Starting phenix.real_space_refine on Wed Mar 4 05:43:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vqr_21355/03_2026/6vqr_21355.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vqr_21355/03_2026/6vqr_21355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vqr_21355/03_2026/6vqr_21355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vqr_21355/03_2026/6vqr_21355.map" model { file = "/net/cci-nas-00/data/ceres_data/6vqr_21355/03_2026/6vqr_21355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vqr_21355/03_2026/6vqr_21355.cif" } resolution = 2.78 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= 0.312 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: 5 Type Number sf(0) Gaussians S 70 5.16 5 C 7482 2.51 5 N 1744 2.21 5 O 1933 1.98 5 F 25 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 11254 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2205 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 3, 'TRANS': 277} Chain: "B" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2240 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "C" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2213 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 4, 'TRANS': 277} Chain: "D" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2228 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 4, 'TRANS': 279} Chain: "E" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2263 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 4, 'TRANS': 283} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'R7M': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'R7M': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'R7M': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'R7M': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'R7M': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.70, per 1000 atoms: 0.24 Number of scatterers: 11254 At special positions: 0 Unit cell: (90.72, 99.36, 97.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 F 25 9.00 O 1933 8.00 N 1744 7.00 C 7482 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 553.4 milliseconds 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2620 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 2 sheets defined 81.5% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 21 through 35 removed outlier: 4.037A pdb=" N LYS A 35 " --> pdb=" O TYR A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 38 No H-bonds generated for 'chain 'A' and resid 36 through 38' Processing helix chain 'A' and resid 39 through 68 removed outlier: 3.726A pdb=" N LEU A 44 " --> pdb=" O ASN A 40 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 78 removed outlier: 3.722A pdb=" N GLU A 75 " --> pdb=" O HIS A 71 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 removed outlier: 3.743A pdb=" N VAL A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.378A pdb=" N MET A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 119 removed outlier: 4.063A pdb=" N LEU A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 148 removed outlier: 3.664A pdb=" N PHE A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 177 removed outlier: 3.910A pdb=" N LEU A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 206 removed outlier: 3.663A pdb=" N LEU A 204 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 226 removed outlier: 3.551A pdb=" N ALA A 226 " --> pdb=" O ALA A 222 " (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 281 removed outlier: 3.544A pdb=" N TYR A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 removed outlier: 4.092A pdb=" N TYR A 285 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR A 286 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 35 removed outlier: 3.990A pdb=" N LYS B 35 " --> pdb=" O TYR B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 68 Processing helix chain 'B' and resid 70 through 78 removed outlier: 3.552A pdb=" N ARG B 74 " --> pdb=" O TYR B 70 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU B 75 " --> pdb=" O HIS B 71 " (cutoff:3.500A) removed outlier: 4.538A 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 101 removed outlier: 4.169A pdb=" N MET B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 118 removed outlier: 4.526A pdb=" N LEU B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B 118 " --> pdb=" O MET B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 148 Processing helix chain 'B' and resid 164 through 179 removed outlier: 4.024A pdb=" N LEU B 170 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 207 removed outlier: 4.112A pdb=" N LYS B 207 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 226 Processing helix chain 'B' and resid 230 through 245 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 257 through 271 removed outlier: 3.530A pdb=" N THR B 261 " --> pdb=" O ASN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 296 removed outlier: 5.676A pdb=" N GLU B 283 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N HIS B 284 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 35 removed outlier: 3.932A pdb=" N TYR C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 68 removed outlier: 3.648A pdb=" N PHE C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 78 removed outlier: 4.057A pdb=" N ILE C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.548A pdb=" N VAL C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 99 removed outlier: 4.307A pdb=" N MET C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 118 removed outlier: 4.809A pdb=" N LEU C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 148 removed outlier: 3.533A pdb=" N VAL C 148 " --> pdb=" O PHE C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 176 removed outlier: 4.155A pdb=" N LEU C 170 " --> pdb=" O PHE C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 206 removed outlier: 3.543A pdb=" N CYS C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 226 removed outlier: 4.065A pdb=" N VAL C 216 " --> pdb=" O TYR C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 244 Processing helix chain 'C' and resid 249 through 255 Processing helix chain 'C' and resid 257 through 271 Processing helix chain 'C' and resid 274 through 281 Processing helix chain 'C' and resid 281 through 290 removed outlier: 3.505A pdb=" N TYR C 285 " --> pdb=" O TYR C 281 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR C 286 " --> pdb=" O LYS C 282 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE C 288 " --> pdb=" O HIS C 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 35 Processing helix chain 'D' and resid 39 through 68 Processing helix chain 'D' and resid 70 through 78 removed outlier: 3.833A pdb=" N GLU D 75 " --> pdb=" O HIS D 71 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 90 removed outlier: 3.563A pdb=" N VAL D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 100 removed outlier: 3.528A pdb=" N CYS D 96 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR D 100 " --> pdb=" O CYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 118 removed outlier: 3.547A pdb=" N ASN D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 148 Processing helix chain 'D' and resid 166 through 179 removed outlier: 3.558A pdb=" N LEU D 170 " --> pdb=" O PHE D 166 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 207 removed outlier: 3.780A pdb=" N VAL D 203 " --> pdb=" O ALA D 199 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU D 204 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR D 205 " --> pdb=" O TYR D 201 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS D 207 " --> pdb=" O VAL D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 227 removed outlier: 3.713A pdb=" N GLY D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 250 through 255 Processing helix chain 'D' and resid 257 through 271 Processing helix chain 'D' and resid 273 through 281 removed outlier: 3.545A pdb=" N LEU D 277 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 291 removed outlier: 3.943A pdb=" N PHE D 288 " --> pdb=" O HIS D 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 36 removed outlier: 4.028A pdb=" N ALA E 36 " --> pdb=" O GLY E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 68 removed outlier: 3.640A pdb=" N LEU E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU E 44 " --> pdb=" O ASN E 40 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA E 45 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 78 Processing helix chain 'E' and resid 80 through 90 Processing helix chain 'E' and resid 91 through 101 removed outlier: 4.336A pdb=" N MET E 95 " --> pdb=" O PRO E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 118 removed outlier: 3.906A pdb=" N ASN E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR E 109 " --> pdb=" O PHE E 105 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR E 113 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET E 114 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 148 Processing helix chain 'E' and resid 164 through 179 removed outlier: 3.589A pdb=" N PHE E 169 " --> pdb=" O HIS E 165 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 206 Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.024A pdb=" N SER E 215 " --> pdb=" O GLY E 211 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL E 216 " --> pdb=" O TYR E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 244 Processing helix chain 'E' and resid 257 through 271 Processing helix chain 'E' and resid 274 through 290 removed outlier: 5.661A pdb=" N GLU E 283 " --> pdb=" O PHE E 279 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N HIS E 284 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 15 through 16 Processing sheet with id=AA2, first strand: chain 'C' and resid 15 through 16 795 hydrogen bonds defined for protein. 2382 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: 1.88 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.25: 1683 1.25 - 1.39: 3321 1.39 - 1.53: 6117 1.53 - 1.67: 328 1.67 - 1.81: 100 Bond restraints: 11549 Sorted by residual: bond pdb=" C19 R7M C 401 " pdb=" C20 R7M C 401 " ideal model delta sigma weight residual 1.402 1.115 0.287 2.00e-02 2.50e+03 2.06e+02 bond pdb=" C19 R7M D 401 " pdb=" C20 R7M D 401 " ideal model delta sigma weight residual 1.402 1.117 0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C13 R7M D 401 " pdb=" C14 R7M D 401 " ideal model delta sigma weight residual 1.460 1.186 0.274 2.00e-02 2.50e+03 1.88e+02 bond pdb=" C13 R7M C 401 " pdb=" C14 R7M C 401 " ideal model delta sigma weight residual 1.460 1.190 0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C19 R7M B 401 " pdb=" C20 R7M B 401 " ideal model delta sigma weight residual 1.402 1.138 0.264 2.00e-02 2.50e+03 1.75e+02 ... (remaining 11544 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 15345 2.81 - 5.62: 274 5.62 - 8.42: 44 8.42 - 11.23: 13 11.23 - 14.04: 8 Bond angle restraints: 15684 Sorted by residual: angle pdb=" N VAL E 77 " pdb=" CA VAL E 77 " pdb=" C VAL E 77 " ideal model delta sigma weight residual 110.72 121.64 -10.92 1.01e+00 9.80e-01 1.17e+02 angle pdb=" N LYS A 120 " pdb=" CA LYS A 120 " pdb=" C LYS A 120 " ideal model delta sigma weight residual 111.07 120.98 -9.91 1.07e+00 8.73e-01 8.58e+01 angle pdb=" N ALA B 270 " pdb=" CA ALA B 270 " pdb=" C ALA B 270 " ideal model delta sigma weight residual 111.36 118.40 -7.04 1.09e+00 8.42e-01 4.17e+01 angle pdb=" N ASN B 108 " pdb=" CA ASN B 108 " pdb=" C ASN B 108 " ideal model delta sigma weight residual 111.07 117.85 -6.78 1.07e+00 8.73e-01 4.01e+01 angle pdb=" N SER B 80 " pdb=" CA SER B 80 " pdb=" C SER B 80 " ideal model delta sigma weight residual 111.07 117.69 -6.62 1.07e+00 8.73e-01 3.82e+01 ... (remaining 15679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.45: 5846 21.45 - 42.89: 657 42.89 - 64.34: 93 64.34 - 85.79: 8 85.79 - 107.23: 13 Dihedral angle restraints: 6617 sinusoidal: 2472 harmonic: 4145 Sorted by residual: dihedral pdb=" N LYS A 119 " pdb=" C LYS A 119 " pdb=" CA LYS A 119 " pdb=" CB LYS A 119 " ideal model delta harmonic sigma weight residual 122.80 137.16 -14.36 0 2.50e+00 1.60e-01 3.30e+01 dihedral pdb=" C LYS A 119 " pdb=" N LYS A 119 " pdb=" CA LYS A 119 " pdb=" CB LYS A 119 " ideal model delta harmonic sigma weight residual -122.60 -135.06 12.46 0 2.50e+00 1.60e-01 2.48e+01 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 -156.16 -23.84 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 6614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1669 0.099 - 0.198: 86 0.198 - 0.297: 14 0.297 - 0.396: 5 0.396 - 0.495: 2 Chirality restraints: 1776 Sorted by residual: chirality pdb=" CA LYS A 119 " pdb=" N LYS A 119 " pdb=" C LYS A 119 " pdb=" CB LYS A 119 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.14e+00 chirality pdb=" CA ALA D 79 " pdb=" N ALA D 79 " pdb=" C ALA D 79 " pdb=" CB ALA D 79 " both_signs ideal model delta sigma weight residual False 2.48 2.03 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CA LYS C 256 " pdb=" N LYS C 256 " pdb=" C LYS C 256 " pdb=" CB LYS C 256 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.89e+00 ... (remaining 1773 not shown) Planarity restraints: 1904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 269 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C GLY B 269 " -0.065 2.00e-02 2.50e+03 pdb=" O GLY B 269 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA B 270 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 38 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.15e+00 pdb=" C TYR B 38 " -0.052 2.00e-02 2.50e+03 pdb=" O TYR B 38 " 0.019 2.00e-02 2.50e+03 pdb=" N SER B 39 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 105 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C PHE A 105 " -0.046 2.00e-02 2.50e+03 pdb=" O PHE A 105 " 0.017 2.00e-02 2.50e+03 pdb=" N THR A 106 " 0.015 2.00e-02 2.50e+03 ... (remaining 1901 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 135 2.60 - 3.17: 10469 3.17 - 3.75: 17751 3.75 - 4.32: 25949 4.32 - 4.90: 42847 Nonbonded interactions: 97151 Sorted by model distance: nonbonded pdb=" F05 R7M C 401 " pdb=" O07 R7M C 401 " model vdw 2.021 2.990 nonbonded pdb=" F05 R7M E 401 " pdb=" O07 R7M E 401 " model vdw 2.129 2.990 nonbonded pdb=" F05 R7M A 401 " pdb=" O07 R7M A 401 " model vdw 2.134 2.990 nonbonded pdb=" F05 R7M B 401 " pdb=" O07 R7M B 401 " model vdw 2.137 2.990 nonbonded pdb=" O SER A 17 " pdb=" OG SER A 17 " model vdw 2.213 3.040 ... (remaining 97146 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 290 or resid 401)) selection = (chain 'B' and (resid 12 through 290 or resid 401)) selection = (chain 'C' and resid 12 through 401) selection = (chain 'D' and (resid 12 through 290 or resid 401)) selection = (chain 'E' and (resid 12 through 290 or resid 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: 0.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.220 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 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:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 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 : 0.013 0.287 11549 Z= 0.669 Angle : 0.969 14.040 15684 Z= 0.538 Chirality : 0.058 0.495 1776 Planarity : 0.005 0.058 1904 Dihedral : 17.675 107.234 3997 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 8.21 % Allowed : 25.21 % Favored : 66.58 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.20), residues: 1410 helix: -1.20 (0.14), residues: 1086 sheet: None (None), residues: 0 loop : -3.68 (0.28), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 293 TYR 0.018 0.002 TYR C 212 PHE 0.021 0.002 PHE B 223 HIS 0.008 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.01340 (11549) covalent geometry : angle 0.96866 (15684) hydrogen bonds : bond 0.13674 ( 795) hydrogen bonds : angle 6.39368 ( 2382) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 301 time to evaluate : 0.397 Fit side-chains REVERT: A 33 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6829 (pptt) REVERT: A 72 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8033 (mmtp) REVERT: A 81 MET cc_start: 0.7225 (mmm) cc_final: 0.6968 (mmm) REVERT: A 95 MET cc_start: 0.7731 (mmm) cc_final: 0.7465 (tpp) REVERT: A 147 PHE cc_start: 0.7520 (m-80) cc_final: 0.7093 (m-80) REVERT: A 212 TYR cc_start: 0.7018 (OUTLIER) cc_final: 0.6214 (m-10) REVERT: A 273 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8566 (tp) REVERT: A 282 LYS cc_start: 0.7476 (tttt) cc_final: 0.7244 (ttmt) REVERT: A 290 ARG cc_start: 0.7049 (mmm-85) cc_final: 0.6752 (mmm160) REVERT: B 164 ASN cc_start: 0.8514 (t0) cc_final: 0.8286 (t160) REVERT: B 202 PHE cc_start: 0.8149 (m-10) cc_final: 0.7889 (m-10) REVERT: B 247 LYS cc_start: 0.7025 (ttmm) cc_final: 0.6818 (ttmm) REVERT: B 251 TYR cc_start: 0.6228 (m-80) cc_final: 0.5973 (m-80) REVERT: C 81 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.6585 (mtp) REVERT: C 201 TYR cc_start: 0.7855 (t80) cc_final: 0.7569 (t80) REVERT: D 33 LYS cc_start: 0.7015 (tmtm) cc_final: 0.6715 (tmtt) REVERT: D 35 LYS cc_start: 0.7907 (tptt) cc_final: 0.7698 (tptp) REVERT: D 106 THR cc_start: 0.8884 (m) cc_final: 0.8466 (p) REVERT: D 120 LYS cc_start: 0.7832 (mmmt) cc_final: 0.7430 (mptt) REVERT: D 271 ILE cc_start: 0.8563 (mm) cc_final: 0.8248 (mp) REVERT: E 33 LYS cc_start: 0.7845 (tttt) cc_final: 0.7532 (tttm) REVERT: E 35 LYS cc_start: 0.8432 (ttmm) cc_final: 0.8158 (mtpp) REVERT: E 52 MET cc_start: 0.7111 (tpp) cc_final: 0.6778 (tpp) REVERT: E 72 LYS cc_start: 0.7102 (mmtt) cc_final: 0.6822 (mmtm) REVERT: E 83 VAL cc_start: 0.8634 (t) cc_final: 0.8391 (t) REVERT: E 95 MET cc_start: 0.6499 (mpp) cc_final: 0.6194 (mpp) REVERT: E 162 GLU cc_start: 0.7478 (mm-30) cc_final: 0.5979 (mm-30) REVERT: E 185 CYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6724 (t) outliers start: 96 outliers final: 58 residues processed: 377 average time/residue: 0.3359 time to fit residues: 143.1667 Evaluate side-chains 333 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 270 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 HIS B 165 HIS B 193 ASN ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN C 137 ASN C 239 ASN D 40 ASN D 59 HIS D 171 ASN E 59 HIS ** E 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.168758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.153465 restraints weight = 13854.995| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.84 r_work: 0.3722 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11549 Z= 0.168 Angle : 0.635 8.785 15684 Z= 0.337 Chirality : 0.043 0.189 1776 Planarity : 0.004 0.038 1904 Dihedral : 12.898 95.929 1758 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 6.32 % Allowed : 27.09 % Favored : 66.58 % 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: 1410 helix: 0.19 (0.15), residues: 1100 sheet: None (None), residues: 0 loop : -3.50 (0.28), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 290 TYR 0.023 0.002 TYR E 31 PHE 0.022 0.002 PHE B 279 HIS 0.006 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00374 (11549) covalent geometry : angle 0.63471 (15684) hydrogen bonds : bond 0.05218 ( 795) hydrogen bonds : angle 4.71358 ( 2382) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 255 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8243 (mmtp) REVERT: A 81 MET cc_start: 0.8202 (mmm) cc_final: 0.7958 (mmm) REVERT: A 95 MET cc_start: 0.7944 (mmm) cc_final: 0.7441 (tpp) REVERT: A 116 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8051 (tp) REVERT: A 202 PHE cc_start: 0.7175 (m-10) cc_final: 0.6861 (m-10) REVERT: A 273 LEU cc_start: 0.8831 (mt) cc_final: 0.8476 (tp) REVERT: A 282 LYS cc_start: 0.7705 (tttt) cc_final: 0.7397 (ttmm) REVERT: A 290 ARG cc_start: 0.7065 (mmm-85) cc_final: 0.6857 (mmm160) REVERT: B 30 GLU cc_start: 0.8140 (tp30) cc_final: 0.7885 (mm-30) REVERT: B 194 ILE cc_start: 0.7992 (mt) cc_final: 0.7667 (mm) REVERT: B 201 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.6673 (m-80) REVERT: B 279 PHE cc_start: 0.8414 (t80) cc_final: 0.8211 (OUTLIER) REVERT: C 16 LYS cc_start: 0.7839 (ttpm) cc_final: 0.7565 (ttpp) REVERT: C 122 LYS cc_start: 0.7250 (mmmt) cc_final: 0.6895 (tptt) REVERT: C 134 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7164 (tt) REVERT: D 72 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7565 (mttp) REVERT: D 163 LYS cc_start: 0.8314 (mptt) cc_final: 0.7992 (mptt) REVERT: D 198 LEU cc_start: 0.8066 (mp) cc_final: 0.7750 (mp) REVERT: D 232 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7781 (mm) REVERT: D 271 ILE cc_start: 0.8489 (mm) cc_final: 0.8164 (mp) REVERT: D 289 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6836 (mp0) REVERT: E 33 LYS cc_start: 0.7710 (tttt) cc_final: 0.7464 (tttp) REVERT: E 37 HIS cc_start: 0.7726 (OUTLIER) cc_final: 0.7211 (t-90) REVERT: E 52 MET cc_start: 0.7261 (tpp) cc_final: 0.6885 (tpp) REVERT: E 72 LYS cc_start: 0.7212 (mmtt) cc_final: 0.6926 (mmtm) REVERT: E 95 MET cc_start: 0.6653 (mpp) cc_final: 0.6390 (mpp) REVERT: E 212 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.7375 (m-80) REVERT: E 217 PHE cc_start: 0.7673 (t80) cc_final: 0.7281 (t80) outliers start: 74 outliers final: 43 residues processed: 305 average time/residue: 0.3258 time to fit residues: 112.7941 Evaluate side-chains 292 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 242 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 98 optimal weight: 0.0030 chunk 76 optimal weight: 20.0000 chunk 2 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 overall best weight: 4.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.169755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.154633 restraints weight = 13996.305| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.77 r_work: 0.3744 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11549 Z= 0.159 Angle : 0.597 7.443 15684 Z= 0.319 Chirality : 0.041 0.173 1776 Planarity : 0.003 0.037 1904 Dihedral : 11.569 95.433 1693 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 7.18 % Allowed : 27.18 % Favored : 65.64 % 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: -0.22 (0.22), residues: 1410 helix: 0.70 (0.16), residues: 1112 sheet: None (None), residues: 0 loop : -3.33 (0.28), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 290 TYR 0.020 0.001 TYR E 31 PHE 0.022 0.001 PHE A 288 HIS 0.010 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00352 (11549) covalent geometry : angle 0.59745 (15684) hydrogen bonds : bond 0.04953 ( 795) hydrogen bonds : angle 4.50812 ( 2382) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 236 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8575 (mmtt) cc_final: 0.8177 (mmtp) REVERT: A 81 MET cc_start: 0.8136 (mmm) cc_final: 0.7889 (mmm) REVERT: A 116 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8078 (tp) REVERT: A 202 PHE cc_start: 0.7161 (m-10) cc_final: 0.6821 (m-10) REVERT: A 212 TYR cc_start: 0.6403 (OUTLIER) cc_final: 0.6148 (m-10) REVERT: A 273 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8451 (tp) REVERT: A 282 LYS cc_start: 0.7635 (tttt) cc_final: 0.7301 (ttmm) REVERT: B 88 PHE cc_start: 0.8137 (t80) cc_final: 0.7703 (t80) REVERT: B 194 ILE cc_start: 0.7984 (mt) cc_final: 0.7677 (mm) REVERT: B 201 TYR cc_start: 0.7374 (OUTLIER) cc_final: 0.6638 (m-80) REVERT: B 243 MET cc_start: 0.7766 (mtt) cc_final: 0.7495 (mtp) REVERT: B 279 PHE cc_start: 0.8312 (t80) cc_final: 0.8111 (t80) REVERT: C 16 LYS cc_start: 0.7813 (ttpm) cc_final: 0.7483 (ttpp) REVERT: C 122 LYS cc_start: 0.7336 (mmmt) cc_final: 0.7012 (tptt) REVERT: C 195 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.5292 (m-80) REVERT: D 72 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7559 (mttp) REVERT: D 262 LEU cc_start: 0.7998 (pp) cc_final: 0.7724 (pp) REVERT: D 271 ILE cc_start: 0.8453 (mm) cc_final: 0.8150 (mp) REVERT: E 33 LYS cc_start: 0.7725 (tttt) cc_final: 0.7470 (tttp) REVERT: E 37 HIS cc_start: 0.7660 (OUTLIER) cc_final: 0.7231 (t-90) REVERT: E 52 MET cc_start: 0.7230 (tpp) cc_final: 0.6832 (tpp) REVERT: E 72 LYS cc_start: 0.7200 (mmtt) cc_final: 0.6918 (mmtm) REVERT: E 95 MET cc_start: 0.6618 (mpp) cc_final: 0.6247 (mpp) REVERT: E 217 PHE cc_start: 0.7591 (t80) cc_final: 0.7203 (t80) outliers start: 84 outliers final: 43 residues processed: 301 average time/residue: 0.3287 time to fit residues: 112.2314 Evaluate side-chains 275 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 225 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 108 optimal weight: 0.4980 chunk 42 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 115 optimal weight: 0.0970 chunk 18 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 80 optimal weight: 0.4980 chunk 101 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 overall best weight: 2.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 HIS ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.173071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.157569 restraints weight = 13868.114| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.87 r_work: 0.3774 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11549 Z= 0.131 Angle : 0.574 8.833 15684 Z= 0.300 Chirality : 0.040 0.172 1776 Planarity : 0.003 0.035 1904 Dihedral : 10.773 94.758 1686 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 6.75 % Allowed : 28.38 % Favored : 64.87 % 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: 0.25 (0.23), residues: 1410 helix: 1.05 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -3.20 (0.28), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 290 TYR 0.018 0.001 TYR C 212 PHE 0.026 0.001 PHE A 279 HIS 0.004 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00285 (11549) covalent geometry : angle 0.57372 (15684) hydrogen bonds : bond 0.04346 ( 795) hydrogen bonds : angle 4.30526 ( 2382) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 234 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8539 (mmtt) cc_final: 0.8165 (mmtp) REVERT: A 81 MET cc_start: 0.8109 (mmm) cc_final: 0.7855 (mmm) REVERT: A 116 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8028 (tp) REVERT: A 202 PHE cc_start: 0.7095 (m-10) cc_final: 0.6740 (m-10) REVERT: A 212 TYR cc_start: 0.6272 (OUTLIER) cc_final: 0.5133 (m-10) REVERT: A 263 LEU cc_start: 0.7973 (tt) cc_final: 0.7758 (tt) REVERT: A 273 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8351 (tp) REVERT: A 282 LYS cc_start: 0.7608 (tttt) cc_final: 0.7296 (ttmm) REVERT: B 88 PHE cc_start: 0.8085 (t80) cc_final: 0.7658 (t80) REVERT: B 194 ILE cc_start: 0.7840 (mt) cc_final: 0.7579 (mm) REVERT: B 201 TYR cc_start: 0.7304 (OUTLIER) cc_final: 0.6661 (m-80) REVERT: B 243 MET cc_start: 0.7739 (mtt) cc_final: 0.7465 (mtp) REVERT: C 16 LYS cc_start: 0.7808 (ttpm) cc_final: 0.7484 (ttpp) REVERT: C 48 ILE cc_start: 0.7724 (mm) cc_final: 0.7462 (mm) REVERT: C 195 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.5223 (m-80) REVERT: D 52 MET cc_start: 0.5797 (mtt) cc_final: 0.5564 (mmm) REVERT: D 72 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7882 (mmmt) REVERT: D 94 PHE cc_start: 0.7747 (t80) cc_final: 0.7120 (t80) REVERT: D 163 LYS cc_start: 0.8270 (mptt) cc_final: 0.8036 (mptt) REVERT: D 289 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: E 33 LYS cc_start: 0.7738 (tttt) cc_final: 0.7480 (tttp) REVERT: E 37 HIS cc_start: 0.7584 (OUTLIER) cc_final: 0.7205 (t-90) REVERT: E 52 MET cc_start: 0.7144 (tpp) cc_final: 0.6809 (tpp) REVERT: E 72 LYS cc_start: 0.7112 (mmtt) cc_final: 0.6836 (mmtm) REVERT: E 217 PHE cc_start: 0.7480 (t80) cc_final: 0.7147 (t80) outliers start: 79 outliers final: 45 residues processed: 293 average time/residue: 0.3242 time to fit residues: 108.1790 Evaluate side-chains 276 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 223 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 115 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 46 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 123 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 HIS ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.170243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.154685 restraints weight = 13918.867| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.87 r_work: 0.3740 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11549 Z= 0.164 Angle : 0.598 9.471 15684 Z= 0.315 Chirality : 0.041 0.177 1776 Planarity : 0.003 0.036 1904 Dihedral : 10.613 94.282 1683 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 7.35 % Allowed : 27.69 % Favored : 64.96 % 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: 0.36 (0.23), residues: 1410 helix: 1.07 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -3.00 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 290 TYR 0.028 0.002 TYR C 70 PHE 0.026 0.001 PHE A 279 HIS 0.005 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00369 (11549) covalent geometry : angle 0.59829 (15684) hydrogen bonds : bond 0.04881 ( 795) hydrogen bonds : angle 4.37052 ( 2382) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 236 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6528 (tttm) REVERT: A 72 LYS cc_start: 0.8555 (mmtt) cc_final: 0.8183 (mmtp) REVERT: A 116 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8081 (tp) REVERT: A 202 PHE cc_start: 0.7184 (m-10) cc_final: 0.6814 (m-10) REVERT: A 212 TYR cc_start: 0.6412 (OUTLIER) cc_final: 0.6162 (m-10) REVERT: A 223 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7582 (t80) REVERT: A 273 LEU cc_start: 0.8802 (mt) cc_final: 0.8490 (tp) REVERT: A 282 LYS cc_start: 0.7622 (tttt) cc_final: 0.7254 (ttmm) REVERT: A 284 HIS cc_start: 0.7376 (OUTLIER) cc_final: 0.6410 (t-170) REVERT: B 88 PHE cc_start: 0.8103 (t80) cc_final: 0.7668 (t80) REVERT: B 194 ILE cc_start: 0.7880 (mt) cc_final: 0.7625 (mm) REVERT: B 201 TYR cc_start: 0.7409 (OUTLIER) cc_final: 0.6757 (m-80) REVERT: C 16 LYS cc_start: 0.7819 (ttpm) cc_final: 0.7485 (ttpp) REVERT: C 35 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7765 (ttpt) REVERT: C 106 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8369 (p) REVERT: C 122 LYS cc_start: 0.7190 (mmmt) cc_final: 0.6919 (tptt) REVERT: C 195 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.5335 (m-80) REVERT: D 52 MET cc_start: 0.5898 (mtt) cc_final: 0.5638 (mmm) REVERT: D 72 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7554 (mttp) REVERT: D 163 LYS cc_start: 0.8315 (mptt) cc_final: 0.7988 (mptt) REVERT: E 33 LYS cc_start: 0.7759 (tttt) cc_final: 0.7491 (tttp) REVERT: E 37 HIS cc_start: 0.7644 (OUTLIER) cc_final: 0.7227 (t-90) REVERT: E 52 MET cc_start: 0.7157 (tpp) cc_final: 0.6649 (tpp) REVERT: E 72 LYS cc_start: 0.7074 (mmtt) cc_final: 0.6796 (mmtm) REVERT: E 95 MET cc_start: 0.6517 (mpp) cc_final: 0.5865 (mpp) REVERT: E 113 THR cc_start: 0.7446 (OUTLIER) cc_final: 0.7214 (m) REVERT: E 122 LYS cc_start: 0.5935 (OUTLIER) cc_final: 0.5172 (mmtm) REVERT: E 162 GLU cc_start: 0.7448 (mm-30) cc_final: 0.6732 (mm-30) REVERT: E 217 PHE cc_start: 0.7585 (t80) cc_final: 0.7219 (t80) REVERT: E 281 TYR cc_start: 0.8032 (m-80) cc_final: 0.7787 (m-80) outliers start: 86 outliers final: 46 residues processed: 302 average time/residue: 0.3517 time to fit residues: 119.3746 Evaluate side-chains 282 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 223 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 263 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 89 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 12 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 HIS B 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.169801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.154551 restraints weight = 13915.624| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.78 r_work: 0.3758 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11549 Z= 0.169 Angle : 0.609 10.811 15684 Z= 0.317 Chirality : 0.041 0.178 1776 Planarity : 0.003 0.036 1904 Dihedral : 10.454 94.075 1674 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 7.52 % Allowed : 27.44 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.44 (0.23), residues: 1410 helix: 1.12 (0.16), residues: 1114 sheet: None (None), residues: 0 loop : -2.91 (0.31), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 290 TYR 0.028 0.002 TYR C 70 PHE 0.027 0.001 PHE A 279 HIS 0.005 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00381 (11549) covalent geometry : angle 0.60935 (15684) hydrogen bonds : bond 0.04919 ( 795) hydrogen bonds : angle 4.36219 ( 2382) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 234 time to evaluate : 0.339 Fit side-chains REVERT: A 33 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6523 (tttm) REVERT: A 49 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7927 (mp) REVERT: A 72 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8130 (mmtp) REVERT: A 116 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8081 (tp) REVERT: A 202 PHE cc_start: 0.7187 (m-10) cc_final: 0.6863 (m-10) REVERT: A 212 TYR cc_start: 0.6410 (OUTLIER) cc_final: 0.6204 (m-10) REVERT: A 223 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7603 (t80) REVERT: A 263 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7730 (tt) REVERT: A 273 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8535 (tp) REVERT: A 282 LYS cc_start: 0.7602 (tttt) cc_final: 0.7159 (ttmt) REVERT: A 284 HIS cc_start: 0.7411 (OUTLIER) cc_final: 0.6457 (t-170) REVERT: A 288 PHE cc_start: 0.7750 (t80) cc_final: 0.7439 (t80) REVERT: B 88 PHE cc_start: 0.8104 (t80) cc_final: 0.7663 (t80) REVERT: B 194 ILE cc_start: 0.7863 (mt) cc_final: 0.7606 (mm) REVERT: B 201 TYR cc_start: 0.7351 (OUTLIER) cc_final: 0.6743 (m-80) REVERT: B 243 MET cc_start: 0.7813 (mtt) cc_final: 0.7515 (mtp) REVERT: C 16 LYS cc_start: 0.7800 (ttpm) cc_final: 0.7472 (ttpp) REVERT: C 35 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7680 (ttpt) REVERT: C 48 ILE cc_start: 0.7751 (mm) cc_final: 0.7533 (mm) REVERT: C 106 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8366 (p) REVERT: C 195 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.5340 (m-80) REVERT: D 52 MET cc_start: 0.5939 (mtt) cc_final: 0.5632 (mmm) REVERT: D 72 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7529 (mttp) REVERT: D 163 LYS cc_start: 0.8338 (mptt) cc_final: 0.7995 (mptt) REVERT: D 202 PHE cc_start: 0.8206 (m-10) cc_final: 0.7903 (m-10) REVERT: E 33 LYS cc_start: 0.7748 (tttt) cc_final: 0.7481 (tttp) REVERT: E 37 HIS cc_start: 0.7647 (OUTLIER) cc_final: 0.7229 (t-90) REVERT: E 52 MET cc_start: 0.7175 (tpp) cc_final: 0.6775 (tpp) REVERT: E 72 LYS cc_start: 0.7087 (mmtt) cc_final: 0.6814 (mmtm) REVERT: E 95 MET cc_start: 0.6538 (mpp) cc_final: 0.5883 (mpp) REVERT: E 122 LYS cc_start: 0.5918 (OUTLIER) cc_final: 0.5161 (mmtm) REVERT: E 162 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6702 (mm-30) REVERT: E 217 PHE cc_start: 0.7600 (t80) cc_final: 0.7269 (t80) REVERT: E 281 TYR cc_start: 0.8017 (m-80) cc_final: 0.7782 (m-80) outliers start: 88 outliers final: 50 residues processed: 297 average time/residue: 0.3504 time to fit residues: 117.0116 Evaluate side-chains 292 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 227 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 83 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 84 optimal weight: 50.0000 chunk 49 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 139 optimal weight: 0.9990 chunk 102 optimal weight: 20.0000 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 257 ASN B 165 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.169967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.154414 restraints weight = 13922.521| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.86 r_work: 0.3734 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11549 Z= 0.165 Angle : 0.613 10.805 15684 Z= 0.318 Chirality : 0.041 0.175 1776 Planarity : 0.003 0.036 1904 Dihedral : 10.467 94.004 1671 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 6.92 % Allowed : 28.38 % Favored : 64.70 % 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: 0.51 (0.23), residues: 1410 helix: 1.17 (0.16), residues: 1105 sheet: None (None), residues: 0 loop : -2.81 (0.31), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 290 TYR 0.025 0.002 TYR C 70 PHE 0.026 0.001 PHE A 279 HIS 0.005 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00372 (11549) covalent geometry : angle 0.61255 (15684) hydrogen bonds : bond 0.04860 ( 795) hydrogen bonds : angle 4.35452 ( 2382) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 235 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7158 (OUTLIER) cc_final: 0.6705 (tmtm) REVERT: A 49 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7927 (mp) REVERT: A 72 LYS cc_start: 0.8534 (mmtt) cc_final: 0.8141 (mmtp) REVERT: A 116 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8115 (tp) REVERT: A 202 PHE cc_start: 0.7192 (m-10) cc_final: 0.6884 (m-10) REVERT: A 223 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7611 (t80) REVERT: A 263 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7739 (tt) REVERT: A 273 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8536 (tp) REVERT: A 282 LYS cc_start: 0.7620 (tttt) cc_final: 0.7233 (ttmt) REVERT: A 284 HIS cc_start: 0.7314 (OUTLIER) cc_final: 0.6406 (t-170) REVERT: A 288 PHE cc_start: 0.7743 (t80) cc_final: 0.7390 (t80) REVERT: B 88 PHE cc_start: 0.8105 (t80) cc_final: 0.7670 (t80) REVERT: B 194 ILE cc_start: 0.7865 (mt) cc_final: 0.7620 (mm) REVERT: B 201 TYR cc_start: 0.7337 (OUTLIER) cc_final: 0.6730 (m-80) REVERT: C 16 LYS cc_start: 0.7771 (ttpm) cc_final: 0.7468 (ttpp) REVERT: C 35 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7545 (ttpt) REVERT: C 106 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8357 (p) REVERT: C 195 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.5338 (m-80) REVERT: D 52 MET cc_start: 0.5945 (mtt) cc_final: 0.5670 (mmm) REVERT: D 72 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7562 (mttp) REVERT: D 163 LYS cc_start: 0.8351 (mptt) cc_final: 0.7997 (mptt) REVERT: D 202 PHE cc_start: 0.8251 (m-10) cc_final: 0.7930 (m-10) REVERT: D 289 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: E 33 LYS cc_start: 0.7746 (tttt) cc_final: 0.7479 (tttp) REVERT: E 37 HIS cc_start: 0.7639 (OUTLIER) cc_final: 0.7230 (t-90) REVERT: E 52 MET cc_start: 0.7182 (tpp) cc_final: 0.6782 (tpp) REVERT: E 72 LYS cc_start: 0.7070 (mmtt) cc_final: 0.6792 (mmtm) REVERT: E 122 LYS cc_start: 0.5915 (OUTLIER) cc_final: 0.5224 (mmtp) REVERT: E 162 GLU cc_start: 0.7443 (mm-30) cc_final: 0.6705 (mm-30) REVERT: E 217 PHE cc_start: 0.7613 (t80) cc_final: 0.7287 (t80) REVERT: E 281 TYR cc_start: 0.8017 (m-80) cc_final: 0.7775 (m-80) outliers start: 81 outliers final: 51 residues processed: 290 average time/residue: 0.3419 time to fit residues: 111.6595 Evaluate side-chains 293 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 227 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 25 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 HIS D 234 ASN D 257 ASN D 284 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.166875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.151539 restraints weight = 13814.567| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.76 r_work: 0.3722 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11549 Z= 0.219 Angle : 0.663 11.568 15684 Z= 0.347 Chirality : 0.043 0.180 1776 Planarity : 0.003 0.037 1904 Dihedral : 10.237 93.416 1671 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 6.92 % Allowed : 28.72 % Favored : 64.36 % 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: 0.31 (0.22), residues: 1410 helix: 1.02 (0.16), residues: 1100 sheet: None (None), residues: 0 loop : -2.74 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 290 TYR 0.033 0.002 TYR C 70 PHE 0.027 0.002 PHE A 279 HIS 0.006 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00496 (11549) covalent geometry : angle 0.66325 (15684) hydrogen bonds : bond 0.05603 ( 795) hydrogen bonds : angle 4.53758 ( 2382) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 238 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6935 (tttm) REVERT: A 49 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7939 (mp) REVERT: A 72 LYS cc_start: 0.8522 (mmtt) cc_final: 0.8137 (mmtp) REVERT: A 116 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8181 (tp) REVERT: A 202 PHE cc_start: 0.7258 (m-10) cc_final: 0.6949 (m-10) REVERT: A 223 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7613 (t80) REVERT: A 263 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7727 (tt) REVERT: A 273 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8589 (tp) REVERT: A 282 LYS cc_start: 0.7634 (tttt) cc_final: 0.7174 (ttmm) REVERT: A 284 HIS cc_start: 0.7200 (OUTLIER) cc_final: 0.6256 (t-170) REVERT: A 288 PHE cc_start: 0.7746 (t80) cc_final: 0.7436 (t80) REVERT: B 88 PHE cc_start: 0.8099 (t80) cc_final: 0.7649 (t80) REVERT: B 194 ILE cc_start: 0.7982 (mt) cc_final: 0.7722 (mm) REVERT: B 201 TYR cc_start: 0.7379 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: C 16 LYS cc_start: 0.7786 (ttpm) cc_final: 0.7502 (ttpp) REVERT: C 48 ILE cc_start: 0.7833 (mm) cc_final: 0.7588 (mm) REVERT: C 81 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7805 (mtp) REVERT: C 106 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8353 (p) REVERT: C 195 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.5290 (m-80) REVERT: D 52 MET cc_start: 0.6027 (mtt) cc_final: 0.5690 (mmm) REVERT: D 72 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7609 (mttp) REVERT: D 215 SER cc_start: 0.7595 (p) cc_final: 0.7226 (p) REVERT: D 266 TYR cc_start: 0.7908 (t80) cc_final: 0.7304 (t80) REVERT: D 289 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: E 33 LYS cc_start: 0.7753 (tttt) cc_final: 0.7480 (tttp) REVERT: E 35 LYS cc_start: 0.8598 (ttmm) cc_final: 0.8285 (mtpp) REVERT: E 37 HIS cc_start: 0.7664 (OUTLIER) cc_final: 0.7244 (t-90) REVERT: E 52 MET cc_start: 0.7358 (tpp) cc_final: 0.7068 (tpp) REVERT: E 72 LYS cc_start: 0.7156 (mmtt) cc_final: 0.6892 (mmtm) REVERT: E 95 MET cc_start: 0.6447 (mpp) cc_final: 0.5791 (mpp) REVERT: E 122 LYS cc_start: 0.5964 (OUTLIER) cc_final: 0.5253 (mmtm) REVERT: E 162 GLU cc_start: 0.7503 (mm-30) cc_final: 0.6520 (mm-30) REVERT: E 217 PHE cc_start: 0.7648 (t80) cc_final: 0.7297 (t80) outliers start: 81 outliers final: 53 residues processed: 294 average time/residue: 0.3487 time to fit residues: 115.3089 Evaluate side-chains 302 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 234 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 105 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 6 optimal weight: 0.0670 chunk 131 optimal weight: 6.9990 overall best weight: 4.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 HIS D 234 ASN D 257 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.169498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.153936 restraints weight = 13715.137| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.86 r_work: 0.3729 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11549 Z= 0.172 Angle : 0.630 12.162 15684 Z= 0.327 Chirality : 0.041 0.179 1776 Planarity : 0.003 0.037 1904 Dihedral : 9.941 94.179 1671 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 6.58 % Allowed : 29.40 % Favored : 64.02 % 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: 0.46 (0.22), residues: 1410 helix: 1.14 (0.16), residues: 1100 sheet: None (None), residues: 0 loop : -2.75 (0.30), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 290 TYR 0.028 0.002 TYR C 70 PHE 0.027 0.002 PHE A 279 HIS 0.005 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00389 (11549) covalent geometry : angle 0.62971 (15684) hydrogen bonds : bond 0.04984 ( 795) hydrogen bonds : angle 4.42213 ( 2382) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 227 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6671 (tmtm) REVERT: A 49 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7928 (mp) REVERT: A 72 LYS cc_start: 0.8522 (mmtt) cc_final: 0.8127 (mmtp) REVERT: A 116 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8122 (tp) REVERT: A 202 PHE cc_start: 0.7184 (m-10) cc_final: 0.6880 (m-10) REVERT: A 263 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7688 (tt) REVERT: A 273 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8580 (tp) REVERT: A 282 LYS cc_start: 0.7618 (tttt) cc_final: 0.7214 (ttmt) REVERT: A 284 HIS cc_start: 0.7205 (OUTLIER) cc_final: 0.6315 (t-170) REVERT: A 288 PHE cc_start: 0.7746 (t80) cc_final: 0.7421 (t80) REVERT: B 88 PHE cc_start: 0.8094 (t80) cc_final: 0.7638 (t80) REVERT: B 165 HIS cc_start: 0.7867 (OUTLIER) cc_final: 0.7636 (m90) REVERT: B 194 ILE cc_start: 0.7913 (mt) cc_final: 0.7657 (mm) REVERT: B 201 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.6654 (m-80) REVERT: B 243 MET cc_start: 0.7788 (mtt) cc_final: 0.7476 (mtp) REVERT: C 16 LYS cc_start: 0.7801 (ttpm) cc_final: 0.7516 (ttpp) REVERT: C 48 ILE cc_start: 0.7774 (mm) cc_final: 0.7520 (mm) REVERT: C 81 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7801 (mtp) REVERT: C 106 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8355 (p) REVERT: C 195 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.5279 (m-80) REVERT: D 52 MET cc_start: 0.5993 (mtt) cc_final: 0.5683 (mmm) REVERT: D 72 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7557 (mttp) REVERT: D 163 LYS cc_start: 0.8249 (mptt) cc_final: 0.8025 (mptt) REVERT: D 202 PHE cc_start: 0.8135 (m-10) cc_final: 0.7881 (m-80) REVERT: D 289 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: E 33 LYS cc_start: 0.7765 (tttt) cc_final: 0.7496 (tttp) REVERT: E 35 LYS cc_start: 0.8574 (ttmm) cc_final: 0.8248 (mtpp) REVERT: E 37 HIS cc_start: 0.7639 (OUTLIER) cc_final: 0.7211 (t-90) REVERT: E 52 MET cc_start: 0.7247 (tpp) cc_final: 0.6840 (tpp) REVERT: E 72 LYS cc_start: 0.7147 (mmtt) cc_final: 0.6882 (mmtm) REVERT: E 95 MET cc_start: 0.6474 (mpp) cc_final: 0.5855 (mpp) REVERT: E 122 LYS cc_start: 0.5896 (OUTLIER) cc_final: 0.5208 (mmtp) REVERT: E 162 GLU cc_start: 0.7410 (mm-30) cc_final: 0.6640 (mm-30) REVERT: E 217 PHE cc_start: 0.7631 (t80) cc_final: 0.7269 (t80) outliers start: 77 outliers final: 52 residues processed: 280 average time/residue: 0.3568 time to fit residues: 112.6531 Evaluate side-chains 287 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 220 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 122 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 58 optimal weight: 20.0000 chunk 29 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 HIS D 234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.167201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.151372 restraints weight = 13803.243| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.83 r_work: 0.3694 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11549 Z= 0.209 Angle : 0.666 12.578 15684 Z= 0.346 Chirality : 0.043 0.181 1776 Planarity : 0.003 0.038 1904 Dihedral : 9.893 93.723 1671 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 6.32 % Allowed : 29.74 % Favored : 63.93 % 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: 0.33 (0.22), residues: 1410 helix: 1.03 (0.16), residues: 1100 sheet: None (None), residues: 0 loop : -2.72 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 290 TYR 0.029 0.002 TYR C 70 PHE 0.029 0.002 PHE A 279 HIS 0.006 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00474 (11549) covalent geometry : angle 0.66550 (15684) hydrogen bonds : bond 0.05401 ( 795) hydrogen bonds : angle 4.52316 ( 2382) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 228 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7201 (OUTLIER) cc_final: 0.6923 (tttm) REVERT: A 49 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7941 (mp) REVERT: A 72 LYS cc_start: 0.8512 (mmtt) cc_final: 0.8143 (mmtp) REVERT: A 81 MET cc_start: 0.8143 (mmm) cc_final: 0.7877 (mmm) REVERT: A 116 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8162 (tp) REVERT: A 202 PHE cc_start: 0.7271 (m-10) cc_final: 0.6929 (m-10) REVERT: A 263 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7755 (tt) REVERT: A 273 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8597 (tp) REVERT: A 282 LYS cc_start: 0.7649 (tttt) cc_final: 0.7180 (ttmm) REVERT: A 284 HIS cc_start: 0.7164 (OUTLIER) cc_final: 0.6241 (t-170) REVERT: A 288 PHE cc_start: 0.7689 (t80) cc_final: 0.7394 (t80) REVERT: B 88 PHE cc_start: 0.8102 (t80) cc_final: 0.7644 (t80) REVERT: B 194 ILE cc_start: 0.7945 (mt) cc_final: 0.7679 (mm) REVERT: B 201 TYR cc_start: 0.7334 (OUTLIER) cc_final: 0.6634 (m-80) REVERT: C 16 LYS cc_start: 0.7728 (ttpm) cc_final: 0.7439 (ttpp) REVERT: C 81 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7821 (mtp) REVERT: C 106 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8377 (p) REVERT: C 195 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.5293 (m-80) REVERT: D 52 MET cc_start: 0.5932 (mtt) cc_final: 0.5597 (mmm) REVERT: D 72 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7618 (mttp) REVERT: D 163 LYS cc_start: 0.8241 (mptt) cc_final: 0.8007 (mptt) REVERT: D 202 PHE cc_start: 0.8112 (m-10) cc_final: 0.7871 (m-10) REVERT: D 289 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: E 33 LYS cc_start: 0.7750 (tttt) cc_final: 0.7472 (tttp) REVERT: E 35 LYS cc_start: 0.8625 (ttmm) cc_final: 0.8315 (mtpp) REVERT: E 37 HIS cc_start: 0.7649 (OUTLIER) cc_final: 0.7203 (t-90) REVERT: E 52 MET cc_start: 0.7282 (tpp) cc_final: 0.6889 (tpp) REVERT: E 72 LYS cc_start: 0.7132 (mmtt) cc_final: 0.6868 (mmtm) REVERT: E 95 MET cc_start: 0.6436 (mpp) cc_final: 0.5727 (mpp) REVERT: E 122 LYS cc_start: 0.5904 (OUTLIER) cc_final: 0.5174 (mmtm) REVERT: E 162 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6476 (mm-30) REVERT: E 217 PHE cc_start: 0.7602 (t80) cc_final: 0.7263 (t80) outliers start: 74 outliers final: 55 residues processed: 277 average time/residue: 0.3453 time to fit residues: 108.1436 Evaluate side-chains 294 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 225 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 75 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 4 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 165 HIS D 234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.171787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.156195 restraints weight = 13941.939| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.87 r_work: 0.3759 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11549 Z= 0.146 Angle : 0.611 12.512 15684 Z= 0.315 Chirality : 0.040 0.179 1776 Planarity : 0.003 0.036 1904 Dihedral : 9.640 94.624 1671 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 6.07 % Allowed : 30.17 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.65 (0.23), residues: 1410 helix: 1.27 (0.16), residues: 1100 sheet: None (None), residues: 0 loop : -2.65 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 290 TYR 0.026 0.001 TYR C 70 PHE 0.028 0.001 PHE A 279 HIS 0.005 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00327 (11549) covalent geometry : angle 0.61050 (15684) hydrogen bonds : bond 0.04542 ( 795) hydrogen bonds : angle 4.33240 ( 2382) =============================================================================== Job complete usr+sys time: 3632.61 seconds wall clock time: 62 minutes 54.82 seconds (3774.82 seconds total)