Starting phenix.real_space_refine on Tue Jul 29 10:45:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vqr_21355/07_2025/6vqr_21355.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vqr_21355/07_2025/6vqr_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_21355/07_2025/6vqr_21355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vqr_21355/07_2025/6vqr_21355.map" model { file = "/net/cci-nas-00/data/ceres_data/6vqr_21355/07_2025/6vqr_21355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vqr_21355/07_2025/6vqr_21355.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.70, per 1000 atoms: 0.68 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: 3.67 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 0.94 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: 3.12 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 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 290 or resid 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: 0.050 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 29.860 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.040 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:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.050 ------------------------------------------------------------------------------- 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 : 15.78 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (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 HIS 0.008 0.001 HIS C 165 PHE 0.021 0.002 PHE B 223 TYR 0.018 0.002 TYR C 212 ARG 0.008 0.001 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.13674 ( 795) hydrogen bonds : angle 6.39368 ( 2382) covalent geometry : bond 0.01340 (11549) covalent geometry : angle 0.96866 (15684) *********************** 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 : 1.234 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: 0.6969 (OUTLIER) cc_final: 0.6724 (t) outliers start: 96 outliers final: 58 residues processed: 377 average time/residue: 0.7515 time to fit residues: 320.7840 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 : 1.264 ------------------------------------------------------------------------------- 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 118 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 30.0000 chunk 109 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN B 59 HIS B 165 HIS B 193 ASN B 230 HIS ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN C 137 ASN C 239 ASN D 59 HIS D 171 ASN E 59 HIS E 257 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.171015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.156090 restraints weight = 13680.462| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.74 r_work: 0.3765 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11549 Z= 0.142 Angle : 0.612 9.225 15684 Z= 0.323 Chirality : 0.042 0.178 1776 Planarity : 0.004 0.036 1904 Dihedral : 12.703 96.443 1758 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 6.15 % Allowed : 26.41 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.22), residues: 1410 helix: 0.30 (0.15), residues: 1100 sheet: None (None), residues: 0 loop : -3.45 (0.28), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 71 PHE 0.022 0.001 PHE B 279 TYR 0.022 0.001 TYR E 31 ARG 0.004 0.000 ARG B 290 Details of bonding type rmsd hydrogen bonds : bond 0.04761 ( 795) hydrogen bonds : angle 4.62052 ( 2382) covalent geometry : bond 0.00309 (11549) covalent geometry : angle 0.61243 (15684) *********************** 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 323 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 251 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8201 (mmtp) REVERT: A 80 SER cc_start: 0.9108 (t) cc_final: 0.8839 (p) REVERT: A 81 MET cc_start: 0.8107 (mmm) cc_final: 0.7867 (mmm) REVERT: A 95 MET cc_start: 0.7890 (mmm) cc_final: 0.7382 (tpp) REVERT: A 116 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8023 (tp) REVERT: A 212 TYR cc_start: 0.6204 (OUTLIER) cc_final: 0.5044 (m-10) REVERT: A 273 LEU cc_start: 0.8841 (mt) cc_final: 0.8441 (tp) REVERT: A 282 LYS cc_start: 0.7648 (tttt) cc_final: 0.7348 (ttmm) REVERT: A 290 ARG cc_start: 0.7038 (mmm-85) cc_final: 0.6836 (mmm160) REVERT: B 30 GLU cc_start: 0.8080 (tp30) cc_final: 0.7830 (mm-30) REVERT: B 119 LYS cc_start: 0.7795 (mttp) cc_final: 0.7594 (mmtm) REVERT: B 194 ILE cc_start: 0.7907 (mt) cc_final: 0.7586 (mm) REVERT: B 201 TYR cc_start: 0.7333 (OUTLIER) cc_final: 0.6605 (m-80) REVERT: B 279 PHE cc_start: 0.8383 (t80) cc_final: 0.8181 (OUTLIER) REVERT: C 16 LYS cc_start: 0.7810 (ttpm) cc_final: 0.7548 (ttpp) REVERT: C 104 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7109 (tm) REVERT: C 122 LYS cc_start: 0.7292 (mmmt) cc_final: 0.6962 (tptt) REVERT: C 173 ILE cc_start: 0.8151 (mm) cc_final: 0.7945 (mm) REVERT: D 72 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7881 (mmmt) REVERT: D 94 PHE cc_start: 0.7786 (t80) cc_final: 0.7119 (t80) REVERT: D 163 LYS cc_start: 0.8308 (mptt) cc_final: 0.8054 (mptt) REVERT: D 232 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7698 (mm) REVERT: D 271 ILE cc_start: 0.8493 (mm) cc_final: 0.8160 (mp) REVERT: D 289 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: E 33 LYS cc_start: 0.7701 (tttt) cc_final: 0.7459 (tttp) REVERT: E 37 HIS cc_start: 0.7643 (OUTLIER) cc_final: 0.7172 (t-90) REVERT: E 52 MET cc_start: 0.7185 (tpp) cc_final: 0.6668 (tpp) REVERT: E 72 LYS cc_start: 0.7150 (mmtt) cc_final: 0.6859 (mmtm) REVERT: E 95 MET cc_start: 0.6578 (mpp) cc_final: 0.6332 (mpp) REVERT: E 212 TYR cc_start: 0.7742 (OUTLIER) cc_final: 0.7383 (m-80) REVERT: E 217 PHE cc_start: 0.7627 (t80) cc_final: 0.7247 (t80) outliers start: 72 outliers final: 39 residues processed: 301 average time/residue: 0.7246 time to fit residues: 247.6770 Evaluate side-chains 283 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 236 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 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 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 104 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 148 VAL 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 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 6 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 58 optimal weight: 0.0870 chunk 71 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 56 optimal weight: 30.0000 chunk 38 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.170470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.154976 restraints weight = 13942.041| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.87 r_work: 0.3744 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11549 Z= 0.151 Angle : 0.588 7.390 15684 Z= 0.313 Chirality : 0.041 0.170 1776 Planarity : 0.003 0.036 1904 Dihedral : 11.433 95.241 1690 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 6.92 % Allowed : 26.67 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.22), residues: 1410 helix: 0.75 (0.16), residues: 1114 sheet: None (None), residues: 0 loop : -3.26 (0.28), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 165 PHE 0.023 0.001 PHE A 288 TYR 0.022 0.001 TYR C 70 ARG 0.006 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.04807 ( 795) hydrogen bonds : angle 4.46620 ( 2382) covalent geometry : bond 0.00332 (11549) covalent geometry : angle 0.58812 (15684) *********************** 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 317 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 236 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8578 (mmtt) cc_final: 0.8185 (mmtp) REVERT: A 81 MET cc_start: 0.8103 (mmm) cc_final: 0.7887 (mmm) REVERT: A 116 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8073 (tp) REVERT: A 202 PHE cc_start: 0.7134 (m-10) cc_final: 0.6769 (m-10) REVERT: A 212 TYR cc_start: 0.6389 (OUTLIER) cc_final: 0.5183 (m-10) REVERT: A 273 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8403 (tp) REVERT: A 282 LYS cc_start: 0.7681 (tttt) cc_final: 0.7343 (ttmt) REVERT: B 194 ILE cc_start: 0.7929 (mt) cc_final: 0.7628 (mm) REVERT: B 201 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.6642 (m-80) REVERT: C 16 LYS cc_start: 0.7801 (ttpm) cc_final: 0.7492 (ttpp) REVERT: C 173 ILE cc_start: 0.8187 (mm) cc_final: 0.7981 (mm) REVERT: D 72 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7501 (mttp) REVERT: D 198 LEU cc_start: 0.8063 (mp) cc_final: 0.7766 (mp) REVERT: D 232 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7721 (mm) REVERT: D 262 LEU cc_start: 0.8037 (pp) cc_final: 0.7740 (pp) REVERT: E 33 LYS cc_start: 0.7727 (tttt) cc_final: 0.7475 (tttp) REVERT: E 37 HIS cc_start: 0.7646 (OUTLIER) cc_final: 0.7247 (t-90) REVERT: E 52 MET cc_start: 0.7170 (tpp) cc_final: 0.6671 (tpp) REVERT: E 72 LYS cc_start: 0.7182 (mmtt) cc_final: 0.6901 (mmtm) REVERT: E 95 MET cc_start: 0.6609 (mpp) cc_final: 0.6332 (mpp) REVERT: E 217 PHE cc_start: 0.7571 (t80) cc_final: 0.7223 (t80) outliers start: 81 outliers final: 39 residues processed: 297 average time/residue: 0.7136 time to fit residues: 241.2407 Evaluate side-chains 271 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 225 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 13 VAL 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 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 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 40 ASN 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 152 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 291 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS 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 273 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 43 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 136 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 134 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 89 optimal weight: 9.9990 chunk 84 optimal weight: 50.0000 chunk 46 optimal weight: 20.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 HIS B 165 HIS ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.171649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.156093 restraints weight = 13849.436| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.88 r_work: 0.3753 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11549 Z= 0.147 Angle : 0.584 8.585 15684 Z= 0.308 Chirality : 0.040 0.173 1776 Planarity : 0.003 0.035 1904 Dihedral : 10.824 94.227 1686 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 6.84 % Allowed : 27.95 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.22), residues: 1410 helix: 0.99 (0.16), residues: 1113 sheet: None (None), residues: 0 loop : -3.11 (0.29), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 165 PHE 0.027 0.001 PHE A 279 TYR 0.027 0.001 TYR C 70 ARG 0.002 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.04624 ( 795) hydrogen bonds : angle 4.35006 ( 2382) covalent geometry : bond 0.00324 (11549) covalent geometry : angle 0.58448 (15684) *********************** 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 312 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 232 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6340 (tttm) REVERT: A 72 LYS cc_start: 0.8544 (mmtt) cc_final: 0.8171 (mmtp) REVERT: A 81 MET cc_start: 0.8121 (mmm) cc_final: 0.7871 (mmm) REVERT: A 116 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8061 (tp) REVERT: A 212 TYR cc_start: 0.6354 (OUTLIER) cc_final: 0.5205 (m-10) REVERT: A 273 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8428 (tp) REVERT: A 282 LYS cc_start: 0.7619 (tttt) cc_final: 0.7256 (ttmt) REVERT: B 88 PHE cc_start: 0.8098 (t80) cc_final: 0.7680 (t80) REVERT: B 194 ILE cc_start: 0.7839 (mt) cc_final: 0.7577 (mm) REVERT: B 201 TYR cc_start: 0.7293 (OUTLIER) cc_final: 0.6644 (m-80) REVERT: C 16 LYS cc_start: 0.7782 (ttpm) cc_final: 0.7459 (ttpp) REVERT: C 48 ILE cc_start: 0.7772 (mm) cc_final: 0.7483 (mm) REVERT: C 173 ILE cc_start: 0.8170 (mm) cc_final: 0.7956 (mm) REVERT: C 195 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.5375 (m-80) REVERT: D 52 MET cc_start: 0.5875 (mtt) cc_final: 0.5602 (mmm) REVERT: D 72 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7903 (mmmt) REVERT: D 94 PHE cc_start: 0.7762 (t80) cc_final: 0.7147 (t80) REVERT: D 163 LYS cc_start: 0.8287 (mptt) cc_final: 0.8053 (mptt) REVERT: D 232 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7712 (mm) REVERT: E 33 LYS cc_start: 0.7767 (tttt) cc_final: 0.7504 (tttp) REVERT: E 37 HIS cc_start: 0.7605 (OUTLIER) cc_final: 0.7209 (t-90) REVERT: E 52 MET cc_start: 0.7147 (tpp) cc_final: 0.6811 (tpp) REVERT: E 72 LYS cc_start: 0.7117 (mmtt) cc_final: 0.6839 (mmtm) REVERT: E 217 PHE cc_start: 0.7542 (t80) cc_final: 0.7193 (t80) outliers start: 80 outliers final: 43 residues processed: 291 average time/residue: 0.7041 time to fit residues: 233.6117 Evaluate side-chains 272 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 220 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 82 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 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 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 165 HIS Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 201 TYR 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 212 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 271 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 96 CYS Chi-restraints excluded: chain D residue 124 LEU 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 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 98 ILE Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE 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 61 optimal weight: 20.0000 chunk 98 optimal weight: 0.0980 chunk 49 optimal weight: 10.0000 chunk 86 optimal weight: 30.0000 chunk 56 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 42 optimal weight: 0.0470 chunk 138 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 overall best weight: 3.0284 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.172735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.157556 restraints weight = 13839.584| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 1.78 r_work: 0.3793 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 11549 Z= 0.134 Angle : 0.565 8.710 15684 Z= 0.296 Chirality : 0.040 0.172 1776 Planarity : 0.003 0.034 1904 Dihedral : 10.628 94.931 1682 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 6.84 % Allowed : 27.86 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.23), residues: 1410 helix: 1.18 (0.16), residues: 1117 sheet: None (None), residues: 0 loop : -2.96 (0.30), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 165 PHE 0.026 0.001 PHE A 279 TYR 0.028 0.001 TYR C 70 ARG 0.002 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.04365 ( 795) hydrogen bonds : angle 4.26086 ( 2382) covalent geometry : bond 0.00296 (11549) covalent geometry : angle 0.56476 (15684) *********************** 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 311 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 231 time to evaluate : 1.131 Fit side-chains REVERT: A 72 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8176 (mmtp) REVERT: A 81 MET cc_start: 0.8127 (mmm) cc_final: 0.7868 (mmm) REVERT: A 98 ILE cc_start: 0.7868 (mm) cc_final: 0.7666 (mm) REVERT: A 116 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8039 (tp) REVERT: A 212 TYR cc_start: 0.6421 (OUTLIER) cc_final: 0.5159 (m-10) REVERT: A 223 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7622 (t80) REVERT: A 263 LEU cc_start: 0.7941 (tt) cc_final: 0.7738 (tt) REVERT: A 273 LEU cc_start: 0.8773 (mt) cc_final: 0.8467 (tp) REVERT: A 282 LYS cc_start: 0.7505 (tttt) cc_final: 0.7171 (ttmt) REVERT: A 284 HIS cc_start: 0.7330 (OUTLIER) cc_final: 0.6380 (t-170) REVERT: A 288 PHE cc_start: 0.7746 (t80) cc_final: 0.7411 (t80) REVERT: B 88 PHE cc_start: 0.8072 (t80) cc_final: 0.7603 (t80) REVERT: B 194 ILE cc_start: 0.7816 (mt) cc_final: 0.7564 (mm) REVERT: B 201 TYR cc_start: 0.7267 (OUTLIER) cc_final: 0.6695 (m-80) REVERT: C 16 LYS cc_start: 0.7754 (ttpm) cc_final: 0.7438 (ttpp) REVERT: C 35 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7768 (ttpt) REVERT: C 106 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8340 (p) REVERT: C 173 ILE cc_start: 0.8157 (mm) cc_final: 0.7953 (mm) REVERT: C 195 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.5303 (m-80) REVERT: D 52 MET cc_start: 0.5818 (mtt) cc_final: 0.5572 (mmm) REVERT: D 72 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7895 (mmmt) REVERT: D 94 PHE cc_start: 0.7803 (t80) cc_final: 0.7215 (t80) REVERT: D 163 LYS cc_start: 0.8291 (mptt) cc_final: 0.8033 (mptt) REVERT: D 232 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7679 (mm) REVERT: D 289 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: E 33 LYS cc_start: 0.7738 (tttt) cc_final: 0.7477 (tttp) REVERT: E 37 HIS cc_start: 0.7530 (OUTLIER) cc_final: 0.7155 (t-90) REVERT: E 52 MET cc_start: 0.7100 (tpp) cc_final: 0.6753 (tpp) REVERT: E 72 LYS cc_start: 0.7126 (mmtt) cc_final: 0.6849 (mmtm) REVERT: E 113 THR cc_start: 0.7361 (OUTLIER) cc_final: 0.7157 (m) REVERT: E 217 PHE cc_start: 0.7550 (t80) cc_final: 0.7227 (t80) outliers start: 80 outliers final: 42 residues processed: 294 average time/residue: 0.7180 time to fit residues: 240.4307 Evaluate side-chains 274 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 219 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 22 GLU 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 124 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 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 35 LYS 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 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 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 223 PHE Chi-restraints excluded: chain D residue 232 ILE 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 39 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 113 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 97 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 58 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.175409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.160308 restraints weight = 13878.316| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.80 r_work: 0.3779 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11549 Z= 0.116 Angle : 0.556 10.983 15684 Z= 0.286 Chirality : 0.039 0.169 1776 Planarity : 0.003 0.032 1904 Dihedral : 10.407 94.553 1679 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 6.41 % Allowed : 27.86 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.23), residues: 1410 helix: 1.45 (0.16), residues: 1105 sheet: None (None), residues: 0 loop : -2.75 (0.30), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 71 PHE 0.025 0.001 PHE A 279 TYR 0.025 0.001 TYR C 70 ARG 0.004 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 795) hydrogen bonds : angle 4.12198 ( 2382) covalent geometry : bond 0.00251 (11549) covalent geometry : angle 0.55560 (15684) *********************** 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 303 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 228 time to evaluate : 1.181 Fit side-chains REVERT: A 72 LYS cc_start: 0.8581 (mmtt) cc_final: 0.8206 (mmtp) REVERT: A 81 MET cc_start: 0.8159 (mmm) cc_final: 0.7906 (mmm) REVERT: A 202 PHE cc_start: 0.7094 (m-10) cc_final: 0.6729 (m-10) REVERT: A 212 TYR cc_start: 0.6282 (OUTLIER) cc_final: 0.5093 (m-10) REVERT: A 273 LEU cc_start: 0.8813 (mt) cc_final: 0.8444 (tp) REVERT: A 282 LYS cc_start: 0.7517 (tttt) cc_final: 0.7186 (ttmt) REVERT: A 284 HIS cc_start: 0.7454 (OUTLIER) cc_final: 0.6546 (t-170) REVERT: A 288 PHE cc_start: 0.7649 (t80) cc_final: 0.7355 (t80) REVERT: B 194 ILE cc_start: 0.7798 (mt) cc_final: 0.7551 (mm) REVERT: B 201 TYR cc_start: 0.7281 (OUTLIER) cc_final: 0.6723 (m-80) REVERT: C 16 LYS cc_start: 0.7751 (ttpm) cc_final: 0.7404 (ttpp) REVERT: C 104 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7052 (tm) REVERT: C 106 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8393 (p) REVERT: C 126 TYR cc_start: 0.7936 (t80) cc_final: 0.7730 (t80) REVERT: C 195 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.5347 (m-80) REVERT: D 52 MET cc_start: 0.6045 (mtt) cc_final: 0.5552 (mmm) REVERT: D 72 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7958 (mmmt) REVERT: D 94 PHE cc_start: 0.7815 (t80) cc_final: 0.7309 (t80) REVERT: D 163 LYS cc_start: 0.8201 (mptt) cc_final: 0.7951 (mptt) REVERT: D 202 PHE cc_start: 0.8145 (m-10) cc_final: 0.7701 (m-80) REVERT: D 232 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7611 (mm) REVERT: D 267 ILE cc_start: 0.8031 (mt) cc_final: 0.7758 (mt) REVERT: E 37 HIS cc_start: 0.7305 (OUTLIER) cc_final: 0.6930 (t-90) REVERT: E 41 LEU cc_start: 0.7978 (pt) cc_final: 0.7547 (mt) REVERT: E 52 MET cc_start: 0.7068 (tpp) cc_final: 0.6707 (tpp) REVERT: E 72 LYS cc_start: 0.7162 (mmtt) cc_final: 0.6860 (mmtm) REVERT: E 95 MET cc_start: 0.6501 (mpp) cc_final: 0.5920 (mpp) REVERT: E 98 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7536 (mp) REVERT: E 122 LYS cc_start: 0.5768 (OUTLIER) cc_final: 0.5043 (mmtm) REVERT: E 217 PHE cc_start: 0.7624 (t80) cc_final: 0.7306 (t80) outliers start: 75 outliers final: 40 residues processed: 285 average time/residue: 0.7840 time to fit residues: 253.4852 Evaluate side-chains 262 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 211 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 22 GLU 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 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 156 THR 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 263 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 104 LEU 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 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 40 ASN Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 232 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 71 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.170777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.155320 restraints weight = 13981.432| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.80 r_work: 0.3752 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2292 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= 0.170 Angle : 0.629 13.842 15684 Z= 0.321 Chirality : 0.041 0.174 1776 Planarity : 0.003 0.034 1904 Dihedral : 10.600 93.466 1678 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 6.50 % Allowed : 28.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.23), residues: 1410 helix: 1.27 (0.16), residues: 1109 sheet: None (None), residues: 0 loop : -2.72 (0.31), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 165 PHE 0.026 0.001 PHE A 279 TYR 0.028 0.002 TYR C 70 ARG 0.005 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.04911 ( 795) hydrogen bonds : angle 4.31729 ( 2382) covalent geometry : bond 0.00382 (11549) covalent geometry : angle 0.62939 (15684) *********************** 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 302 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 226 time to evaluate : 1.303 Fit side-chains REVERT: A 72 LYS cc_start: 0.8532 (mmtt) cc_final: 0.8146 (mmtp) REVERT: A 81 MET cc_start: 0.8093 (mmm) cc_final: 0.7851 (mmm) REVERT: A 116 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8112 (tp) REVERT: A 202 PHE cc_start: 0.7231 (m-10) cc_final: 0.6849 (m-10) REVERT: A 212 TYR cc_start: 0.6490 (OUTLIER) cc_final: 0.6237 (m-10) REVERT: A 273 LEU cc_start: 0.8910 (mt) cc_final: 0.8569 (tp) REVERT: A 282 LYS cc_start: 0.7578 (tttt) cc_final: 0.7208 (ttmt) REVERT: A 284 HIS cc_start: 0.7425 (OUTLIER) cc_final: 0.6511 (t-170) REVERT: A 288 PHE cc_start: 0.7727 (t80) cc_final: 0.7395 (t80) REVERT: B 88 PHE cc_start: 0.8075 (t80) cc_final: 0.7570 (t80) REVERT: B 194 ILE cc_start: 0.7875 (mt) cc_final: 0.7620 (mm) REVERT: B 201 TYR cc_start: 0.7371 (OUTLIER) cc_final: 0.6766 (m-80) REVERT: C 16 LYS cc_start: 0.7783 (ttpm) cc_final: 0.7507 (ttpp) REVERT: C 81 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7925 (mtp) REVERT: C 104 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.7007 (tm) REVERT: C 106 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8318 (p) REVERT: C 173 ILE cc_start: 0.8246 (mm) cc_final: 0.8022 (mm) REVERT: C 177 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7827 (mttm) REVERT: C 195 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.5282 (m-80) REVERT: D 52 MET cc_start: 0.6022 (mtt) cc_final: 0.5676 (mmm) REVERT: D 72 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7962 (mmmt) REVERT: D 94 PHE cc_start: 0.7869 (t80) cc_final: 0.7334 (t80) REVERT: D 163 LYS cc_start: 0.8312 (mptt) cc_final: 0.7993 (mptt) REVERT: E 35 LYS cc_start: 0.8417 (ttmm) cc_final: 0.8076 (mtpp) REVERT: E 37 HIS cc_start: 0.7607 (OUTLIER) cc_final: 0.7202 (t-90) REVERT: E 52 MET cc_start: 0.7131 (tpp) cc_final: 0.6778 (tpp) REVERT: E 72 LYS cc_start: 0.7119 (mmtt) cc_final: 0.6851 (mmtm) REVERT: E 122 LYS cc_start: 0.5938 (OUTLIER) cc_final: 0.5191 (mmtm) REVERT: E 162 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6695 (mm-30) REVERT: E 217 PHE cc_start: 0.7615 (t80) cc_final: 0.7270 (t80) REVERT: E 281 TYR cc_start: 0.8004 (m-80) cc_final: 0.7771 (m-80) outliers start: 76 outliers final: 47 residues processed: 281 average time/residue: 0.9665 time to fit residues: 306.3175 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 : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE 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 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 124 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 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 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 52 MET Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 114 MET 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 177 LYS 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 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 20 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS D 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.169491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.154086 restraints weight = 13870.451| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.79 r_work: 0.3737 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2248 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= 0.188 Angle : 0.643 11.915 15684 Z= 0.330 Chirality : 0.042 0.179 1776 Planarity : 0.003 0.035 1904 Dihedral : 10.501 93.313 1674 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 6.58 % Allowed : 29.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.23), residues: 1410 helix: 1.17 (0.16), residues: 1108 sheet: None (None), residues: 0 loop : -2.77 (0.31), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 165 PHE 0.026 0.002 PHE A 279 TYR 0.031 0.002 TYR C 70 ARG 0.005 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.05118 ( 795) hydrogen bonds : angle 4.39873 ( 2382) covalent geometry : bond 0.00424 (11549) covalent geometry : angle 0.64271 (15684) *********************** 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 303 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 226 time to evaluate : 1.298 Fit side-chains REVERT: A 72 LYS cc_start: 0.8524 (mmtt) cc_final: 0.8136 (mmtp) REVERT: A 81 MET cc_start: 0.8107 (mmm) cc_final: 0.7900 (mmm) REVERT: A 116 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8142 (tp) REVERT: A 202 PHE cc_start: 0.7241 (m-10) cc_final: 0.6904 (m-10) REVERT: A 212 TYR cc_start: 0.6490 (OUTLIER) cc_final: 0.6180 (m-10) REVERT: A 273 LEU cc_start: 0.8888 (mt) cc_final: 0.8591 (tp) REVERT: A 282 LYS cc_start: 0.7611 (tttt) cc_final: 0.7229 (ttmt) REVERT: A 284 HIS cc_start: 0.7471 (OUTLIER) cc_final: 0.6545 (t-170) REVERT: A 288 PHE cc_start: 0.7766 (t80) cc_final: 0.7418 (t80) REVERT: B 88 PHE cc_start: 0.8096 (t80) cc_final: 0.7638 (t80) REVERT: B 165 HIS cc_start: 0.7841 (OUTLIER) cc_final: 0.7632 (m-70) REVERT: B 194 ILE cc_start: 0.7886 (mt) cc_final: 0.7634 (mm) REVERT: B 201 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.6672 (m-80) REVERT: C 16 LYS cc_start: 0.7797 (ttpm) cc_final: 0.7496 (ttpp) REVERT: C 81 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7854 (mtp) REVERT: C 104 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6999 (tm) REVERT: C 106 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8249 (p) REVERT: C 173 ILE cc_start: 0.8268 (mm) cc_final: 0.8031 (mm) REVERT: C 177 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7857 (mttm) REVERT: C 195 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.5313 (m-80) REVERT: D 52 MET cc_start: 0.5981 (mtt) cc_final: 0.5594 (tpt) REVERT: D 72 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7955 (mmmt) REVERT: D 94 PHE cc_start: 0.7900 (t80) cc_final: 0.7408 (t80) REVERT: D 163 LYS cc_start: 0.8338 (mptt) cc_final: 0.8000 (mptt) REVERT: E 35 LYS cc_start: 0.8437 (ttmm) cc_final: 0.8099 (mtpp) REVERT: E 37 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.7200 (t-90) REVERT: E 52 MET cc_start: 0.7153 (tpp) cc_final: 0.6643 (tpp) REVERT: E 72 LYS cc_start: 0.7130 (mmtt) cc_final: 0.6868 (mmtm) REVERT: E 95 MET cc_start: 0.6556 (mpp) cc_final: 0.5898 (mpp) REVERT: E 122 LYS cc_start: 0.5944 (OUTLIER) cc_final: 0.5203 (mmtm) REVERT: E 162 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6500 (mm-30) REVERT: E 217 PHE cc_start: 0.7635 (t80) cc_final: 0.7302 (t80) REVERT: E 281 TYR cc_start: 0.8038 (m-80) cc_final: 0.7801 (m-80) outliers start: 77 outliers final: 49 residues processed: 281 average time/residue: 0.7629 time to fit residues: 242.5061 Evaluate side-chains 286 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 224 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE 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 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 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 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 52 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 104 LEU 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 177 LYS Chi-restraints excluded: chain C residue 184 GLU 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 72 LYS Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 156 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 112 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.170203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.154482 restraints weight = 13928.912| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.88 r_work: 0.3735 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2273 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= 0.171 Angle : 0.632 12.252 15684 Z= 0.325 Chirality : 0.041 0.178 1776 Planarity : 0.003 0.035 1904 Dihedral : 10.274 93.685 1674 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 6.75 % Allowed : 29.15 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.23), residues: 1410 helix: 1.23 (0.16), residues: 1104 sheet: None (None), residues: 0 loop : -2.74 (0.31), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 165 PHE 0.028 0.002 PHE A 279 TYR 0.028 0.002 TYR C 70 ARG 0.005 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.04936 ( 795) hydrogen bonds : angle 4.37093 ( 2382) covalent geometry : bond 0.00385 (11549) covalent geometry : angle 0.63238 (15684) *********************** 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 311 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 232 time to evaluate : 1.222 Fit side-chains REVERT: A 33 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6710 (tttm) REVERT: A 72 LYS cc_start: 0.8515 (mmtt) cc_final: 0.8125 (mmtp) REVERT: A 116 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8126 (tp) REVERT: A 202 PHE cc_start: 0.7173 (m-10) cc_final: 0.6851 (m-10) REVERT: A 212 TYR cc_start: 0.6478 (OUTLIER) cc_final: 0.6166 (m-10) REVERT: A 273 LEU cc_start: 0.8919 (mt) cc_final: 0.8601 (tp) REVERT: A 282 LYS cc_start: 0.7569 (tttt) cc_final: 0.7181 (ttmt) REVERT: A 284 HIS cc_start: 0.7315 (OUTLIER) cc_final: 0.6395 (t-170) REVERT: A 288 PHE cc_start: 0.7759 (t80) cc_final: 0.7420 (t80) REVERT: B 88 PHE cc_start: 0.8087 (t80) cc_final: 0.7619 (t80) REVERT: B 194 ILE cc_start: 0.7847 (mt) cc_final: 0.7598 (mm) REVERT: B 201 TYR cc_start: 0.7344 (OUTLIER) cc_final: 0.6705 (m-80) REVERT: C 48 ILE cc_start: 0.7869 (mm) cc_final: 0.7637 (mm) REVERT: C 81 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7868 (mtp) REVERT: C 104 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6983 (tm) REVERT: C 106 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8310 (p) REVERT: C 173 ILE cc_start: 0.8264 (mm) cc_final: 0.8020 (mm) REVERT: C 177 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7827 (mttm) REVERT: C 195 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.5291 (m-80) REVERT: D 52 MET cc_start: 0.5985 (mtt) cc_final: 0.5595 (tpt) REVERT: D 72 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7943 (mmmt) REVERT: D 94 PHE cc_start: 0.7884 (t80) cc_final: 0.7384 (t80) REVERT: D 163 LYS cc_start: 0.8338 (mptt) cc_final: 0.8003 (mptt) REVERT: D 289 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6842 (mm-30) REVERT: E 35 LYS cc_start: 0.8427 (ttmm) cc_final: 0.8090 (mtpp) REVERT: E 37 HIS cc_start: 0.7619 (OUTLIER) cc_final: 0.7192 (t-90) REVERT: E 52 MET cc_start: 0.7151 (tpp) cc_final: 0.6731 (tpp) REVERT: E 72 LYS cc_start: 0.7095 (mmtt) cc_final: 0.6832 (mmtm) REVERT: E 95 MET cc_start: 0.6538 (mpp) cc_final: 0.5847 (mpp) REVERT: E 122 LYS cc_start: 0.5922 (OUTLIER) cc_final: 0.5179 (mmtm) REVERT: E 162 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6447 (mm-30) REVERT: E 217 PHE cc_start: 0.7614 (t80) cc_final: 0.7273 (t80) outliers start: 79 outliers final: 52 residues processed: 286 average time/residue: 0.7389 time to fit residues: 239.5295 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 : 1.190 ------------------------------------------------------------------------------- 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 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 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 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 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 30 GLU 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 104 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 114 MET 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 177 LYS 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 16 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 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 = 0.3973 r_free = 0.3973 target = 0.168764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.153012 restraints weight = 13917.495| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.88 r_work: 0.3727 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2230 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= 0.194 Angle : 0.660 12.684 15684 Z= 0.340 Chirality : 0.042 0.179 1776 Planarity : 0.003 0.036 1904 Dihedral : 10.082 93.534 1674 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 6.41 % Allowed : 29.74 % Favored : 63.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.23), residues: 1410 helix: 1.15 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : -2.61 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 165 PHE 0.028 0.002 PHE A 279 TYR 0.029 0.002 TYR C 70 ARG 0.005 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.05255 ( 795) hydrogen bonds : angle 4.44863 ( 2382) covalent geometry : bond 0.00440 (11549) covalent geometry : angle 0.65983 (15684) ********************** 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 306 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 231 time to evaluate : 1.201 Fit side-chains REVERT: A 33 LYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6765 (tttm) REVERT: A 72 LYS cc_start: 0.8498 (mmtt) cc_final: 0.8104 (mmtp) REVERT: A 116 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8160 (tp) REVERT: A 202 PHE cc_start: 0.7205 (m-10) cc_final: 0.6845 (m-10) REVERT: A 212 TYR cc_start: 0.6563 (OUTLIER) cc_final: 0.6262 (m-10) REVERT: A 273 LEU cc_start: 0.8928 (mt) cc_final: 0.8725 (tp) REVERT: A 282 LYS cc_start: 0.7616 (tttt) cc_final: 0.7211 (ttmt) REVERT: A 284 HIS cc_start: 0.7208 (OUTLIER) cc_final: 0.6330 (t-170) REVERT: A 288 PHE cc_start: 0.7788 (t80) cc_final: 0.7455 (t80) REVERT: B 88 PHE cc_start: 0.8092 (t80) cc_final: 0.7621 (t80) REVERT: B 194 ILE cc_start: 0.7930 (mt) cc_final: 0.7689 (mm) REVERT: B 201 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.6677 (m-80) REVERT: C 48 ILE cc_start: 0.7908 (mm) cc_final: 0.7701 (mm) REVERT: C 81 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7871 (mtp) REVERT: C 104 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7008 (tm) REVERT: C 106 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8319 (p) REVERT: C 173 ILE cc_start: 0.8284 (mm) cc_final: 0.8048 (mm) REVERT: C 177 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7843 (mttm) REVERT: C 195 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.5290 (m-80) REVERT: D 52 MET cc_start: 0.6020 (mtt) cc_final: 0.5607 (tpt) REVERT: D 72 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7584 (mttp) REVERT: D 163 LYS cc_start: 0.8353 (mptt) cc_final: 0.8009 (mptt) REVERT: D 175 GLU cc_start: 0.8136 (tt0) cc_final: 0.7922 (tt0) REVERT: E 35 LYS cc_start: 0.8429 (ttmm) cc_final: 0.8088 (mtpp) REVERT: E 37 HIS cc_start: 0.7653 (OUTLIER) cc_final: 0.7197 (t-90) REVERT: E 52 MET cc_start: 0.7182 (tpp) cc_final: 0.6775 (tpp) REVERT: E 72 LYS cc_start: 0.7081 (mmtt) cc_final: 0.6822 (mmtm) REVERT: E 122 LYS cc_start: 0.5968 (OUTLIER) cc_final: 0.5253 (mmtm) REVERT: E 162 GLU cc_start: 0.7416 (mm-30) cc_final: 0.6480 (mm-30) REVERT: E 217 PHE cc_start: 0.7629 (t80) cc_final: 0.7245 (t80) outliers start: 75 outliers final: 50 residues processed: 285 average time/residue: 0.7777 time to fit residues: 251.7579 Evaluate side-chains 287 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 224 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 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 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 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 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 104 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 114 MET 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 177 LYS 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 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 152 SER Chi-restraints excluded: chain D residue 156 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 49 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 71 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- 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 164 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 = 0.3983 r_free = 0.3983 target = 0.169589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.153866 restraints weight = 13894.532| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.87 r_work: 0.3734 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11549 Z= 0.180 Angle : 0.649 12.563 15684 Z= 0.334 Chirality : 0.042 0.180 1776 Planarity : 0.003 0.035 1904 Dihedral : 9.927 93.850 1674 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 5.90 % Allowed : 30.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.22), residues: 1410 helix: 1.18 (0.16), residues: 1102 sheet: None (None), residues: 0 loop : -2.65 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 165 PHE 0.028 0.002 PHE A 279 TYR 0.027 0.002 TYR C 70 ARG 0.008 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.05053 ( 795) hydrogen bonds : angle 4.41662 ( 2382) covalent geometry : bond 0.00406 (11549) covalent geometry : angle 0.64860 (15684) =============================================================================== Job complete usr+sys time: 8073.91 seconds wall clock time: 141 minutes 27.15 seconds (8487.15 seconds total)