Starting phenix.real_space_refine on Thu Mar 5 01:23:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w55_32314/03_2026/7w55_32314.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w55_32314/03_2026/7w55_32314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w55_32314/03_2026/7w55_32314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w55_32314/03_2026/7w55_32314.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w55_32314/03_2026/7w55_32314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w55_32314/03_2026/7w55_32314.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 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 55 5.16 5 C 5889 2.51 5 N 1580 2.21 5 O 1698 1.98 5 H 9112 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18334 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3799 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5108 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 157 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3493 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 827 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "R" Number of atoms: 4950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 4950 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 14, 'TRANS': 288} Chain breaks: 1 Time building chain proxies: 3.32, per 1000 atoms: 0.18 Number of scatterers: 18334 At special positions: 0 Unit cell: (115.56, 129.6, 113.4, 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 55 16.00 O 1698 8.00 N 1580 7.00 C 5889 6.00 H 9112 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 204 " distance=2.06 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: 1.64 Conformation dependent library (CDL) restraints added in 630.4 milliseconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2190 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 14 sheets defined 42.1% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.720A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.534A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 245 removed outlier: 4.360A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 4.282A pdb=" N THR A 251 " --> pdb=" O TRP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 298 through 318 Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 9 through 30 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 52 through 55 removed outlier: 3.888A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.754A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 28 through 43 Processing helix chain 'G' and resid 44 through 47 Processing helix chain 'G' and resid 54 through 58 removed outlier: 3.750A pdb=" N ASN G 58 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 73 removed outlier: 3.608A pdb=" N VAL R 51 " --> pdb=" O PRO R 47 " (cutoff:3.500A) Proline residue: R 54 - end of helix removed outlier: 3.717A pdb=" N LEU R 71 " --> pdb=" O CYS R 67 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS R 73 " --> pdb=" O VAL R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 77 Processing helix chain 'R' and resid 78 through 108 Proline residue: R 100 - end of helix Processing helix chain 'R' and resid 115 through 150 Processing helix chain 'R' and resid 150 through 158 Processing helix chain 'R' and resid 159 through 184 Proline residue: R 180 - end of helix removed outlier: 3.859A pdb=" N ILE R 184 " --> pdb=" O PRO R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 225 removed outlier: 3.616A pdb=" N TYR R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 245 Processing helix chain 'R' and resid 246 through 250 Processing helix chain 'R' and resid 258 through 294 removed outlier: 4.310A pdb=" N CYS R 262 " --> pdb=" O ILE R 258 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER R 265 " --> pdb=" O PRO R 261 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS R 268 " --> pdb=" O LYS R 264 " (cutoff:3.500A) Proline residue: R 283 - end of helix removed outlier: 3.539A pdb=" N VAL R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 328 removed outlier: 3.565A pdb=" N SER R 320 " --> pdb=" O PHE R 316 " (cutoff:3.500A) Proline residue: R 324 - end of helix Processing helix chain 'R' and resid 331 through 346 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 9.467A pdb=" N ALA A 220 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 5.894A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.618A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.790A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 158 removed outlier: 3.602A pdb=" N CYS B 153 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N CYS B 171 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.583A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.528A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 264 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.803A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.991A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 removed outlier: 4.376A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.316A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 185 through 187 495 hydrogen bonds defined for protein. 1365 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.55 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 9083 1.02 - 1.21: 43 1.21 - 1.41: 3934 1.41 - 1.61: 5398 1.61 - 1.81: 81 Bond restraints: 18539 Sorted by residual: bond pdb=" SG CYS R 204 " pdb=" HG CYS R 204 " ideal model delta sigma weight residual 1.200 1.344 -0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" SG CYS R 67 " pdb=" HG CYS R 67 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" CA GLU E 234 " pdb=" C GLU E 234 " ideal model delta sigma weight residual 1.523 1.439 0.084 1.21e-02 6.83e+03 4.81e+01 bond pdb=" SG CYS R 119 " pdb=" HG CYS R 119 " ideal model delta sigma weight residual 1.200 1.332 -0.132 2.00e-02 2.50e+03 4.32e+01 bond pdb=" CA ALA B 145 " pdb=" C ALA B 145 " ideal model delta sigma weight residual 1.521 1.462 0.059 1.24e-02 6.50e+03 2.26e+01 ... (remaining 18534 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 33215 3.31 - 6.62: 104 6.62 - 9.92: 11 9.92 - 13.23: 4 13.23 - 16.54: 4 Bond angle restraints: 33338 Sorted by residual: angle pdb=" N LEU R 113 " pdb=" CA LEU R 113 " pdb=" C LEU R 113 " ideal model delta sigma weight residual 111.40 127.18 -15.78 1.22e+00 6.72e-01 1.67e+02 angle pdb=" N PHE R 114 " pdb=" CA PHE R 114 " pdb=" C PHE R 114 " ideal model delta sigma weight residual 111.36 124.83 -13.47 1.09e+00 8.42e-01 1.53e+02 angle pdb=" N HIS R 190 " pdb=" CA HIS R 190 " pdb=" C HIS R 190 " ideal model delta sigma weight residual 110.44 99.99 10.45 1.20e+00 6.94e-01 7.59e+01 angle pdb=" N GLU B 231 " pdb=" CA GLU B 231 " pdb=" C GLU B 231 " ideal model delta sigma weight residual 110.44 100.62 9.82 1.20e+00 6.94e-01 6.69e+01 angle pdb=" N TYR E 235 " pdb=" CA TYR E 235 " pdb=" C TYR E 235 " ideal model delta sigma weight residual 109.81 126.35 -16.54 2.21e+00 2.05e-01 5.60e+01 ... (remaining 33333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 8110 17.79 - 35.58: 410 35.58 - 53.36: 160 53.36 - 71.15: 79 71.15 - 88.94: 12 Dihedral angle restraints: 8771 sinusoidal: 4676 harmonic: 4095 Sorted by residual: dihedral pdb=" N TYR E 235 " pdb=" C TYR E 235 " pdb=" CA TYR E 235 " pdb=" CB TYR E 235 " ideal model delta harmonic sigma weight residual 122.80 145.40 -22.60 0 2.50e+00 1.60e-01 8.17e+01 dihedral pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " pdb=" SG CYS R 204 " pdb=" CB CYS R 204 " ideal model delta sinusoidal sigma weight residual 93.00 168.64 -75.64 1 1.00e+01 1.00e-02 7.22e+01 dihedral pdb=" C TYR E 235 " pdb=" N TYR E 235 " pdb=" CA TYR E 235 " pdb=" CB TYR E 235 " ideal model delta harmonic sigma weight residual -122.60 -143.60 21.00 0 2.50e+00 1.60e-01 7.05e+01 ... (remaining 8768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.230: 1427 0.230 - 0.460: 4 0.460 - 0.689: 2 0.689 - 0.919: 0 0.919 - 1.149: 1 Chirality restraints: 1434 Sorted by residual: chirality pdb=" CA TYR E 235 " pdb=" N TYR E 235 " pdb=" C TYR E 235 " pdb=" CB TYR E 235 " both_signs ideal model delta sigma weight residual False 2.51 1.36 1.15 2.00e-01 2.50e+01 3.30e+01 chirality pdb=" CA PHE R 114 " pdb=" N PHE R 114 " pdb=" C PHE R 114 " pdb=" CB PHE R 114 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.39e+00 chirality pdb=" CA TYR B 64 " pdb=" N TYR B 64 " pdb=" C TYR B 64 " pdb=" CB TYR B 64 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.42e+00 ... (remaining 1431 not shown) Planarity restraints: 2740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS R 204 " -0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C CYS R 204 " 0.058 2.00e-02 2.50e+03 pdb=" O CYS R 204 " -0.021 2.00e-02 2.50e+03 pdb=" N THR R 205 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 145 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.86e+00 pdb=" N GLY B 146 " 0.048 2.00e-02 2.50e+03 pdb=" CA GLY B 146 " -0.013 2.00e-02 2.50e+03 pdb=" H GLY B 146 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 145 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.85e+00 pdb=" C ALA B 145 " 0.048 2.00e-02 2.50e+03 pdb=" O ALA B 145 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY B 146 " -0.016 2.00e-02 2.50e+03 ... (remaining 2737 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 695 2.16 - 2.77: 35930 2.77 - 3.38: 52764 3.38 - 3.99: 68568 3.99 - 4.60: 107025 Nonbonded interactions: 264982 Sorted by model distance: nonbonded pdb=" HG1 THR B 279 " pdb=" O VAL B 320 " model vdw 1.551 2.450 nonbonded pdb="HH12 ARG A 208 " pdb=" OD1 ASP A 239 " model vdw 1.580 2.450 nonbonded pdb="HH11 ARG C 24 " pdb=" OE2 GLU R 102 " model vdw 1.605 2.450 nonbonded pdb=" OD2 ASP B 175 " pdb=" HG1 THR B 178 " model vdw 1.635 2.450 nonbonded pdb=" HG SER B 250 " pdb=" OD1 ASP B 252 " model vdw 1.637 2.450 ... (remaining 264977 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 0.570 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: 0.100 Extract box with map and model: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 18.350 Find NCS groups from input model: 0.060 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:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 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 : 0.005 0.084 9428 Z= 0.305 Angle : 0.723 16.538 12775 Z= 0.455 Chirality : 0.058 1.149 1434 Planarity : 0.004 0.033 1622 Dihedral : 11.825 88.940 3392 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.50 % Allowed : 4.95 % Favored : 94.55 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.25), residues: 1148 helix: 1.24 (0.24), residues: 420 sheet: 0.28 (0.32), residues: 278 loop : -0.12 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 108 TYR 0.021 0.002 TYR E 235 PHE 0.019 0.001 PHE R 284 TRP 0.010 0.002 TRP A 211 HIS 0.009 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 9427) covalent geometry : angle 0.72146 (12773) SS BOND : bond 0.03225 ( 1) SS BOND : angle 3.45340 ( 2) hydrogen bonds : bond 0.14859 ( 488) hydrogen bonds : angle 6.66495 ( 1365) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Evaluate side-chains 317 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 312 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASN cc_start: 0.7524 (p0) cc_final: 0.6887 (p0) REVERT: A 229 ASP cc_start: 0.7118 (t0) cc_final: 0.6639 (t0) REVERT: A 230 TYR cc_start: 0.8340 (m-10) cc_final: 0.8086 (m-10) REVERT: A 231 ASN cc_start: 0.8050 (m-40) cc_final: 0.7646 (m-40) REVERT: A 232 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7828 (mmm-85) REVERT: A 263 LEU cc_start: 0.8201 (mt) cc_final: 0.7983 (mt) REVERT: A 284 ARG cc_start: 0.7526 (ptp-170) cc_final: 0.7319 (ptp-110) REVERT: A 311 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7145 (mm-30) REVERT: A 348 ASP cc_start: 0.7408 (t70) cc_final: 0.7187 (t70) REVERT: B 42 ILE cc_start: 0.8677 (tt) cc_final: 0.8464 (tt) REVERT: B 141 SER cc_start: 0.7973 (t) cc_final: 0.7706 (p) REVERT: B 273 ASN cc_start: 0.6809 (m110) cc_final: 0.6526 (m110) REVERT: C 24 ARG cc_start: 0.7639 (ttm-80) cc_final: 0.7303 (ttm-80) REVERT: E 17 ARG cc_start: 0.7944 (tpp80) cc_final: 0.7668 (tpp80) REVERT: E 66 ARG cc_start: 0.7736 (mtm-85) cc_final: 0.7307 (mtm-85) REVERT: E 82 MET cc_start: 0.7794 (mtt) cc_final: 0.7579 (mtp) REVERT: E 214 LEU cc_start: 0.8312 (tp) cc_final: 0.8083 (tp) REVERT: G 18 LEU cc_start: 0.7933 (mm) cc_final: 0.7552 (mt) REVERT: G 29 VAL cc_start: 0.8890 (t) cc_final: 0.8569 (t) REVERT: R 49 SER cc_start: 0.7652 (t) cc_final: 0.7451 (m) REVERT: R 76 MET cc_start: 0.6543 (tpt) cc_final: 0.6334 (mmm) REVERT: R 204 CYS cc_start: 0.5915 (t) cc_final: 0.5552 (t) REVERT: R 242 ARG cc_start: 0.7319 (tpp80) cc_final: 0.6905 (tpt170) REVERT: R 291 PHE cc_start: 0.7918 (t80) cc_final: 0.7672 (t80) REVERT: R 320 SER cc_start: 0.8363 (m) cc_final: 0.8099 (t) outliers start: 5 outliers final: 1 residues processed: 316 average time/residue: 1.1975 time to fit residues: 405.3014 Evaluate side-chains 271 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 270 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 235 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 190 GLN B 41 ASN B 80 GLN B 180 GLN B 225 GLN R 81 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.134088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.118454 restraints weight = 36965.447| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.96 r_work: 0.3461 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9428 Z= 0.214 Angle : 0.586 6.872 12775 Z= 0.320 Chirality : 0.042 0.225 1434 Planarity : 0.005 0.042 1622 Dihedral : 5.610 39.768 1273 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.18 % Allowed : 16.14 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.25), residues: 1148 helix: 1.43 (0.24), residues: 421 sheet: -0.26 (0.31), residues: 271 loop : -0.28 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 208 TYR 0.026 0.002 TYR E 235 PHE 0.020 0.002 PHE R 284 TRP 0.016 0.002 TRP B 87 HIS 0.005 0.001 HIS R 185 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 9427) covalent geometry : angle 0.58583 (12773) SS BOND : bond 0.00266 ( 1) SS BOND : angle 0.13246 ( 2) hydrogen bonds : bond 0.04666 ( 488) hydrogen bonds : angle 5.29909 ( 1365) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Evaluate side-chains 288 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 266 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8028 (m-30) cc_final: 0.7807 (m-30) REVERT: A 53 MET cc_start: 0.7572 (mtt) cc_final: 0.7340 (mtt) REVERT: A 231 ASN cc_start: 0.8259 (m-40) cc_final: 0.8044 (m-40) REVERT: A 284 ARG cc_start: 0.7896 (ptp-170) cc_final: 0.7652 (ptp-110) REVERT: A 314 ASP cc_start: 0.7583 (t70) cc_final: 0.7318 (t70) REVERT: A 341 ARG cc_start: 0.8319 (mtt-85) cc_final: 0.8022 (mtt90) REVERT: B 42 ILE cc_start: 0.8727 (tt) cc_final: 0.8443 (tt) REVERT: B 135 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7596 (mt-10) REVERT: B 269 TYR cc_start: 0.8463 (m-80) cc_final: 0.8102 (m-80) REVERT: B 273 ASN cc_start: 0.7371 (m110) cc_final: 0.6999 (m110) REVERT: B 282 SER cc_start: 0.8562 (t) cc_final: 0.8206 (m) REVERT: C 24 ARG cc_start: 0.7816 (ttm-80) cc_final: 0.7483 (mtm-85) REVERT: E 12 GLN cc_start: 0.8188 (mp10) cc_final: 0.7985 (mp10) REVERT: E 82 MET cc_start: 0.8230 (mtt) cc_final: 0.7979 (mtp) REVERT: E 210 THR cc_start: 0.8581 (t) cc_final: 0.8311 (m) REVERT: G 18 LEU cc_start: 0.7893 (mm) cc_final: 0.7538 (mt) REVERT: G 29 VAL cc_start: 0.8871 (t) cc_final: 0.8663 (t) REVERT: R 96 LEU cc_start: 0.7811 (mp) cc_final: 0.7596 (mm) REVERT: R 106 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7513 (mtm) REVERT: R 208 LYS cc_start: 0.8399 (mmmm) cc_final: 0.8168 (mmmm) REVERT: R 320 SER cc_start: 0.8710 (m) cc_final: 0.8371 (t) outliers start: 22 outliers final: 13 residues processed: 275 average time/residue: 1.2451 time to fit residues: 365.9605 Evaluate side-chains 273 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 259 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain R residue 106 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 23 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 41 ASN B 93 ASN ** R 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.135177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.119706 restraints weight = 36932.429| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.94 r_work: 0.3476 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9428 Z= 0.163 Angle : 0.547 6.874 12775 Z= 0.297 Chirality : 0.041 0.224 1434 Planarity : 0.004 0.039 1622 Dihedral : 5.181 27.080 1271 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.48 % Allowed : 17.62 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.25), residues: 1148 helix: 1.89 (0.25), residues: 409 sheet: -0.53 (0.30), residues: 272 loop : -0.20 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 139 TYR 0.027 0.001 TYR E 235 PHE 0.018 0.001 PHE R 284 TRP 0.016 0.002 TRP B 174 HIS 0.006 0.001 HIS R 43 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9427) covalent geometry : angle 0.54752 (12773) SS BOND : bond 0.00089 ( 1) SS BOND : angle 0.14508 ( 2) hydrogen bonds : bond 0.04353 ( 488) hydrogen bonds : angle 5.01463 ( 1365) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Evaluate side-chains 290 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 265 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7609 (mtt) cc_final: 0.7383 (mtt) REVERT: A 231 ASN cc_start: 0.8279 (m-40) cc_final: 0.8041 (m-40) REVERT: A 284 ARG cc_start: 0.7896 (ptp-170) cc_final: 0.7650 (ptp-110) REVERT: B 42 ILE cc_start: 0.8698 (tt) cc_final: 0.8440 (tt) REVERT: B 135 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7542 (mt-10) REVERT: B 139 ARG cc_start: 0.7633 (mtm110) cc_final: 0.7383 (mtm110) REVERT: B 269 TYR cc_start: 0.8493 (m-80) cc_final: 0.8204 (m-80) REVERT: B 273 ASN cc_start: 0.7415 (m110) cc_final: 0.7041 (m110) REVERT: B 282 SER cc_start: 0.8590 (t) cc_final: 0.8256 (m) REVERT: B 306 LYS cc_start: 0.8531 (mmmm) cc_final: 0.8306 (mmpt) REVERT: C 24 ARG cc_start: 0.7785 (ttm-80) cc_final: 0.7280 (mtm-85) REVERT: E 12 GLN cc_start: 0.8195 (mp10) cc_final: 0.7934 (mp10) REVERT: E 18 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8425 (ttmm) REVERT: E 82 MET cc_start: 0.8207 (mtt) cc_final: 0.7952 (mtp) REVERT: E 138 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8210 (mp) REVERT: E 210 THR cc_start: 0.8527 (t) cc_final: 0.8279 (m) REVERT: G 29 VAL cc_start: 0.8876 (t) cc_final: 0.8651 (t) REVERT: R 96 LEU cc_start: 0.7807 (mp) cc_final: 0.7564 (mm) REVERT: R 106 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7500 (mtm) REVERT: R 208 LYS cc_start: 0.8383 (mmmm) cc_final: 0.8143 (mmmm) REVERT: R 320 SER cc_start: 0.8685 (m) cc_final: 0.8360 (t) outliers start: 25 outliers final: 16 residues processed: 275 average time/residue: 1.3081 time to fit residues: 383.7802 Evaluate side-chains 279 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 261 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 169 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 89 optimal weight: 0.5980 chunk 109 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 96 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 85 optimal weight: 0.0870 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 181 ASN ** 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 = 0.3809 r_free = 0.3809 target = 0.136554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.121161 restraints weight = 36814.401| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.95 r_work: 0.3498 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9428 Z= 0.114 Angle : 0.512 5.549 12775 Z= 0.273 Chirality : 0.040 0.177 1434 Planarity : 0.004 0.040 1622 Dihedral : 4.858 24.882 1271 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.28 % Allowed : 18.02 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.25), residues: 1148 helix: 2.06 (0.25), residues: 419 sheet: -0.64 (0.30), residues: 269 loop : -0.28 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 160 TYR 0.022 0.001 TYR E 235 PHE 0.015 0.001 PHE R 284 TRP 0.016 0.001 TRP B 174 HIS 0.007 0.001 HIS R 43 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9427) covalent geometry : angle 0.51163 (12773) SS BOND : bond 0.00126 ( 1) SS BOND : angle 0.29364 ( 2) hydrogen bonds : bond 0.03907 ( 488) hydrogen bonds : angle 4.78523 ( 1365) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Evaluate side-chains 293 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 270 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7561 (mtt) cc_final: 0.7342 (mtt) REVERT: A 216 ASN cc_start: 0.7374 (p0) cc_final: 0.7007 (p0) REVERT: A 231 ASN cc_start: 0.8267 (m-40) cc_final: 0.8035 (m-40) REVERT: A 284 ARG cc_start: 0.7881 (ptp-170) cc_final: 0.7638 (ptp-110) REVERT: B 42 ILE cc_start: 0.8695 (tt) cc_final: 0.8451 (tt) REVERT: B 135 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7527 (mt-10) REVERT: B 139 ARG cc_start: 0.7630 (mtm110) cc_final: 0.7318 (mtm110) REVERT: B 224 ARG cc_start: 0.7825 (mtp180) cc_final: 0.7358 (ttm110) REVERT: B 259 ASP cc_start: 0.7786 (t70) cc_final: 0.7532 (t0) REVERT: B 269 TYR cc_start: 0.8490 (m-80) cc_final: 0.8232 (m-80) REVERT: B 273 ASN cc_start: 0.7419 (m110) cc_final: 0.7053 (m110) REVERT: B 282 SER cc_start: 0.8608 (t) cc_final: 0.8264 (m) REVERT: C 24 ARG cc_start: 0.7772 (ttm-80) cc_final: 0.7541 (ttm-80) REVERT: E 12 GLN cc_start: 0.8143 (mp10) cc_final: 0.7939 (mp10) REVERT: E 18 LYS cc_start: 0.8673 (ttmm) cc_final: 0.8418 (ttmm) REVERT: E 46 TRP cc_start: 0.8574 (t60) cc_final: 0.8171 (t60) REVERT: E 82 MET cc_start: 0.8206 (mtt) cc_final: 0.8004 (mtt) REVERT: E 210 THR cc_start: 0.8512 (t) cc_final: 0.8260 (m) REVERT: G 18 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7562 (mt) REVERT: G 29 VAL cc_start: 0.8893 (t) cc_final: 0.8667 (t) REVERT: R 96 LEU cc_start: 0.7724 (mp) cc_final: 0.7479 (mm) REVERT: R 106 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7429 (mtm) REVERT: R 208 LYS cc_start: 0.8355 (mmmm) cc_final: 0.8106 (mmmm) REVERT: R 320 SER cc_start: 0.8674 (m) cc_final: 0.8415 (t) outliers start: 23 outliers final: 15 residues processed: 277 average time/residue: 1.2555 time to fit residues: 372.1246 Evaluate side-chains 283 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 266 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 169 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN B 41 ASN B 80 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.134086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.118606 restraints weight = 36831.845| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.94 r_work: 0.3468 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9428 Z= 0.232 Angle : 0.551 6.172 12775 Z= 0.298 Chirality : 0.042 0.207 1434 Planarity : 0.004 0.045 1622 Dihedral : 4.954 24.281 1271 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.97 % Allowed : 18.32 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.25), residues: 1148 helix: 1.94 (0.25), residues: 420 sheet: -0.76 (0.29), residues: 269 loop : -0.32 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 300 TYR 0.023 0.002 TYR E 235 PHE 0.024 0.002 PHE R 224 TRP 0.016 0.002 TRP B 174 HIS 0.007 0.001 HIS R 43 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 9427) covalent geometry : angle 0.55117 (12773) SS BOND : bond 0.00039 ( 1) SS BOND : angle 0.22340 ( 2) hydrogen bonds : bond 0.04248 ( 488) hydrogen bonds : angle 4.85800 ( 1365) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Evaluate side-chains 298 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 268 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7602 (mtt) cc_final: 0.7388 (mtt) REVERT: A 182 SER cc_start: 0.8505 (p) cc_final: 0.8299 (m) REVERT: A 185 PHE cc_start: 0.7398 (t80) cc_final: 0.7071 (t80) REVERT: A 284 ARG cc_start: 0.7889 (ptp-170) cc_final: 0.7610 (ptp-110) REVERT: A 356 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7840 (mtp180) REVERT: B 42 ILE cc_start: 0.8744 (tt) cc_final: 0.8505 (tt) REVERT: B 135 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7606 (mt-10) REVERT: B 139 ARG cc_start: 0.7660 (mtm110) cc_final: 0.7357 (mtm110) REVERT: B 224 ARG cc_start: 0.7847 (mtp180) cc_final: 0.7392 (ttm110) REVERT: B 256 ARG cc_start: 0.8659 (mtt90) cc_final: 0.8413 (mtt90) REVERT: B 261 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8096 (mtp180) REVERT: B 269 TYR cc_start: 0.8589 (m-80) cc_final: 0.8351 (m-10) REVERT: B 273 ASN cc_start: 0.7467 (m110) cc_final: 0.7102 (m110) REVERT: B 282 SER cc_start: 0.8605 (t) cc_final: 0.8239 (m) REVERT: C 24 ARG cc_start: 0.7857 (ttm-80) cc_final: 0.7569 (ttm-80) REVERT: E 12 GLN cc_start: 0.8086 (mp10) cc_final: 0.7812 (mp10) REVERT: E 18 LYS cc_start: 0.8677 (ttmm) cc_final: 0.8470 (ttmm) REVERT: E 22 SER cc_start: 0.8328 (OUTLIER) cc_final: 0.7907 (p) REVERT: E 67 PHE cc_start: 0.8297 (m-10) cc_final: 0.8046 (m-10) REVERT: E 210 THR cc_start: 0.8523 (t) cc_final: 0.8303 (m) REVERT: G 29 VAL cc_start: 0.8912 (t) cc_final: 0.8690 (t) REVERT: R 77 LYS cc_start: 0.7981 (tttt) cc_final: 0.7578 (tttt) REVERT: R 96 LEU cc_start: 0.7750 (mp) cc_final: 0.7497 (mm) REVERT: R 106 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7449 (mtm) REVERT: R 208 LYS cc_start: 0.8362 (mmmm) cc_final: 0.8103 (mmmm) REVERT: R 320 SER cc_start: 0.8740 (m) cc_final: 0.8319 (t) outliers start: 30 outliers final: 20 residues processed: 279 average time/residue: 1.2782 time to fit residues: 380.9541 Evaluate side-chains 285 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 261 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 287 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 0.0970 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN B 80 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 181 ASN ** 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 = 0.3798 r_free = 0.3798 target = 0.135880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.120387 restraints weight = 36822.071| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.95 r_work: 0.3490 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9428 Z= 0.130 Angle : 0.511 5.139 12775 Z= 0.273 Chirality : 0.040 0.169 1434 Planarity : 0.004 0.043 1622 Dihedral : 4.730 24.191 1271 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.38 % Allowed : 19.50 % Favored : 78.12 % 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: 0.66 (0.25), residues: 1148 helix: 2.15 (0.25), residues: 414 sheet: -0.82 (0.29), residues: 271 loop : -0.26 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 160 TYR 0.019 0.001 TYR E 235 PHE 0.016 0.001 PHE R 284 TRP 0.016 0.001 TRP B 174 HIS 0.008 0.001 HIS R 43 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9427) covalent geometry : angle 0.51138 (12773) SS BOND : bond 0.00216 ( 1) SS BOND : angle 0.23519 ( 2) hydrogen bonds : bond 0.03852 ( 488) hydrogen bonds : angle 4.71504 ( 1365) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Evaluate side-chains 290 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 266 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7580 (mtt) cc_final: 0.7362 (mtt) REVERT: A 185 PHE cc_start: 0.7384 (t80) cc_final: 0.7042 (t80) REVERT: A 195 ASN cc_start: 0.8239 (m-40) cc_final: 0.8013 (m-40) REVERT: A 284 ARG cc_start: 0.7814 (ptp-170) cc_final: 0.7566 (ptp-110) REVERT: A 356 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7890 (mtp180) REVERT: B 42 ILE cc_start: 0.8744 (tt) cc_final: 0.8509 (tt) REVERT: B 135 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7617 (mt-10) REVERT: B 224 ARG cc_start: 0.7842 (mtp180) cc_final: 0.7390 (ttm110) REVERT: B 256 ARG cc_start: 0.8640 (mtt90) cc_final: 0.8419 (mtt90) REVERT: B 261 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8034 (mtp180) REVERT: B 269 TYR cc_start: 0.8579 (m-80) cc_final: 0.8323 (m-10) REVERT: B 273 ASN cc_start: 0.7476 (m110) cc_final: 0.7110 (m110) REVERT: B 282 SER cc_start: 0.8563 (t) cc_final: 0.8233 (m) REVERT: E 22 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.7925 (p) REVERT: E 67 PHE cc_start: 0.8227 (m-10) cc_final: 0.7995 (m-10) REVERT: E 210 THR cc_start: 0.8512 (t) cc_final: 0.8299 (m) REVERT: E 219 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8440 (mt) REVERT: G 18 LEU cc_start: 0.7887 (mm) cc_final: 0.7686 (mt) REVERT: G 29 VAL cc_start: 0.8894 (t) cc_final: 0.8666 (t) REVERT: R 77 LYS cc_start: 0.7974 (tttt) cc_final: 0.7567 (tttt) REVERT: R 96 LEU cc_start: 0.7749 (mp) cc_final: 0.7493 (mm) REVERT: R 106 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7404 (mtm) REVERT: R 320 SER cc_start: 0.8753 (m) cc_final: 0.8370 (t) outliers start: 24 outliers final: 15 residues processed: 274 average time/residue: 1.2453 time to fit residues: 364.8731 Evaluate side-chains 282 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 262 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 106 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 5 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN B 41 ASN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 181 ASN ** 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 = 0.3760 r_free = 0.3760 target = 0.132341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.116992 restraints weight = 36957.882| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.92 r_work: 0.3450 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 9428 Z= 0.291 Angle : 0.577 5.847 12775 Z= 0.312 Chirality : 0.043 0.210 1434 Planarity : 0.005 0.048 1622 Dihedral : 4.948 24.309 1271 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.07 % Allowed : 19.21 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.25), residues: 1148 helix: 1.93 (0.25), residues: 415 sheet: -0.93 (0.29), residues: 271 loop : -0.39 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 32 TYR 0.022 0.002 TYR E 235 PHE 0.026 0.002 PHE R 284 TRP 0.017 0.002 TRP B 174 HIS 0.008 0.002 HIS R 43 Details of bonding type rmsd covalent geometry : bond 0.00656 ( 9427) covalent geometry : angle 0.57660 (12773) SS BOND : bond 0.00095 ( 1) SS BOND : angle 0.25744 ( 2) hydrogen bonds : bond 0.04356 ( 488) hydrogen bonds : angle 4.88920 ( 1365) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Evaluate side-chains 290 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 259 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 PHE cc_start: 0.7377 (t80) cc_final: 0.7055 (t80) REVERT: A 284 ARG cc_start: 0.7836 (ptp-170) cc_final: 0.7577 (ptp-110) REVERT: A 309 ARG cc_start: 0.7995 (tmm-80) cc_final: 0.7710 (ttt-90) REVERT: A 356 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7835 (mtp180) REVERT: B 42 ILE cc_start: 0.8787 (tt) cc_final: 0.8548 (tt) REVERT: B 135 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7650 (mt-10) REVERT: B 195 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7570 (mp) REVERT: B 224 ARG cc_start: 0.7876 (mtp180) cc_final: 0.7432 (ttm110) REVERT: B 269 TYR cc_start: 0.8644 (m-80) cc_final: 0.8443 (m-10) REVERT: B 273 ASN cc_start: 0.7465 (m110) cc_final: 0.7098 (m110) REVERT: B 282 SER cc_start: 0.8552 (t) cc_final: 0.8197 (m) REVERT: B 339 SER cc_start: 0.8115 (OUTLIER) cc_final: 0.7740 (p) REVERT: E 22 SER cc_start: 0.8346 (OUTLIER) cc_final: 0.7942 (p) REVERT: R 77 LYS cc_start: 0.8034 (tttt) cc_final: 0.7644 (tttt) REVERT: R 96 LEU cc_start: 0.7779 (mp) cc_final: 0.7521 (mm) REVERT: R 106 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7451 (mtm) outliers start: 31 outliers final: 18 residues processed: 270 average time/residue: 1.1104 time to fit residues: 322.4685 Evaluate side-chains 278 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 255 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 311 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 41 ASN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 181 ASN ** 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 = 0.3792 r_free = 0.3792 target = 0.135451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.119904 restraints weight = 36965.550| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.94 r_work: 0.3481 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9428 Z= 0.147 Angle : 0.530 5.249 12775 Z= 0.283 Chirality : 0.040 0.175 1434 Planarity : 0.004 0.048 1622 Dihedral : 4.775 23.665 1271 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.57 % Allowed : 20.00 % Favored : 77.43 % 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: 0.57 (0.25), residues: 1148 helix: 2.12 (0.25), residues: 414 sheet: -0.91 (0.29), residues: 271 loop : -0.32 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 32 TYR 0.020 0.001 TYR E 235 PHE 0.020 0.002 PHE R 224 TRP 0.016 0.002 TRP B 174 HIS 0.009 0.001 HIS R 43 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9427) covalent geometry : angle 0.52963 (12773) SS BOND : bond 0.00202 ( 1) SS BOND : angle 0.34504 ( 2) hydrogen bonds : bond 0.03957 ( 488) hydrogen bonds : angle 4.74518 ( 1365) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Evaluate side-chains 277 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 251 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 PHE cc_start: 0.7391 (t80) cc_final: 0.7076 (t80) REVERT: A 284 ARG cc_start: 0.7831 (ptp-170) cc_final: 0.7578 (ptp-110) REVERT: A 309 ARG cc_start: 0.7953 (tmm-80) cc_final: 0.7681 (ttt-90) REVERT: A 356 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7881 (mtp180) REVERT: B 42 ILE cc_start: 0.8775 (tt) cc_final: 0.8548 (tt) REVERT: B 135 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7637 (mt-10) REVERT: B 195 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7480 (mp) REVERT: B 224 ARG cc_start: 0.7841 (mtp180) cc_final: 0.7404 (ttm110) REVERT: B 269 TYR cc_start: 0.8638 (m-80) cc_final: 0.8379 (m-10) REVERT: B 273 ASN cc_start: 0.7451 (m110) cc_final: 0.7077 (m110) REVERT: B 282 SER cc_start: 0.8559 (t) cc_final: 0.8204 (m) REVERT: B 339 SER cc_start: 0.8113 (OUTLIER) cc_final: 0.7820 (p) REVERT: E 67 PHE cc_start: 0.8209 (m-10) cc_final: 0.7972 (m-10) REVERT: G 18 LEU cc_start: 0.7889 (mm) cc_final: 0.7581 (mt) REVERT: R 77 LYS cc_start: 0.8028 (tttt) cc_final: 0.7636 (tttt) REVERT: R 96 LEU cc_start: 0.7763 (mp) cc_final: 0.7504 (mm) outliers start: 26 outliers final: 17 residues processed: 260 average time/residue: 1.2200 time to fit residues: 339.8877 Evaluate side-chains 269 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 249 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 311 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 73 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 chunk 62 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN B 41 ASN B 80 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.134607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.119056 restraints weight = 36723.804| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.93 r_work: 0.3482 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9428 Z= 0.151 Angle : 0.525 4.900 12775 Z= 0.280 Chirality : 0.040 0.162 1434 Planarity : 0.004 0.051 1622 Dihedral : 4.683 23.386 1271 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.18 % Allowed : 20.30 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.25), residues: 1148 helix: 2.22 (0.25), residues: 414 sheet: -0.83 (0.29), residues: 266 loop : -0.35 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 32 TYR 0.017 0.001 TYR E 235 PHE 0.018 0.001 PHE R 45 TRP 0.036 0.002 TRP R 297 HIS 0.010 0.001 HIS R 43 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9427) covalent geometry : angle 0.52508 (12773) SS BOND : bond 0.00186 ( 1) SS BOND : angle 0.40663 ( 2) hydrogen bonds : bond 0.03899 ( 488) hydrogen bonds : angle 4.68589 ( 1365) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Evaluate side-chains 279 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 257 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 PHE cc_start: 0.7376 (t80) cc_final: 0.7065 (t80) REVERT: A 284 ARG cc_start: 0.7838 (ptp-170) cc_final: 0.7582 (ptp-110) REVERT: A 309 ARG cc_start: 0.7962 (tmm-80) cc_final: 0.7702 (ttt-90) REVERT: A 356 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7894 (mtp180) REVERT: B 135 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7646 (mt-10) REVERT: B 195 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7469 (mp) REVERT: B 263 ASP cc_start: 0.7792 (t0) cc_final: 0.7470 (t70) REVERT: B 269 TYR cc_start: 0.8635 (m-80) cc_final: 0.8374 (m-10) REVERT: B 273 ASN cc_start: 0.7454 (m110) cc_final: 0.7087 (m110) REVERT: B 282 SER cc_start: 0.8555 (t) cc_final: 0.8202 (m) REVERT: B 319 ARG cc_start: 0.8078 (ttt-90) cc_final: 0.7863 (ttt180) REVERT: B 339 SER cc_start: 0.8104 (OUTLIER) cc_final: 0.7815 (p) REVERT: E 22 SER cc_start: 0.8358 (OUTLIER) cc_final: 0.7958 (p) REVERT: G 18 LEU cc_start: 0.7873 (mm) cc_final: 0.7548 (mt) REVERT: R 77 LYS cc_start: 0.8038 (tttt) cc_final: 0.7625 (tttt) REVERT: R 96 LEU cc_start: 0.7762 (mp) cc_final: 0.7510 (mm) outliers start: 22 outliers final: 18 residues processed: 265 average time/residue: 1.2264 time to fit residues: 347.9061 Evaluate side-chains 276 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 254 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 311 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 49 optimal weight: 4.9990 chunk 62 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 0.0870 chunk 9 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN B 80 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 181 ASN ** 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 = 0.3804 r_free = 0.3804 target = 0.136260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.120708 restraints weight = 37001.976| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.95 r_work: 0.3490 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9428 Z= 0.128 Angle : 0.519 4.798 12775 Z= 0.275 Chirality : 0.040 0.152 1434 Planarity : 0.004 0.050 1622 Dihedral : 4.584 22.067 1271 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.08 % Allowed : 20.89 % Favored : 77.03 % 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: 0.73 (0.25), residues: 1148 helix: 2.29 (0.25), residues: 413 sheet: -0.78 (0.30), residues: 266 loop : -0.30 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 160 TYR 0.017 0.001 TYR E 235 PHE 0.021 0.001 PHE E 67 TRP 0.019 0.001 TRP R 297 HIS 0.010 0.001 HIS R 43 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9427) covalent geometry : angle 0.51889 (12773) SS BOND : bond 0.00223 ( 1) SS BOND : angle 0.48910 ( 2) hydrogen bonds : bond 0.03778 ( 488) hydrogen bonds : angle 4.63016 ( 1365) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Evaluate side-chains 277 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 256 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 PHE cc_start: 0.7372 (t80) cc_final: 0.7035 (t80) REVERT: A 263 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8254 (mp) REVERT: A 284 ARG cc_start: 0.7836 (ptp-170) cc_final: 0.7577 (ptp-110) REVERT: A 309 ARG cc_start: 0.7940 (tmm-80) cc_final: 0.7664 (ttt-90) REVERT: A 356 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7843 (mtp-110) REVERT: B 135 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7616 (mt-10) REVERT: B 195 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7417 (mp) REVERT: B 224 ARG cc_start: 0.7779 (mtp180) cc_final: 0.7572 (mtp180) REVERT: B 263 ASP cc_start: 0.7791 (t0) cc_final: 0.7472 (t70) REVERT: B 269 TYR cc_start: 0.8637 (m-80) cc_final: 0.8370 (m-10) REVERT: B 273 ASN cc_start: 0.7450 (m110) cc_final: 0.7080 (m110) REVERT: B 282 SER cc_start: 0.8556 (t) cc_final: 0.8205 (m) REVERT: B 319 ARG cc_start: 0.8067 (ttt-90) cc_final: 0.7851 (ttt180) REVERT: E 22 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.7954 (p) REVERT: E 67 PHE cc_start: 0.8117 (m-10) cc_final: 0.7857 (m-10) REVERT: G 18 LEU cc_start: 0.7875 (mm) cc_final: 0.7566 (mt) REVERT: R 77 LYS cc_start: 0.8043 (tttt) cc_final: 0.7617 (tttt) REVERT: R 96 LEU cc_start: 0.7758 (mp) cc_final: 0.7510 (mm) outliers start: 21 outliers final: 17 residues processed: 265 average time/residue: 1.1693 time to fit residues: 332.6290 Evaluate side-chains 279 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 258 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 311 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 0.0010 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 41 ASN B 80 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.135384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.119780 restraints weight = 36740.104| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.94 r_work: 0.3484 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9428 Z= 0.163 Angle : 0.531 4.900 12775 Z= 0.281 Chirality : 0.040 0.160 1434 Planarity : 0.004 0.041 1622 Dihedral : 4.599 22.033 1271 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.08 % Allowed : 21.19 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.25), residues: 1148 helix: 2.27 (0.25), residues: 414 sheet: -0.77 (0.30), residues: 266 loop : -0.31 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 160 TYR 0.017 0.001 TYR E 235 PHE 0.018 0.001 PHE R 45 TRP 0.018 0.002 TRP R 297 HIS 0.011 0.001 HIS R 43 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 9427) covalent geometry : angle 0.53105 (12773) SS BOND : bond 0.00199 ( 1) SS BOND : angle 0.50693 ( 2) hydrogen bonds : bond 0.03859 ( 488) hydrogen bonds : angle 4.64286 ( 1365) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8549.74 seconds wall clock time: 145 minutes 3.66 seconds (8703.66 seconds total)