Starting phenix.real_space_refine on Fri Sep 11 19:46:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vqr_21355/09_2026/6vqr_21355.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vqr_21355/09_2026/6vqr_21355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6vqr_21355/09_2026/6vqr_21355.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vqr_21355/09_2026/6vqr_21355.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vqr_21355/09_2026/6vqr_21355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vqr_21355/09_2026/6vqr_21355.map" model { file = "/net/cci-nas-00/data/ceres_data/6vqr_21355/09_2026/6vqr_21355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vqr_21355/09_2026/6vqr_21355.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.312 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 70 5.16 5 C 7482 2.51 5 N 1744 2.21 5 O 1933 1.98 5 F 25 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11254 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2205 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 3, 'TRANS': 277} Chain: "B" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2240 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "C" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2213 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 4, 'TRANS': 277} Chain: "D" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2228 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 4, 'TRANS': 279} Chain: "E" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2263 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 4, 'TRANS': 283} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'R7M': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'R7M': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'R7M': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'R7M': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'R7M': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.74, per 1000 atoms: 0.24 Number of scatterers: 11254 At special positions: 0 Unit cell: (90.72, 99.36, 97.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 F 25 9.00 O 1933 8.00 N 1744 7.00 C 7482 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 268.5 milliseconds 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2620 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 2 sheets defined 81.5% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 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: 2.11 Time building geometry restraints manager: 1.16 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 - 17.97: 5618 17.97 - 35.95: 714 35.95 - 53.92: 176 53.92 - 71.90: 20 71.90 - 89.87: 4 Dihedral angle restraints: 6532 sinusoidal: 2387 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 6529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1669 0.099 - 0.198: 86 0.198 - 0.297: 14 0.297 - 0.396: 5 0.396 - 0.495: 2 Chirality restraints: 1776 Sorted by residual: chirality pdb=" CA LYS A 119 " pdb=" N LYS A 119 " pdb=" C LYS A 119 " pdb=" CB LYS A 119 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.14e+00 chirality pdb=" CA ALA D 79 " pdb=" N ALA D 79 " pdb=" C ALA D 79 " pdb=" CB ALA D 79 " both_signs ideal model delta sigma weight residual False 2.48 2.03 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CA LYS C 256 " pdb=" N LYS C 256 " pdb=" C LYS C 256 " pdb=" CB LYS C 256 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.89e+00 ... (remaining 1773 not shown) Planarity restraints: 1904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 269 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C GLY B 269 " -0.065 2.00e-02 2.50e+03 pdb=" O GLY B 269 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA B 270 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 38 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.15e+00 pdb=" C TYR B 38 " -0.052 2.00e-02 2.50e+03 pdb=" O TYR B 38 " 0.019 2.00e-02 2.50e+03 pdb=" N SER B 39 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 105 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C PHE A 105 " -0.046 2.00e-02 2.50e+03 pdb=" O PHE A 105 " 0.017 2.00e-02 2.50e+03 pdb=" N THR A 106 " 0.015 2.00e-02 2.50e+03 ... (remaining 1901 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 135 2.60 - 3.17: 10469 3.17 - 3.75: 17751 3.75 - 4.32: 25949 4.32 - 4.90: 42847 Nonbonded interactions: 97151 Sorted by model distance: nonbonded pdb=" F05 R7M C 401 " pdb=" O07 R7M C 401 " model vdw 2.021 2.990 nonbonded pdb=" F05 R7M E 401 " pdb=" O07 R7M E 401 " model vdw 2.129 2.990 nonbonded pdb=" F05 R7M A 401 " pdb=" O07 R7M A 401 " model vdw 2.134 2.990 nonbonded pdb=" F05 R7M B 401 " pdb=" O07 R7M B 401 " model vdw 2.137 2.990 nonbonded pdb=" O SER A 17 " pdb=" OG SER A 17 " model vdw 2.213 3.040 ... (remaining 97146 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 290 or resid 401)) selection = (chain 'B' and (resid 12 through 290 or resid 401)) selection = (chain 'C' and resid 12 through 401) selection = (chain 'D' and (resid 12 through 290 or resid 401)) selection = (chain 'E' and (resid 12 through 290 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.050 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.450 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 : 16.455 89.872 3912 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 8.21 % Allowed : 25.21 % Favored : 66.58 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.20), residues: 1410 helix: -1.20 (0.14), residues: 1086 sheet: None (None), residues: 0 loop : -3.68 (0.28), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 293 TYR 0.018 0.002 TYR C 212 PHE 0.021 0.002 PHE B 223 HIS 0.008 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.01340 / 0.67 (11549) covalent geometry : angle 0.96866 / 0.54 (15684) hydrogen bonds : bond 0.13674 / 8.93 ( 795) hydrogen bonds : angle 6.39368 / 4.68 ( 2382) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 301 time to evaluate : 0.376 Fit side-chains REVERT: A 33 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6829 (pptt) REVERT: A 72 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8033 (mmtp) REVERT: A 81 MET cc_start: 0.7225 (mmm) cc_final: 0.6968 (mmm) REVERT: A 95 MET cc_start: 0.7731 (mmm) cc_final: 0.7465 (tpp) REVERT: A 147 PHE cc_start: 0.7520 (m-80) cc_final: 0.7093 (m-80) REVERT: A 212 TYR cc_start: 0.7018 (OUTLIER) cc_final: 0.6214 (m-10) REVERT: A 273 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8566 (tp) REVERT: A 282 LYS cc_start: 0.7476 (tttt) cc_final: 0.7244 (ttmt) REVERT: A 290 ARG cc_start: 0.7049 (mmm-85) cc_final: 0.6752 (mmm160) REVERT: B 164 ASN cc_start: 0.8514 (t0) cc_final: 0.8286 (t160) REVERT: B 202 PHE cc_start: 0.8149 (m-10) cc_final: 0.7889 (m-10) REVERT: B 247 LYS cc_start: 0.7025 (ttmm) cc_final: 0.6818 (ttmm) REVERT: B 251 TYR cc_start: 0.6228 (m-80) cc_final: 0.5973 (m-80) REVERT: C 81 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.6585 (mtp) REVERT: C 201 TYR cc_start: 0.7855 (t80) cc_final: 0.7569 (t80) REVERT: D 33 LYS cc_start: 0.7015 (tmtm) cc_final: 0.6715 (tmtt) REVERT: D 35 LYS cc_start: 0.7907 (tptt) cc_final: 0.7698 (tptp) REVERT: D 106 THR cc_start: 0.8884 (m) cc_final: 0.8466 (p) REVERT: D 120 LYS cc_start: 0.7832 (mmmt) cc_final: 0.7430 (mptt) REVERT: D 271 ILE cc_start: 0.8563 (mm) cc_final: 0.8248 (mp) REVERT: E 33 LYS cc_start: 0.7845 (tttt) cc_final: 0.7532 (tttm) REVERT: E 35 LYS cc_start: 0.8432 (ttmm) cc_final: 0.8158 (mtpp) REVERT: E 52 MET cc_start: 0.7111 (tpp) cc_final: 0.6778 (tpp) REVERT: E 72 LYS cc_start: 0.7102 (mmtt) cc_final: 0.6822 (mmtm) REVERT: E 83 VAL cc_start: 0.8634 (t) cc_final: 0.8391 (t) REVERT: E 95 MET cc_start: 0.6499 (mpp) cc_final: 0.6194 (mpp) REVERT: E 162 GLU cc_start: 0.7478 (mm-30) cc_final: 0.5979 (mm-30) REVERT: E 185 CYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6724 (t) outliers start: 96 outliers final: 58 residues processed: 377 average time/residue: 0.3241 time to fit residues: 138.4024 Evaluate side-chains 333 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 270 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 HIS B 165 HIS B 193 ASN ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN C 137 ASN C 239 ASN D 59 HIS D 171 ASN E 59 HIS ** E 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.168620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.153658 restraints weight = 13845.603| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.74 r_work: 0.3729 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11549 Z= 0.168 Angle : 0.641 8.833 15684 Z= 0.339 Chirality : 0.043 0.189 1776 Planarity : 0.004 0.038 1904 Dihedral : 9.061 59.656 1673 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 6.41 % Allowed : 27.35 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.22), residues: 1410 helix: 0.17 (0.15), residues: 1100 sheet: None (None), residues: 0 loop : -3.51 (0.28), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 290 TYR 0.023 0.002 TYR E 31 PHE 0.022 0.002 PHE B 279 HIS 0.006 0.001 HIS C 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (11549) covalent geometry : angle 0.64098 / 0.34 (15684) hydrogen bonds : bond 0.05234 / 3.63 ( 795) hydrogen bonds : angle 4.72205 / 3.44 ( 2382) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 256 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8236 (mmtp) REVERT: A 81 MET cc_start: 0.8183 (mmm) cc_final: 0.7937 (mmm) REVERT: A 95 MET cc_start: 0.7944 (mmm) cc_final: 0.7437 (tpp) REVERT: A 116 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8069 (tp) REVERT: A 202 PHE cc_start: 0.7187 (m-10) cc_final: 0.6878 (m-10) REVERT: A 273 LEU cc_start: 0.8829 (mt) cc_final: 0.8471 (tp) REVERT: A 282 LYS cc_start: 0.7688 (tttt) cc_final: 0.7371 (ttmm) REVERT: A 290 ARG cc_start: 0.7062 (mmm-85) cc_final: 0.6853 (mmm160) REVERT: B 30 GLU cc_start: 0.8180 (tp30) cc_final: 0.7898 (mm-30) REVERT: B 194 ILE cc_start: 0.7982 (mt) cc_final: 0.7649 (mm) REVERT: B 201 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.6679 (m-80) REVERT: B 279 PHE cc_start: 0.8412 (t80) cc_final: 0.8206 (OUTLIER) REVERT: C 16 LYS cc_start: 0.7866 (ttpm) cc_final: 0.7591 (ttpp) REVERT: C 104 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7131 (tm) REVERT: C 122 LYS cc_start: 0.7346 (mmmt) cc_final: 0.7010 (tptt) REVERT: C 134 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7160 (tt) REVERT: D 72 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7564 (mttp) REVERT: D 163 LYS cc_start: 0.8314 (mptt) cc_final: 0.7990 (mptt) REVERT: D 232 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7786 (mm) REVERT: D 271 ILE cc_start: 0.8492 (mm) cc_final: 0.8166 (mp) REVERT: D 289 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6848 (mp0) REVERT: E 33 LYS cc_start: 0.7719 (tttt) cc_final: 0.7472 (tttp) REVERT: E 37 HIS cc_start: 0.7733 (OUTLIER) cc_final: 0.7218 (t-90) REVERT: E 52 MET cc_start: 0.7256 (tpp) cc_final: 0.6878 (tpp) REVERT: E 72 LYS cc_start: 0.7209 (mmtt) cc_final: 0.6924 (mmtm) REVERT: E 95 MET cc_start: 0.6642 (mpp) cc_final: 0.6377 (mpp) REVERT: E 212 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.7387 (m-80) REVERT: E 217 PHE cc_start: 0.7688 (t80) cc_final: 0.7303 (t80) outliers start: 75 outliers final: 43 residues processed: 308 average time/residue: 0.3055 time to fit residues: 107.2793 Evaluate side-chains 292 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 241 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 2 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3955 r_free = 0.3955 target = 0.167534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.152420 restraints weight = 14061.941| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.78 r_work: 0.3728 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11549 Z= 0.191 Angle : 0.628 7.610 15684 Z= 0.336 Chirality : 0.042 0.176 1776 Planarity : 0.003 0.039 1904 Dihedral : 7.462 58.499 1608 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 7.09 % Allowed : 27.44 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.22), residues: 1410 helix: 0.58 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -3.29 (0.30), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 290 TYR 0.021 0.002 TYR E 31 PHE 0.023 0.002 PHE A 288 HIS 0.006 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (11549) covalent geometry : angle 0.62755 / 0.34 (15684) hydrogen bonds : bond 0.05420 / 3.76 ( 795) hydrogen bonds : angle 4.62450 / 3.36 ( 2382) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 247 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8183 (mmtp) REVERT: A 81 MET cc_start: 0.8160 (mmm) cc_final: 0.7884 (mmm) REVERT: A 95 MET cc_start: 0.7896 (mmm) cc_final: 0.7400 (tpp) REVERT: A 116 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8087 (tp) REVERT: A 202 PHE cc_start: 0.7208 (m-10) cc_final: 0.6870 (m-10) REVERT: A 212 TYR cc_start: 0.6559 (OUTLIER) cc_final: 0.6221 (m-10) REVERT: A 273 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8535 (tp) REVERT: A 282 LYS cc_start: 0.7666 (tttt) cc_final: 0.7328 (ttmm) REVERT: B 88 PHE cc_start: 0.8140 (t80) cc_final: 0.7704 (t80) REVERT: B 194 ILE cc_start: 0.7956 (mt) cc_final: 0.7611 (mm) REVERT: B 201 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.6645 (m-80) REVERT: B 279 PHE cc_start: 0.8347 (t80) cc_final: 0.8144 (t80) REVERT: C 16 LYS cc_start: 0.7834 (ttpm) cc_final: 0.7527 (ttpp) REVERT: C 104 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7160 (tm) REVERT: C 122 LYS cc_start: 0.7181 (mmmt) cc_final: 0.6857 (tptt) REVERT: C 195 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.5334 (m-80) REVERT: D 72 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7602 (mttp) REVERT: D 271 ILE cc_start: 0.8481 (mm) cc_final: 0.8177 (mp) REVERT: D 289 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: E 33 LYS cc_start: 0.7731 (tttt) cc_final: 0.7472 (tttp) REVERT: E 35 LYS cc_start: 0.8508 (ttmm) cc_final: 0.8173 (mtpp) REVERT: E 37 HIS cc_start: 0.7701 (OUTLIER) cc_final: 0.7194 (t-90) REVERT: E 52 MET cc_start: 0.7281 (tpp) cc_final: 0.6902 (tpp) REVERT: E 72 LYS cc_start: 0.7167 (mmtt) cc_final: 0.6889 (mmtm) REVERT: E 95 MET cc_start: 0.6695 (mpp) cc_final: 0.6329 (mpp) REVERT: E 217 PHE cc_start: 0.7655 (t80) cc_final: 0.7264 (t80) outliers start: 83 outliers final: 47 residues processed: 311 average time/residue: 0.3092 time to fit residues: 109.7378 Evaluate side-chains 294 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 238 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 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 250 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 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 121 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 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 192 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 110 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 108 optimal weight: 0.6980 chunk 42 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.169062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.153454 restraints weight = 13903.227| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.87 r_work: 0.3727 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11549 Z= 0.173 Angle : 0.614 8.644 15684 Z= 0.324 Chirality : 0.041 0.178 1776 Planarity : 0.003 0.037 1904 Dihedral : 6.924 54.273 1598 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 7.78 % Allowed : 26.84 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.22), residues: 1410 helix: 0.87 (0.16), residues: 1108 sheet: None (None), residues: 0 loop : -3.24 (0.29), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 290 TYR 0.020 0.002 TYR E 31 PHE 0.027 0.001 PHE A 279 HIS 0.005 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (11549) covalent geometry : angle 0.61365 / 0.32 (15684) hydrogen bonds : bond 0.05087 / 3.53 ( 795) hydrogen bonds : angle 4.47867 / 3.25 ( 2382) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 231 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8540 (mmtt) cc_final: 0.8169 (mmtp) REVERT: A 116 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8108 (tp) REVERT: A 147 PHE cc_start: 0.8013 (m-80) cc_final: 0.7373 (m-80) REVERT: A 202 PHE cc_start: 0.7161 (m-10) cc_final: 0.6827 (m-10) REVERT: A 212 TYR cc_start: 0.6511 (OUTLIER) cc_final: 0.6103 (m-10) REVERT: A 273 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8374 (tp) REVERT: A 282 LYS cc_start: 0.7658 (tttt) cc_final: 0.7302 (ttmm) REVERT: B 194 ILE cc_start: 0.7952 (mt) cc_final: 0.7679 (mm) REVERT: B 201 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.6713 (m-80) REVERT: C 16 LYS cc_start: 0.7808 (ttpm) cc_final: 0.7490 (ttpp) REVERT: C 104 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7141 (tm) REVERT: C 122 LYS cc_start: 0.7258 (mmmt) cc_final: 0.6936 (tptt) REVERT: C 195 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.5308 (m-80) REVERT: D 72 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7564 (mttp) REVERT: D 94 PHE cc_start: 0.7830 (t80) cc_final: 0.7159 (t80) REVERT: D 163 LYS cc_start: 0.8315 (mptt) cc_final: 0.8077 (mptt) REVERT: D 289 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6820 (mp0) REVERT: E 33 LYS cc_start: 0.7745 (tttt) cc_final: 0.7486 (tttp) REVERT: E 37 HIS cc_start: 0.7672 (OUTLIER) cc_final: 0.7219 (t-90) REVERT: E 52 MET cc_start: 0.7266 (tpp) cc_final: 0.6881 (tpp) REVERT: E 72 LYS cc_start: 0.7156 (mmtt) cc_final: 0.6883 (mmtm) REVERT: E 95 MET cc_start: 0.6673 (mpp) cc_final: 0.6309 (mpp) REVERT: E 217 PHE cc_start: 0.7576 (t80) cc_final: 0.7256 (t80) outliers start: 91 outliers final: 56 residues processed: 300 average time/residue: 0.3240 time to fit residues: 110.1634 Evaluate side-chains 291 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 226 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 250 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 279 PHE 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 121 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 80 SER 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 192 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 110 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 115 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 chunk 112 optimal weight: 30.0000 chunk 123 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.168079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.152292 restraints weight = 13907.818| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.87 r_work: 0.3725 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11549 Z= 0.193 Angle : 0.628 8.809 15684 Z= 0.332 Chirality : 0.042 0.180 1776 Planarity : 0.003 0.038 1904 Dihedral : 6.819 54.595 1596 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 7.78 % Allowed : 26.84 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.23), residues: 1410 helix: 0.91 (0.16), residues: 1111 sheet: None (None), residues: 0 loop : -3.24 (0.30), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 290 TYR 0.026 0.002 TYR C 70 PHE 0.026 0.002 PHE A 279 HIS 0.006 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (11549) covalent geometry : angle 0.62826 / 0.33 (15684) hydrogen bonds : bond 0.05298 / 3.68 ( 795) hydrogen bonds : angle 4.48105 / 3.25 ( 2382) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 234 time to evaluate : 0.321 Fit side-chains REVERT: A 72 LYS cc_start: 0.8566 (mmtt) cc_final: 0.8197 (mmtp) REVERT: A 81 MET cc_start: 0.8348 (mmm) cc_final: 0.7878 (mmm) REVERT: A 116 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8136 (tp) REVERT: A 202 PHE cc_start: 0.7180 (m-10) cc_final: 0.6851 (m-10) REVERT: A 212 TYR cc_start: 0.6516 (OUTLIER) cc_final: 0.6149 (m-10) REVERT: A 273 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8531 (tp) REVERT: A 282 LYS cc_start: 0.7642 (tttt) cc_final: 0.7283 (ttmm) REVERT: B 88 PHE cc_start: 0.8149 (t80) cc_final: 0.7732 (t80) REVERT: B 194 ILE cc_start: 0.7972 (mt) cc_final: 0.7699 (mm) REVERT: B 201 TYR cc_start: 0.7391 (OUTLIER) cc_final: 0.6673 (m-80) REVERT: B 243 MET cc_start: 0.7727 (mtt) cc_final: 0.7449 (mtp) REVERT: C 104 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7096 (tm) REVERT: C 106 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8233 (p) REVERT: C 122 LYS cc_start: 0.7176 (mmmt) cc_final: 0.6887 (tptt) REVERT: C 195 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.5372 (m-80) REVERT: D 33 LYS cc_start: 0.7042 (tmtm) cc_final: 0.6645 (tmtt) REVERT: D 72 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7601 (mttp) REVERT: D 163 LYS cc_start: 0.8319 (mptt) cc_final: 0.7974 (mptt) REVERT: D 289 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: E 33 LYS cc_start: 0.7749 (tttt) cc_final: 0.7481 (tttp) REVERT: E 35 LYS cc_start: 0.8501 (ttmm) cc_final: 0.8173 (mtpp) REVERT: E 37 HIS cc_start: 0.7695 (OUTLIER) cc_final: 0.7226 (t-90) REVERT: E 52 MET cc_start: 0.7276 (tpp) cc_final: 0.6896 (tpp) REVERT: E 72 LYS cc_start: 0.7107 (mmtt) cc_final: 0.6829 (mmtm) REVERT: E 95 MET cc_start: 0.6659 (mpp) cc_final: 0.6270 (mpp) REVERT: E 122 LYS cc_start: 0.5935 (OUTLIER) cc_final: 0.5214 (tmmt) REVERT: E 162 GLU cc_start: 0.7487 (mm-30) cc_final: 0.6695 (mm-30) REVERT: E 217 PHE cc_start: 0.7587 (t80) cc_final: 0.7236 (t80) outliers start: 91 outliers final: 60 residues processed: 302 average time/residue: 0.3249 time to fit residues: 111.0284 Evaluate side-chains 298 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 227 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 98 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 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 163 LYS Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 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 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 24 SER Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 263 LEU 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 89 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.167778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.152366 restraints weight = 13922.260| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.78 r_work: 0.3728 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11549 Z= 0.198 Angle : 0.631 9.652 15684 Z= 0.334 Chirality : 0.042 0.182 1776 Planarity : 0.003 0.038 1904 Dihedral : 6.529 56.624 1591 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 8.03 % Allowed : 26.58 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.23), residues: 1410 helix: 0.94 (0.16), residues: 1103 sheet: None (None), residues: 0 loop : -3.11 (0.30), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 290 TYR 0.023 0.002 TYR C 70 PHE 0.027 0.002 PHE A 279 HIS 0.006 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (11549) covalent geometry : angle 0.63066 / 0.33 (15684) hydrogen bonds : bond 0.05350 / 3.71 ( 795) hydrogen bonds : angle 4.49977 / 3.27 ( 2382) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 232 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7938 (mp) REVERT: A 72 LYS cc_start: 0.8551 (mmtt) cc_final: 0.8185 (mmtp) REVERT: A 81 MET cc_start: 0.8324 (mmm) cc_final: 0.7843 (mmm) REVERT: A 98 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7945 (mm) REVERT: A 116 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8138 (tp) REVERT: A 202 PHE cc_start: 0.7190 (m-10) cc_final: 0.6857 (m-10) REVERT: A 212 TYR cc_start: 0.6566 (OUTLIER) cc_final: 0.6194 (m-10) REVERT: A 223 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7631 (t80) REVERT: A 263 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7689 (tt) REVERT: A 273 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8507 (tp) REVERT: A 282 LYS cc_start: 0.7647 (tttt) cc_final: 0.7193 (ttmm) REVERT: A 288 PHE cc_start: 0.7792 (t80) cc_final: 0.7450 (t80) REVERT: B 88 PHE cc_start: 0.8140 (t80) cc_final: 0.7719 (t80) REVERT: B 165 HIS cc_start: 0.7981 (OUTLIER) cc_final: 0.7761 (m-70) REVERT: B 194 ILE cc_start: 0.7950 (mt) cc_final: 0.7674 (mm) REVERT: B 201 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.6657 (m-80) REVERT: B 243 MET cc_start: 0.7726 (mtt) cc_final: 0.7448 (mtp) REVERT: B 279 PHE cc_start: 0.8422 (t80) cc_final: 0.8204 (t80) REVERT: C 35 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7671 (ttpt) REVERT: C 104 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7046 (tm) REVERT: C 106 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8251 (p) REVERT: C 122 LYS cc_start: 0.7206 (mmmt) cc_final: 0.6874 (tptt) REVERT: C 195 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.5379 (m-80) REVERT: D 72 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7607 (mttp) REVERT: D 290 ARG cc_start: 0.7420 (tpp80) cc_final: 0.7172 (tpp80) REVERT: E 33 LYS cc_start: 0.7742 (tttt) cc_final: 0.7474 (tttp) REVERT: E 35 LYS cc_start: 0.8567 (ttmm) cc_final: 0.8285 (mtpp) REVERT: E 37 HIS cc_start: 0.7693 (OUTLIER) cc_final: 0.7221 (t-90) REVERT: E 52 MET cc_start: 0.7272 (tpp) cc_final: 0.6892 (tpp) REVERT: E 72 LYS cc_start: 0.7072 (mmtt) cc_final: 0.6801 (mmtm) REVERT: E 95 MET cc_start: 0.6654 (mpp) cc_final: 0.6256 (mpp) REVERT: E 113 THR cc_start: 0.7442 (OUTLIER) cc_final: 0.7226 (m) REVERT: E 122 LYS cc_start: 0.5927 (OUTLIER) cc_final: 0.5205 (tmmt) REVERT: E 162 GLU cc_start: 0.7487 (mm-30) cc_final: 0.6662 (mm-30) REVERT: E 217 PHE cc_start: 0.7610 (t80) cc_final: 0.7269 (t80) outliers start: 94 outliers final: 56 residues processed: 299 average time/residue: 0.3331 time to fit residues: 112.5816 Evaluate side-chains 301 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 228 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 35 LYS 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 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 156 THR Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 24 SER 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 192 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 83 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 118 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 114 optimal weight: 30.0000 chunk 139 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.170256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.154468 restraints weight = 13930.215| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.89 r_work: 0.3737 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 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 : 0.004 0.049 11549 Z= 0.157 Angle : 0.600 10.988 15684 Z= 0.316 Chirality : 0.041 0.178 1776 Planarity : 0.003 0.036 1904 Dihedral : 6.353 56.605 1591 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 7.18 % Allowed : 27.44 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.23), residues: 1410 helix: 1.10 (0.16), residues: 1105 sheet: None (None), residues: 0 loop : -3.02 (0.30), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 290 TYR 0.028 0.001 TYR C 70 PHE 0.024 0.001 PHE A 279 HIS 0.005 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (11549) covalent geometry : angle 0.60022 / 0.32 (15684) hydrogen bonds : bond 0.04817 / 3.34 ( 795) hydrogen bonds : angle 4.38473 / 3.18 ( 2382) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 236 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7910 (mp) REVERT: A 72 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8158 (mmtp) REVERT: A 81 MET cc_start: 0.8296 (mmm) cc_final: 0.7796 (mmm) REVERT: A 98 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7813 (mm) REVERT: A 116 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8080 (tp) REVERT: A 202 PHE cc_start: 0.7116 (m-10) cc_final: 0.6792 (m-10) REVERT: A 212 TYR cc_start: 0.6456 (OUTLIER) cc_final: 0.6152 (m-10) REVERT: A 223 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7630 (t80) REVERT: A 273 LEU cc_start: 0.8928 (mt) cc_final: 0.8524 (tp) REVERT: A 282 LYS cc_start: 0.7606 (tttt) cc_final: 0.7164 (ttmm) REVERT: A 288 PHE cc_start: 0.7751 (t80) cc_final: 0.7418 (t80) REVERT: B 88 PHE cc_start: 0.8096 (t80) cc_final: 0.7656 (t80) REVERT: B 165 HIS cc_start: 0.7987 (OUTLIER) cc_final: 0.7739 (m-70) REVERT: B 194 ILE cc_start: 0.7912 (mt) cc_final: 0.7652 (mm) REVERT: B 201 TYR cc_start: 0.7398 (OUTLIER) cc_final: 0.6758 (m-80) REVERT: B 243 MET cc_start: 0.7796 (mtt) cc_final: 0.7516 (mtp) REVERT: B 279 PHE cc_start: 0.8373 (t80) cc_final: 0.8172 (t80) REVERT: C 48 ILE cc_start: 0.7565 (mm) cc_final: 0.7353 (mm) REVERT: C 104 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7109 (tm) REVERT: C 106 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8252 (p) REVERT: C 195 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.5276 (m-80) REVERT: D 52 MET cc_start: 0.5958 (mtt) cc_final: 0.5689 (mmm) REVERT: D 72 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7921 (mmmt) REVERT: D 94 PHE cc_start: 0.7903 (t80) cc_final: 0.7295 (t80) REVERT: D 163 LYS cc_start: 0.8247 (mptt) cc_final: 0.8018 (mptt) REVERT: D 289 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: E 33 LYS cc_start: 0.7736 (tttt) cc_final: 0.7472 (tttp) REVERT: E 37 HIS cc_start: 0.7629 (OUTLIER) cc_final: 0.7209 (t-90) REVERT: E 52 MET cc_start: 0.7237 (tpp) cc_final: 0.6847 (tpp) REVERT: E 72 LYS cc_start: 0.7137 (mmtt) cc_final: 0.6860 (mmtm) REVERT: E 122 LYS cc_start: 0.5852 (OUTLIER) cc_final: 0.5266 (mptp) REVERT: E 162 GLU cc_start: 0.7472 (mm-30) cc_final: 0.6723 (mm-30) REVERT: E 217 PHE cc_start: 0.7574 (t80) cc_final: 0.7202 (t80) outliers start: 84 outliers final: 61 residues processed: 298 average time/residue: 0.3190 time to fit residues: 108.0807 Evaluate side-chains 299 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 224 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 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 37 HIS Chi-restraints excluded: chain C residue 38 TYR 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 156 THR 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 24 SER 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 134 LEU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 25 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS B 284 HIS D 234 ASN D 257 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.166350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.150890 restraints weight = 13774.966| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.77 r_work: 0.3698 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11549 Z= 0.233 Angle : 0.676 11.442 15684 Z= 0.355 Chirality : 0.044 0.182 1776 Planarity : 0.003 0.039 1904 Dihedral : 6.500 56.849 1589 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 7.78 % Allowed : 27.35 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.22), residues: 1410 helix: 0.88 (0.16), residues: 1102 sheet: None (None), residues: 0 loop : -2.98 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 290 TYR 0.032 0.002 TYR C 70 PHE 0.026 0.002 PHE A 279 HIS 0.007 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.23 (11549) covalent geometry : angle 0.67592 / 0.35 (15684) hydrogen bonds : bond 0.05728 / 3.97 ( 795) hydrogen bonds : angle 4.57946 / 3.33 ( 2382) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 235 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7957 (mp) REVERT: A 72 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8168 (mmtp) REVERT: A 81 MET cc_start: 0.8379 (mmm) cc_final: 0.7885 (mmm) REVERT: A 98 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7946 (mm) REVERT: A 116 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8190 (tp) REVERT: A 131 THR cc_start: 0.8097 (m) cc_final: 0.7896 (m) REVERT: A 202 PHE cc_start: 0.7314 (m-10) cc_final: 0.6977 (m-10) REVERT: A 212 TYR cc_start: 0.6689 (OUTLIER) cc_final: 0.6373 (m-10) REVERT: A 223 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7715 (t80) REVERT: A 273 LEU cc_start: 0.8909 (mt) cc_final: 0.8591 (tp) REVERT: A 282 LYS cc_start: 0.7671 (tttt) cc_final: 0.7229 (ttmm) REVERT: A 288 PHE cc_start: 0.7839 (t80) cc_final: 0.7509 (t80) REVERT: B 88 PHE cc_start: 0.8121 (t80) cc_final: 0.7685 (t80) REVERT: B 194 ILE cc_start: 0.8026 (mt) cc_final: 0.7755 (mm) REVERT: B 201 TYR cc_start: 0.7395 (OUTLIER) cc_final: 0.6689 (m-80) REVERT: B 243 MET cc_start: 0.7812 (mtt) cc_final: 0.7528 (mtp) REVERT: B 279 PHE cc_start: 0.8398 (t80) cc_final: 0.8182 (t80) REVERT: C 104 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7078 (tm) REVERT: C 106 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8260 (p) REVERT: C 195 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.5318 (m-80) REVERT: D 52 MET cc_start: 0.6061 (mtt) cc_final: 0.5738 (mmm) REVERT: D 72 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7654 (mttp) REVERT: D 123 LEU cc_start: 0.6052 (OUTLIER) cc_final: 0.5770 (pt) REVERT: D 163 LYS cc_start: 0.8279 (mptt) cc_final: 0.8058 (mptt) REVERT: D 215 SER cc_start: 0.7746 (p) cc_final: 0.7423 (p) REVERT: D 266 TYR cc_start: 0.7928 (t80) cc_final: 0.7290 (t80) REVERT: D 289 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: E 33 LYS cc_start: 0.7780 (tttt) cc_final: 0.7506 (tttp) REVERT: E 35 LYS cc_start: 0.8586 (ttmm) cc_final: 0.8302 (mtpp) REVERT: E 37 HIS cc_start: 0.7721 (OUTLIER) cc_final: 0.7297 (t-90) REVERT: E 52 MET cc_start: 0.7393 (tpp) cc_final: 0.7029 (tpp) REVERT: E 72 LYS cc_start: 0.7192 (mmtt) cc_final: 0.6921 (mmtm) REVERT: E 122 LYS cc_start: 0.5983 (OUTLIER) cc_final: 0.5276 (tmmt) REVERT: E 129 VAL cc_start: 0.8052 (t) cc_final: 0.7790 (p) REVERT: E 162 GLU cc_start: 0.7457 (mm-30) cc_final: 0.6563 (mm-30) REVERT: E 217 PHE cc_start: 0.7676 (t80) cc_final: 0.7374 (t80) outliers start: 91 outliers final: 60 residues processed: 300 average time/residue: 0.3213 time to fit residues: 109.3298 Evaluate side-chains 308 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 234 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 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 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 250 VAL Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 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 156 THR Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 105 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 131 optimal weight: 20.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 HIS B 165 HIS D 234 ASN D 257 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.169384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.153458 restraints weight = 13256.622| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.79 r_work: 0.3717 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11549 Z= 0.154 Angle : 0.617 12.203 15684 Z= 0.320 Chirality : 0.041 0.178 1776 Planarity : 0.003 0.038 1904 Dihedral : 6.273 56.517 1589 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 6.84 % Allowed : 28.72 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.23), residues: 1410 helix: 1.15 (0.16), residues: 1100 sheet: None (None), residues: 0 loop : -2.93 (0.30), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 290 TYR 0.028 0.001 TYR C 70 PHE 0.026 0.001 PHE A 279 HIS 0.005 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (11549) covalent geometry : angle 0.61661 / 0.32 (15684) hydrogen bonds : bond 0.04728 / 3.28 ( 795) hydrogen bonds : angle 4.37354 / 3.17 ( 2382) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 227 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.6910 (tmtm) REVERT: A 49 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7948 (mp) REVERT: A 72 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8231 (mmtp) REVERT: A 81 MET cc_start: 0.8210 (mmm) cc_final: 0.7716 (mmm) REVERT: A 98 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7823 (mm) REVERT: A 116 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8068 (tp) REVERT: A 202 PHE cc_start: 0.7106 (m-10) cc_final: 0.6851 (m-10) REVERT: A 212 TYR cc_start: 0.6572 (OUTLIER) cc_final: 0.6273 (m-10) REVERT: A 223 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7637 (t80) REVERT: A 263 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7740 (tt) REVERT: A 273 LEU cc_start: 0.8944 (mt) cc_final: 0.8638 (tp) REVERT: A 282 LYS cc_start: 0.7692 (tttt) cc_final: 0.7226 (ttmm) REVERT: A 284 HIS cc_start: 0.7373 (OUTLIER) cc_final: 0.6493 (t-170) REVERT: A 288 PHE cc_start: 0.7763 (t80) cc_final: 0.7403 (t80) REVERT: B 88 PHE cc_start: 0.8080 (t80) cc_final: 0.7647 (t80) REVERT: B 165 HIS cc_start: 0.7873 (OUTLIER) cc_final: 0.7664 (m90) REVERT: B 194 ILE cc_start: 0.7884 (mt) cc_final: 0.7636 (mm) REVERT: B 201 TYR cc_start: 0.7398 (OUTLIER) cc_final: 0.6711 (m-80) REVERT: B 243 MET cc_start: 0.7801 (mtt) cc_final: 0.7521 (mtp) REVERT: C 104 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7177 (tm) REVERT: C 106 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8258 (p) REVERT: C 195 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.5351 (m-80) REVERT: D 52 MET cc_start: 0.5984 (mtt) cc_final: 0.5733 (mmm) REVERT: D 72 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7981 (mmmt) REVERT: D 163 LYS cc_start: 0.8279 (mptt) cc_final: 0.8056 (mptt) REVERT: D 289 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: E 33 LYS cc_start: 0.7784 (tttt) cc_final: 0.7550 (tttp) REVERT: E 37 HIS cc_start: 0.7622 (OUTLIER) cc_final: 0.7223 (t-90) REVERT: E 52 MET cc_start: 0.7288 (tpp) cc_final: 0.6915 (tpp) REVERT: E 72 LYS cc_start: 0.7247 (mmtt) cc_final: 0.6972 (mmtm) REVERT: E 122 LYS cc_start: 0.5898 (OUTLIER) cc_final: 0.5319 (mptp) REVERT: E 162 GLU cc_start: 0.7462 (mm-30) cc_final: 0.6723 (mm-30) REVERT: E 217 PHE cc_start: 0.7680 (t80) cc_final: 0.7425 (t80) outliers start: 80 outliers final: 51 residues processed: 284 average time/residue: 0.3312 time to fit residues: 106.5829 Evaluate side-chains 290 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 222 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 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 B residue 279 PHE Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 38 TYR 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 156 THR Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 24 SER 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 133 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 122 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 83 optimal weight: 0.1980 chunk 23 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 overall best weight: 5.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.167567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.151596 restraints weight = 13376.465| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.80 r_work: 0.3696 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2111 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= 0.186 Angle : 0.644 12.249 15684 Z= 0.336 Chirality : 0.042 0.181 1776 Planarity : 0.003 0.038 1904 Dihedral : 6.365 56.644 1589 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 6.50 % Allowed : 29.32 % Favored : 64.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.22), residues: 1410 helix: 1.07 (0.16), residues: 1102 sheet: None (None), residues: 0 loop : -2.94 (0.30), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 290 TYR 0.029 0.002 TYR C 70 PHE 0.028 0.002 PHE A 279 HIS 0.005 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (11549) covalent geometry : angle 0.64450 / 0.34 (15684) hydrogen bonds : bond 0.05115 / 3.55 ( 795) hydrogen bonds : angle 4.44695 / 3.22 ( 2382) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 228 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.6951 (tmtm) REVERT: A 49 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7957 (mp) REVERT: A 72 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8232 (mmtp) REVERT: A 81 MET cc_start: 0.8227 (mmm) cc_final: 0.7722 (mmm) REVERT: A 98 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7879 (mm) REVERT: A 116 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8118 (tp) REVERT: A 202 PHE cc_start: 0.7189 (m-10) cc_final: 0.6899 (m-10) REVERT: A 212 TYR cc_start: 0.6602 (OUTLIER) cc_final: 0.6287 (m-10) REVERT: A 223 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7670 (t80) REVERT: A 263 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7778 (tt) REVERT: A 273 LEU cc_start: 0.8958 (mt) cc_final: 0.8649 (tp) REVERT: A 282 LYS cc_start: 0.7715 (tttt) cc_final: 0.7247 (ttmm) REVERT: A 284 HIS cc_start: 0.7462 (OUTLIER) cc_final: 0.6565 (t-170) REVERT: A 288 PHE cc_start: 0.7769 (t80) cc_final: 0.7422 (t80) REVERT: B 88 PHE cc_start: 0.8099 (t80) cc_final: 0.7668 (t80) REVERT: B 194 ILE cc_start: 0.7914 (mt) cc_final: 0.7707 (mm) REVERT: B 201 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.6694 (m-80) REVERT: B 279 PHE cc_start: 0.8468 (t80) cc_final: 0.8223 (t80) REVERT: C 95 MET cc_start: 0.7470 (tpp) cc_final: 0.7239 (mmp) REVERT: C 104 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7149 (tm) REVERT: C 106 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8235 (p) REVERT: C 195 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.5402 (m-80) REVERT: D 52 MET cc_start: 0.6018 (mtt) cc_final: 0.5747 (mmm) REVERT: D 72 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7617 (mttp) REVERT: D 163 LYS cc_start: 0.8288 (mptt) cc_final: 0.8066 (mptt) REVERT: D 289 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: E 33 LYS cc_start: 0.7802 (tttt) cc_final: 0.7557 (tttp) REVERT: E 35 LYS cc_start: 0.8609 (ttmm) cc_final: 0.8324 (mtpp) REVERT: E 37 HIS cc_start: 0.7648 (OUTLIER) cc_final: 0.7222 (t-90) REVERT: E 52 MET cc_start: 0.7265 (tpp) cc_final: 0.6895 (tpp) REVERT: E 72 LYS cc_start: 0.7257 (mmtt) cc_final: 0.6986 (mmtm) REVERT: E 122 LYS cc_start: 0.5970 (OUTLIER) cc_final: 0.5273 (mmtm) REVERT: E 162 GLU cc_start: 0.7418 (mm-30) cc_final: 0.6628 (mm-30) REVERT: E 217 PHE cc_start: 0.7692 (t80) cc_final: 0.7385 (t80) outliers start: 76 outliers final: 53 residues processed: 283 average time/residue: 0.3052 time to fit residues: 97.9291 Evaluate side-chains 290 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 221 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 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 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 37 HIS Chi-restraints excluded: chain C residue 38 TYR 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 156 THR Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain 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 132 ILE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 75 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.170366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.154338 restraints weight = 13395.334| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.81 r_work: 0.3724 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11549 Z= 0.150 Angle : 0.620 12.500 15684 Z= 0.319 Chirality : 0.041 0.176 1776 Planarity : 0.003 0.037 1904 Dihedral : 6.241 56.678 1589 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 6.24 % Allowed : 29.83 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.23), residues: 1410 helix: 1.19 (0.16), residues: 1108 sheet: None (None), residues: 0 loop : -2.87 (0.31), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 290 TYR 0.027 0.001 TYR C 70 PHE 0.033 0.001 PHE B 223 HIS 0.004 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (11549) covalent geometry : angle 0.61967 / 0.32 (15684) hydrogen bonds : bond 0.04601 / 3.20 ( 795) hydrogen bonds : angle 4.33267 / 3.14 ( 2382) =============================================================================== Job complete usr+sys time: 3399.07 seconds wall clock time: 59 minutes 3.30 seconds (3543.30 seconds total)