 restraints weight = 33261.352| |-----------------------------------------------------------------------------| r_work (start): 0.4761 rms_B_bonded: 0.80 r_work: 0.4769 rms_B_bonded: 1.02 restraints_weight: 0.5000 r_work: 0.4711 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work (final): 0.4711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 11424 Z= 0.257 Angle : 0.593 5.390 15507 Z= 0.341 Chirality : 0.041 0.171 1757 Planarity : 0.004 0.054 1886 Dihedral : 7.523 79.690 1576 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 6.40 % Allowed : 27.85 % Favored : 65.74 % 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: 0.72 (0.22), residues: 1396 helix: 1.12 (0.15), residues: 1121 sheet: None (None), residues: 0 loop : -2.11 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 290 TYR 0.019 0.002 TYR B 212 PHE 0.021 0.002 PHE E 223 HIS 0.013 0.002 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00566 (11424) covalent geometry : angle 0.59260 (15507) hydrogen bonds : bond 0.04797 ( 857) hydrogen bonds : angle 4.56319 ( 2559) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 348 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7712 (mmt) cc_final: 0.7478 (mmm) REVERT: A 95 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7191 (mpp) REVERT: A 163 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7191 (mtpt) REVERT: A 247 LYS cc_start: 0.6407 (OUTLIER) cc_final: 0.6141 (mppt) REVERT: B 175 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.6151 (mt-10) REVERT: B 223 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7093 (t80) REVERT: B 279 PHE cc_start: 0.7693 (m-80) cc_final: 0.6591 (t80) REVERT: C 23 GLU cc_start: 0.7067 (mp0) cc_final: 0.6668 (mp0) REVERT: C 86 TYR cc_start: 0.8193 (t80) cc_final: 0.7569 (t80) REVERT: E 86 TYR cc_start: 0.8021 (t80) cc_final: 0.7497 (t80) REVERT: E 283 GLU cc_start: 0.5433 (OUTLIER) cc_final: 0.4290 (mm-30) outliers start: 74 outliers final: 48 residues processed: 387 average time/residue: 0.5744 time to fit residues: 260.6249 Evaluate side-chains 395 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 341 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 284 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 65 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 117 optimal weight: 0.8980 chunk 138 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 overall best weight: 6.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 193 ASN B 245 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.247339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.238830 restraints weight = 33166.344| |-----------------------------------------------------------------------------| r_work (start): 0.4761 rms_B_bonded: 0.80 r_work: 0.4770 rms_B_bonded: 1.02 restraints_weight: 0.5000 r_work: 0.4711 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work (final): 0.4711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 11424 Z= 0.265 Angle : 0.599 6.075 15507 Z= 0.345 Chirality : 0.041 0.170 1757 Planarity : 0.004 0.053 1886 Dihedral : 7.531 77.809 1576 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 6.14 % Allowed : 28.29 % Favored : 65.57 % 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: 0.64 (0.22), residues: 1396 helix: 1.06 (0.15), residues: 1121 sheet: None (None), residues: 0 loop : -2.10 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 290 TYR 0.018 0.002 TYR D 236 PHE 0.021 0.002 PHE E 223 HIS 0.013 0.002 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00584 (11424) covalent geometry : angle 0.59923 (15507) hydrogen bonds : bond 0.04816 ( 857) hydrogen bonds : angle 4.58872 ( 2559) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 349 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7747 (mmt) cc_final: 0.7518 (mmm) REVERT: A 95 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7198 (mpp) REVERT: A 163 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7132 (mtpt) REVERT: A 247 LYS cc_start: 0.6410 (OUTLIER) cc_final: 0.6139 (mppt) REVERT: B 175 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.6141 (mt-10) REVERT: B 223 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.7146 (t80) REVERT: B 279 PHE cc_start: 0.7697 (m-80) cc_final: 0.6615 (t80) REVERT: C 23 GLU cc_start: 0.7042 (mp0) cc_final: 0.6658 (mp0) REVERT: C 86 TYR cc_start: 0.8202 (t80) cc_final: 0.7596 (t80) REVERT: E 22 GLU cc_start: 0.7297 (pt0) cc_final: 0.6934 (pt0) REVERT: E 86 TYR cc_start: 0.8038 (t80) cc_final: 0.7464 (t80) REVERT: E 283 GLU cc_start: 0.5449 (OUTLIER) cc_final: 0.4297 (mm-30) outliers start: 71 outliers final: 44 residues processed: 385 average time/residue: 0.5771 time to fit residues: 260.2730 Evaluate side-chains 391 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 341 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 284 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 94 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.247463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.238942 restraints weight = 32988.298| |-----------------------------------------------------------------------------| r_work (start): 0.4767 rms_B_bonded: 0.80 r_work: 0.4777 rms_B_bonded: 1.02 restraints_weight: 0.5000 r_work: 0.4720 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work (final): 0.4720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 11424 Z= 0.254 Angle : 0.598 5.865 15507 Z= 0.344 Chirality : 0.041 0.170 1757 Planarity : 0.004 0.051 1886 Dihedral : 7.510 76.930 1576 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 6.40 % Allowed : 28.55 % Favored : 65.05 % 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: 0.67 (0.22), residues: 1396 helix: 1.09 (0.15), residues: 1121 sheet: None (None), residues: 0 loop : -2.13 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 290 TYR 0.022 0.002 TYR B 286 PHE 0.025 0.002 PHE A 202 HIS 0.013 0.002 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00558 (11424) covalent geometry : angle 0.59821 (15507) hydrogen bonds : bond 0.04774 ( 857) hydrogen bonds : angle 4.57028 ( 2559) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 347 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7737 (mmt) cc_final: 0.7459 (mmm) REVERT: A 95 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7180 (mpp) REVERT: A 163 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7182 (mtpt) REVERT: A 247 LYS cc_start: 0.6421 (OUTLIER) cc_final: 0.6156 (mppt) REVERT: B 175 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.6146 (mt-10) REVERT: B 223 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7080 (t80) REVERT: B 279 PHE cc_start: 0.7702 (m-80) cc_final: 0.6619 (t80) REVERT: C 23 GLU cc_start: 0.7027 (mp0) cc_final: 0.6651 (mp0) REVERT: C 86 TYR cc_start: 0.8249 (t80) cc_final: 0.7683 (t80) REVERT: E 22 GLU cc_start: 0.7270 (pt0) cc_final: 0.6920 (pt0) REVERT: E 86 TYR cc_start: 0.8039 (t80) cc_final: 0.7798 (t80) REVERT: E 283 GLU cc_start: 0.5496 (OUTLIER) cc_final: 0.4378 (mm-30) outliers start: 74 outliers final: 50 residues processed: 390 average time/residue: 0.5939 time to fit residues: 271.9495 Evaluate side-chains 398 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 342 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 284 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 85 optimal weight: 10.0000 chunk 42 optimal weight: 0.0170 chunk 58 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 overall best weight: 5.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.248188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.239657 restraints weight = 33165.718| |-----------------------------------------------------------------------------| r_work (start): 0.4772 rms_B_bonded: 0.80 r_work: 0.4785 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.4727 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work (final): 0.4727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 11424 Z= 0.236 Angle : 0.587 5.936 15507 Z= 0.337 Chirality : 0.040 0.168 1757 Planarity : 0.004 0.048 1886 Dihedral : 7.401 76.946 1576 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.62 % Allowed : 28.89 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.22), residues: 1396 helix: 1.15 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -2.12 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 290 TYR 0.018 0.002 TYR D 236 PHE 0.032 0.002 PHE A 202 HIS 0.013 0.002 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00518 (11424) covalent geometry : angle 0.58676 (15507) hydrogen bonds : bond 0.04663 ( 857) hydrogen bonds : angle 4.54547 ( 2559) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 349 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7735 (mmt) cc_final: 0.7458 (mmm) REVERT: A 95 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7133 (mpp) REVERT: A 163 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7155 (mtpt) REVERT: A 247 LYS cc_start: 0.6423 (OUTLIER) cc_final: 0.6174 (mppt) REVERT: B 175 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.6164 (mt-10) REVERT: B 223 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.7096 (t80) REVERT: B 279 PHE cc_start: 0.7685 (m-80) cc_final: 0.6613 (t80) REVERT: C 23 GLU cc_start: 0.6968 (mp0) cc_final: 0.6605 (mp0) REVERT: C 86 TYR cc_start: 0.8261 (t80) cc_final: 0.7660 (t80) REVERT: E 22 GLU cc_start: 0.7268 (pt0) cc_final: 0.6916 (pt0) REVERT: E 86 TYR cc_start: 0.8039 (t80) cc_final: 0.7772 (t80) REVERT: E 283 GLU cc_start: 0.5399 (OUTLIER) cc_final: 0.4280 (mm-30) outliers start: 65 outliers final: 47 residues processed: 383 average time/residue: 0.5889 time to fit residues: 264.6351 Evaluate side-chains 394 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 341 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 284 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 36 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 193 ASN B 245 ASN ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.235969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.228834 restraints weight = 31510.098| |-----------------------------------------------------------------------------| r_work (start): 0.4676 rms_B_bonded: 0.87 r_work: 0.4623 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.4555 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.4555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11424 Z= 0.200 Angle : 0.562 6.339 15507 Z= 0.322 Chirality : 0.038 0.163 1757 Planarity : 0.004 0.041 1886 Dihedral : 7.211 78.100 1575 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.67 % Allowed : 30.10 % Favored : 65.22 % 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: 0.96 (0.22), residues: 1396 helix: 1.31 (0.15), residues: 1122 sheet: None (None), residues: 0 loop : -2.17 (0.32), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 290 TYR 0.024 0.002 TYR B 286 PHE 0.034 0.002 PHE A 202 HIS 0.012 0.002 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00437 (11424) covalent geometry : angle 0.56198 (15507) hydrogen bonds : bond 0.04394 ( 857) hydrogen bonds : angle 4.46725 ( 2559) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 344 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7850 (mmt) cc_final: 0.7561 (mmm) REVERT: A 95 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7291 (mpp) REVERT: A 122 LYS cc_start: 0.6070 (OUTLIER) cc_final: 0.5541 (mptt) REVERT: A 163 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7175 (mtpt) REVERT: A 247 LYS cc_start: 0.6453 (OUTLIER) cc_final: 0.6189 (mppt) REVERT: B 175 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.6186 (mt-10) REVERT: B 223 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7006 (t80) REVERT: B 279 PHE cc_start: 0.7671 (m-80) cc_final: 0.6595 (t80) REVERT: C 23 GLU cc_start: 0.7005 (mp0) cc_final: 0.6670 (mp0) REVERT: C 86 TYR cc_start: 0.8250 (t80) cc_final: 0.7667 (t80) REVERT: E 22 GLU cc_start: 0.7273 (pt0) cc_final: 0.6892 (pt0) REVERT: E 86 TYR cc_start: 0.8064 (t80) cc_final: 0.7823 (t80) outliers start: 54 outliers final: 40 residues processed: 372 average time/residue: 0.5885 time to fit residues: 257.3554 Evaluate side-chains 389 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 343 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 33 LYS Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 284 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS B 193 ASN B 245 ASN ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.234735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.227559 restraints weight = 31382.393| |-----------------------------------------------------------------------------| r_work (start): 0.4664 rms_B_bonded: 0.86 r_work: 0.4613 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.4545 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.4545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 11424 Z= 0.249 Angle : 0.597 6.484 15507 Z= 0.343 Chirality : 0.040 0.168 1757 Planarity : 0.004 0.051 1886 Dihedral : 6.985 78.933 1572 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.02 % Allowed : 30.02 % Favored : 64.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.72 (0.22), residues: 1396 helix: 1.14 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -2.18 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 290 TYR 0.019 0.002 TYR E 221 PHE 0.035 0.002 PHE A 202 HIS 0.013 0.002 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00547 (11424) covalent geometry : angle 0.59696 (15507) hydrogen bonds : bond 0.04738 ( 857) hydrogen bonds : angle 4.55675 ( 2559) =============================================================================== Job complete usr+sys time: 7377.96 seconds wall clock time: 125 minutes 40.90 seconds (7540.90 seconds total)