Starting phenix.real_space_refine on Mon Jun 16 01:25:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w55_32314/06_2025/7w55_32314.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w55_32314/06_2025/7w55_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7w55_32314/06_2025/7w55_32314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w55_32314/06_2025/7w55_32314.map" model { file = "/net/cci-nas-00/data/ceres_data/7w55_32314/06_2025/7w55_32314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w55_32314/06_2025/7w55_32314.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.82, per 1000 atoms: 0.48 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: 5.35 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.42 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: 6.82 Time building geometry restraints manager: 6.06 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: 0.510 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: 0.300 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 40.920 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.430 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (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 TRP 0.010 0.002 TRP A 211 HIS 0.009 0.001 HIS B 147 PHE 0.019 0.001 PHE R 284 TYR 0.021 0.002 TYR E 235 ARG 0.003 0.000 ARG R 108 Details of bonding type rmsd hydrogen bonds : bond 0.14859 ( 488) hydrogen bonds : angle 6.66495 ( 1365) SS BOND : bond 0.03225 ( 1) SS BOND : angle 3.45340 ( 2) covalent geometry : bond 0.00489 ( 9427) covalent geometry : angle 0.72146 (12773) *********************** 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 : 1.461 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: 0.7188 (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 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: 0.7578 (mtp) REVERT: E 214 LEU cc_start: 0.8312 (tp) cc_final: 0.8083 (tp) REVERT: G 18 LEU cc_start: 0.7934 (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: 0.6904 (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: 0.8100 (t) outliers start: 5 outliers final: 1 residues processed: 316 average time/residue: 2.3298 time to fit residues: 795.7681 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 : 1.337 ------------------------------------------------------------------------------- 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 96 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.133784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.118374 restraints weight = 37037.291| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.93 r_work: 0.3459 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9428 Z= 0.236 Angle : 0.596 7.553 12775 Z= 0.328 Chirality : 0.043 0.242 1434 Planarity : 0.004 0.041 1622 Dihedral : 5.674 41.238 1273 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.08 % Allowed : 15.64 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1148 helix: 1.40 (0.24), residues: 420 sheet: -0.24 (0.31), residues: 271 loop : -0.29 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 87 HIS 0.006 0.001 HIS R 185 PHE 0.020 0.002 PHE R 284 TYR 0.030 0.002 TYR E 235 ARG 0.003 0.000 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.04965 ( 488) hydrogen bonds : angle 5.41207 ( 1365) SS BOND : bond 0.00202 ( 1) SS BOND : angle 0.22938 ( 2) covalent geometry : bond 0.00524 ( 9427) covalent geometry : angle 0.59580 (12773) *********************** 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 286 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 265 time to evaluate : 1.534 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: A 53 MET cc_start: 0.7579 (mtt) cc_final: 0.7351 (mtt) REVERT: A 231 ASN cc_start: 0.8262 (m-40) cc_final: 0.8051 (m-40) REVERT: A 284 ARG cc_start: 0.7907 (ptp-170) cc_final: 0.7676 (ptp-110) REVERT: A 314 ASP cc_start: 0.7557 (t70) cc_final: 0.7281 (t70) REVERT: B 42 ILE cc_start: 0.8732 (tt) cc_final: 0.8452 (tt) REVERT: B 53 ARG cc_start: 0.8374 (mmt180) cc_final: 0.8167 (mmm160) REVERT: B 135 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7595 (mt-10) REVERT: B 269 TYR cc_start: 0.8476 (m-80) cc_final: 0.8142 (m-80) REVERT: B 273 ASN cc_start: 0.7368 (m110) cc_final: 0.6994 (m110) REVERT: B 282 SER cc_start: 0.8555 (t) cc_final: 0.8193 (m) REVERT: C 24 ARG cc_start: 0.7844 (ttm-80) cc_final: 0.7335 (mtm-85) REVERT: E 66 ARG cc_start: 0.8031 (mtm-85) cc_final: 0.7661 (mtm-85) REVERT: E 82 MET cc_start: 0.8239 (mtt) cc_final: 0.7989 (mtp) REVERT: E 210 THR cc_start: 0.8546 (t) cc_final: 0.8273 (m) REVERT: G 18 LEU cc_start: 0.7893 (mm) cc_final: 0.7534 (mt) REVERT: G 29 VAL cc_start: 0.8880 (t) cc_final: 0.8665 (t) REVERT: R 96 LEU cc_start: 0.7804 (mp) cc_final: 0.7553 (mm) REVERT: R 106 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7491 (mtm) REVERT: R 208 LYS cc_start: 0.8409 (mmmm) cc_final: 0.8183 (mmmm) REVERT: R 320 SER cc_start: 0.8723 (m) cc_final: 0.8320 (t) outliers start: 21 outliers final: 12 residues processed: 275 average time/residue: 2.9144 time to fit residues: 865.1186 Evaluate side-chains 275 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 262 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 323 ARG Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 142 ARG 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 101 LEU Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 169 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 36 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN B 225 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.135529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.120073 restraints weight = 36769.180| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.94 r_work: 0.3486 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2514 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= 0.146 Angle : 0.540 6.704 12775 Z= 0.291 Chirality : 0.041 0.218 1434 Planarity : 0.004 0.040 1622 Dihedral : 5.165 27.375 1271 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.38 % Allowed : 17.62 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1148 helix: 1.88 (0.25), residues: 410 sheet: -0.49 (0.30), residues: 273 loop : -0.20 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 174 HIS 0.006 0.001 HIS R 43 PHE 0.016 0.001 PHE R 284 TYR 0.027 0.001 TYR E 235 ARG 0.008 0.000 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.04318 ( 488) hydrogen bonds : angle 5.03539 ( 1365) SS BOND : bond 0.00100 ( 1) SS BOND : angle 0.18444 ( 2) covalent geometry : bond 0.00317 ( 9427) covalent geometry : angle 0.53955 (12773) *********************** 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: 24 poor density : 266 time to evaluate : 1.303 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 231 ASN cc_start: 0.8254 (m-40) cc_final: 0.8027 (m-40) REVERT: A 284 ARG cc_start: 0.7893 (ptp-170) cc_final: 0.7646 (ptp-110) REVERT: B 42 ILE cc_start: 0.8704 (tt) cc_final: 0.8437 (tt) REVERT: B 53 ARG cc_start: 0.8343 (mmt180) cc_final: 0.8118 (mmm160) REVERT: B 135 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7554 (mt-10) REVERT: B 139 ARG cc_start: 0.7622 (mtm110) cc_final: 0.7355 (mtm110) REVERT: B 269 TYR cc_start: 0.8497 (m-80) cc_final: 0.8216 (m-80) REVERT: B 273 ASN cc_start: 0.7416 (m110) cc_final: 0.7043 (m110) REVERT: B 282 SER cc_start: 0.8595 (t) cc_final: 0.8255 (m) REVERT: B 306 LYS cc_start: 0.8575 (mmmm) cc_final: 0.8368 (mmmt) REVERT: C 24 ARG cc_start: 0.7791 (ttm-80) cc_final: 0.7319 (mtm-85) REVERT: E 18 LYS cc_start: 0.8700 (ttmm) cc_final: 0.8426 (ttmm) REVERT: E 82 MET cc_start: 0.8195 (mtt) cc_final: 0.7944 (mtp) REVERT: E 210 THR cc_start: 0.8545 (t) cc_final: 0.8286 (m) REVERT: G 29 VAL cc_start: 0.8872 (t) cc_final: 0.8643 (t) REVERT: R 96 LEU cc_start: 0.7804 (mp) cc_final: 0.7557 (mm) REVERT: R 101 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7605 (mt) REVERT: R 106 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7448 (mtm) REVERT: R 208 LYS cc_start: 0.8376 (mmmm) cc_final: 0.8138 (mmmm) REVERT: R 320 SER cc_start: 0.8676 (m) cc_final: 0.8374 (t) outliers start: 24 outliers final: 15 residues processed: 277 average time/residue: 2.5216 time to fit residues: 753.1597 Evaluate side-chains 277 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 260 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN 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 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 212 PHE 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 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 45 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN B 225 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 = 0.3783 r_free = 0.3783 target = 0.134607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.119086 restraints weight = 36761.111| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.94 r_work: 0.3462 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2701 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= 0.212 Angle : 0.554 6.374 12775 Z= 0.300 Chirality : 0.042 0.218 1434 Planarity : 0.004 0.042 1622 Dihedral : 5.100 25.869 1271 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.87 % Allowed : 17.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.25), residues: 1148 helix: 1.81 (0.25), residues: 417 sheet: -0.67 (0.29), residues: 269 loop : -0.28 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 174 HIS 0.006 0.001 HIS R 43 PHE 0.019 0.002 PHE R 224 TYR 0.024 0.002 TYR E 235 ARG 0.004 0.000 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.04304 ( 488) hydrogen bonds : angle 4.95667 ( 1365) SS BOND : bond 0.00752 ( 1) SS BOND : angle 0.23997 ( 2) covalent geometry : bond 0.00471 ( 9427) covalent geometry : angle 0.55446 (12773) *********************** 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 290 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 261 time to evaluate : 1.479 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: 0.7596 (mtt) cc_final: 0.7393 (mtt) REVERT: A 185 PHE cc_start: 0.7433 (t80) cc_final: 0.7073 (t80) REVERT: A 214 CYS cc_start: 0.8162 (m) cc_final: 0.7946 (m) REVERT: A 231 ASN cc_start: 0.8310 (m-40) cc_final: 0.8081 (m-40) REVERT: A 284 ARG cc_start: 0.7893 (ptp-170) cc_final: 0.7646 (ptp-110) REVERT: A 309 ARG cc_start: 0.7945 (tmm-80) cc_final: 0.7704 (ttt-90) REVERT: B 42 ILE cc_start: 0.8712 (tt) cc_final: 0.8461 (tt) REVERT: B 53 ARG cc_start: 0.8374 (mmt180) cc_final: 0.8116 (mmm160) REVERT: B 135 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7603 (mt-10) REVERT: B 224 ARG cc_start: 0.7836 (mtp180) cc_final: 0.7371 (ttm110) REVERT: B 259 ASP cc_start: 0.7794 (t70) cc_final: 0.7538 (t0) REVERT: B 269 TYR cc_start: 0.8508 (m-80) cc_final: 0.8257 (m-10) REVERT: B 273 ASN cc_start: 0.7439 (m110) cc_final: 0.7064 (m110) REVERT: B 282 SER cc_start: 0.8595 (t) cc_final: 0.8237 (m) REVERT: C 24 ARG cc_start: 0.7843 (ttm-80) cc_final: 0.7310 (mtm-85) REVERT: E 18 LYS cc_start: 0.8686 (ttmm) cc_final: 0.8450 (ttmm) REVERT: E 210 THR cc_start: 0.8515 (t) cc_final: 0.8278 (m) REVERT: G 18 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7554 (mt) REVERT: G 29 VAL cc_start: 0.8904 (t) cc_final: 0.8704 (t) REVERT: R 96 LEU cc_start: 0.7739 (mp) cc_final: 0.7485 (mm) REVERT: R 106 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7486 (mtm) REVERT: R 208 LYS cc_start: 0.8380 (mmmm) cc_final: 0.8141 (mmmm) REVERT: R 224 PHE cc_start: 0.7863 (m-80) cc_final: 0.7541 (m-80) REVERT: R 320 SER cc_start: 0.8694 (m) cc_final: 0.8406 (t) outliers start: 29 outliers final: 18 residues processed: 274 average time/residue: 2.4060 time to fit residues: 708.1636 Evaluate side-chains 280 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 260 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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 253 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 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 22 SER Chi-restraints excluded: chain E residue 158 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 3 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 B 225 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 = 0.3785 r_free = 0.3785 target = 0.134814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.119390 restraints weight = 37081.500| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.94 r_work: 0.3473 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9428 Z= 0.188 Angle : 0.536 5.992 12775 Z= 0.287 Chirality : 0.041 0.198 1434 Planarity : 0.004 0.043 1622 Dihedral : 4.948 24.818 1271 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.48 % Allowed : 18.02 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1148 helix: 1.87 (0.25), residues: 420 sheet: -0.83 (0.29), residues: 269 loop : -0.33 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 174 HIS 0.008 0.001 HIS R 43 PHE 0.019 0.002 PHE R 284 TYR 0.022 0.001 TYR E 235 ARG 0.006 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 488) hydrogen bonds : angle 4.86643 ( 1365) SS BOND : bond 0.00121 ( 1) SS BOND : angle 0.12503 ( 2) covalent geometry : bond 0.00416 ( 9427) covalent geometry : angle 0.53652 (12773) *********************** 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 294 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 269 time to evaluate : 1.344 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 26 ASP cc_start: 0.7384 (m-30) cc_final: 0.7181 (m-30) REVERT: A 53 MET cc_start: 0.7617 (mtt) cc_final: 0.7402 (mtt) REVERT: A 185 PHE cc_start: 0.7384 (t80) cc_final: 0.7057 (t80) REVERT: A 284 ARG cc_start: 0.7885 (ptp-170) cc_final: 0.7604 (ptp-110) REVERT: B 42 ILE cc_start: 0.8749 (tt) cc_final: 0.8521 (tt) REVERT: B 123 ASP cc_start: 0.7875 (p0) cc_final: 0.7629 (p0) REVERT: B 135 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7613 (mt-10) REVERT: B 195 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7521 (mp) REVERT: B 224 ARG cc_start: 0.7812 (mtp180) cc_final: 0.7580 (mtp180) REVERT: B 269 TYR cc_start: 0.8604 (m-80) cc_final: 0.8399 (m-80) REVERT: B 273 ASN cc_start: 0.7448 (m110) cc_final: 0.7082 (m110) REVERT: B 282 SER cc_start: 0.8603 (t) cc_final: 0.8229 (m) REVERT: C 24 ARG cc_start: 0.7866 (ttm-80) cc_final: 0.7252 (mtm-85) REVERT: E 18 LYS cc_start: 0.8672 (ttmm) cc_final: 0.8471 (ttmm) REVERT: E 210 THR cc_start: 0.8497 (t) cc_final: 0.8279 (m) REVERT: G 29 VAL cc_start: 0.8905 (t) cc_final: 0.8688 (t) REVERT: R 96 LEU cc_start: 0.7773 (mp) cc_final: 0.7516 (mm) REVERT: R 106 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7484 (mtm) REVERT: R 208 LYS cc_start: 0.8358 (mmmm) cc_final: 0.8098 (mmmm) outliers start: 25 outliers final: 19 residues processed: 277 average time/residue: 2.5026 time to fit residues: 750.1240 Evaluate side-chains 283 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 262 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 331 THR 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 195 LEU 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 158 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 68 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 B 225 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.133048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.117329 restraints weight = 37063.385| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.95 r_work: 0.3462 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9428 Z= 0.228 Angle : 0.553 5.763 12775 Z= 0.298 Chirality : 0.042 0.204 1434 Planarity : 0.005 0.050 1622 Dihedral : 4.947 24.424 1271 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.87 % Allowed : 19.11 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1148 helix: 1.90 (0.25), residues: 414 sheet: -0.93 (0.29), residues: 271 loop : -0.36 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 174 HIS 0.008 0.002 HIS R 43 PHE 0.026 0.002 PHE R 224 TYR 0.020 0.002 TYR E 235 ARG 0.006 0.000 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 488) hydrogen bonds : angle 4.87701 ( 1365) SS BOND : bond 0.00117 ( 1) SS BOND : angle 0.30727 ( 2) covalent geometry : bond 0.00509 ( 9427) covalent geometry : angle 0.55338 (12773) *********************** 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 289 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 260 time to evaluate : 1.369 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: 0.7600 (mtt) cc_final: 0.7383 (mtt) REVERT: A 182 SER cc_start: 0.8496 (p) cc_final: 0.8292 (m) REVERT: A 185 PHE cc_start: 0.7389 (t80) cc_final: 0.7075 (t80) REVERT: A 284 ARG cc_start: 0.7825 (ptp-170) cc_final: 0.7570 (ptp-110) REVERT: A 309 ARG cc_start: 0.7993 (tmm-80) cc_final: 0.7734 (ttt-90) REVERT: B 42 ILE cc_start: 0.8787 (tt) cc_final: 0.8548 (tt) REVERT: B 123 ASP cc_start: 0.7856 (p0) cc_final: 0.7620 (p0) REVERT: B 135 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7685 (mt-10) REVERT: B 195 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7570 (mp) REVERT: B 224 ARG cc_start: 0.7839 (mtp180) cc_final: 0.7397 (ttm110) REVERT: B 269 TYR cc_start: 0.8631 (m-80) cc_final: 0.8413 (m-10) REVERT: B 273 ASN cc_start: 0.7462 (m110) cc_final: 0.7092 (m110) REVERT: B 282 SER cc_start: 0.8567 (t) cc_final: 0.8202 (m) REVERT: B 339 SER cc_start: 0.8115 (OUTLIER) cc_final: 0.7828 (p) REVERT: C 24 ARG cc_start: 0.7906 (ttm-80) cc_final: 0.7627 (ttm-80) REVERT: E 18 LYS cc_start: 0.8666 (ttmm) cc_final: 0.8458 (ttmm) REVERT: E 22 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.7928 (p) REVERT: E 66 ARG cc_start: 0.8175 (mtm-85) cc_final: 0.7876 (mtm-85) REVERT: E 219 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8471 (mt) REVERT: G 18 LEU cc_start: 0.7900 (mm) cc_final: 0.7573 (mt) REVERT: G 29 VAL cc_start: 0.8930 (t) cc_final: 0.8727 (t) REVERT: R 96 LEU cc_start: 0.7779 (mp) cc_final: 0.7515 (mm) REVERT: R 106 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7469 (mtm) REVERT: R 208 LYS cc_start: 0.8370 (mmmm) cc_final: 0.8109 (mmmm) outliers start: 29 outliers final: 20 residues processed: 271 average time/residue: 2.3468 time to fit residues: 683.8151 Evaluate side-chains 280 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 255 time to evaluate : 1.514 ------------------------------------------------------------------------------- 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 331 THR 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 195 LEU 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 158 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 B 225 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 = 0.134099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.118457 restraints weight = 36837.970| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.94 r_work: 0.3460 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9428 Z= 0.209 Angle : 0.546 5.657 12775 Z= 0.293 Chirality : 0.041 0.192 1434 Planarity : 0.005 0.053 1622 Dihedral : 4.892 24.248 1271 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.97 % Allowed : 19.90 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1148 helix: 1.94 (0.25), residues: 414 sheet: -0.94 (0.29), residues: 270 loop : -0.39 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 174 HIS 0.009 0.001 HIS R 43 PHE 0.022 0.002 PHE R 224 TYR 0.021 0.002 TYR E 235 ARG 0.007 0.001 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 488) hydrogen bonds : angle 4.84301 ( 1365) SS BOND : bond 0.00147 ( 1) SS BOND : angle 0.37500 ( 2) covalent geometry : bond 0.00465 ( 9427) covalent geometry : angle 0.54646 (12773) *********************** 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 283 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 253 time to evaluate : 1.352 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: 0.7604 (mtt) cc_final: 0.7391 (mtt) REVERT: A 185 PHE cc_start: 0.7393 (t80) cc_final: 0.7052 (t80) REVERT: A 284 ARG cc_start: 0.7847 (ptp-170) cc_final: 0.7588 (ptp-110) REVERT: A 309 ARG cc_start: 0.7985 (tmm-80) cc_final: 0.7720 (ttt-90) REVERT: A 356 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7733 (mtp-110) REVERT: B 42 ILE cc_start: 0.8776 (tt) cc_final: 0.8535 (tt) REVERT: B 135 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7676 (mt-10) REVERT: B 195 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7535 (mp) REVERT: B 224 ARG cc_start: 0.7828 (mtp180) cc_final: 0.7375 (ttm110) REVERT: B 269 TYR cc_start: 0.8640 (m-80) cc_final: 0.8433 (m-10) REVERT: B 273 ASN cc_start: 0.7464 (m110) cc_final: 0.7090 (m110) REVERT: B 282 SER cc_start: 0.8559 (t) cc_final: 0.8182 (m) REVERT: C 24 ARG cc_start: 0.7898 (ttm-80) cc_final: 0.7558 (ttm-80) REVERT: E 22 SER cc_start: 0.8370 (OUTLIER) cc_final: 0.7942 (p) REVERT: E 66 ARG cc_start: 0.8190 (mtm-85) cc_final: 0.7886 (mtm-85) REVERT: G 18 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7575 (mt) REVERT: G 29 VAL cc_start: 0.8903 (t) cc_final: 0.8690 (t) REVERT: R 96 LEU cc_start: 0.7779 (mp) cc_final: 0.7511 (mm) REVERT: R 106 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7447 (mtm) outliers start: 30 outliers final: 21 residues processed: 263 average time/residue: 2.3260 time to fit residues: 658.7675 Evaluate side-chains 272 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 1.440 ------------------------------------------------------------------------------- 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 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 195 LEU 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 158 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 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 95 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 102 optimal weight: 0.4980 chunk 101 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 B 225 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.134761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.119120 restraints weight = 36835.846| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.94 r_work: 0.3488 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3338 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= 0.133 Angle : 0.520 4.967 12775 Z= 0.277 Chirality : 0.040 0.163 1434 Planarity : 0.004 0.052 1622 Dihedral : 4.716 23.971 1271 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.77 % Allowed : 19.90 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.25), residues: 1148 helix: 2.16 (0.25), residues: 413 sheet: -0.80 (0.29), residues: 265 loop : -0.33 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 297 HIS 0.009 0.001 HIS R 43 PHE 0.018 0.001 PHE R 45 TYR 0.018 0.001 TYR E 235 ARG 0.007 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 488) hydrogen bonds : angle 4.71551 ( 1365) SS BOND : bond 0.00187 ( 1) SS BOND : angle 0.43644 ( 2) covalent geometry : bond 0.00291 ( 9427) covalent geometry : angle 0.51994 (12773) *********************** 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 281 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 253 time to evaluate : 1.304 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: 0.7600 (mtt) cc_final: 0.7381 (mtt) REVERT: A 185 PHE cc_start: 0.7370 (t80) cc_final: 0.7041 (t80) REVERT: A 284 ARG cc_start: 0.7832 (ptp-170) cc_final: 0.7577 (ptp-110) REVERT: A 309 ARG cc_start: 0.7965 (tmm-80) cc_final: 0.7693 (ttt-90) REVERT: A 356 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7787 (mtp-110) REVERT: B 27 ARG cc_start: 0.7603 (mtt180) cc_final: 0.7363 (mtt180) REVERT: B 135 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7681 (mt-10) REVERT: B 195 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7464 (mp) REVERT: B 224 ARG cc_start: 0.7777 (mtp180) cc_final: 0.7345 (ttm110) REVERT: B 269 TYR cc_start: 0.8638 (m-80) cc_final: 0.8425 (m-10) REVERT: B 273 ASN cc_start: 0.7448 (m110) cc_final: 0.7083 (m110) REVERT: B 282 SER cc_start: 0.8561 (t) cc_final: 0.8205 (m) REVERT: E 66 ARG cc_start: 0.8153 (mtm-85) cc_final: 0.7898 (mtm-85) REVERT: E 67 PHE cc_start: 0.8213 (m-10) cc_final: 0.7960 (m-10) REVERT: G 18 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7568 (mt) REVERT: G 29 VAL cc_start: 0.8901 (t) cc_final: 0.8696 (t) REVERT: R 96 LEU cc_start: 0.7767 (mp) cc_final: 0.7525 (mm) outliers start: 28 outliers final: 17 residues processed: 262 average time/residue: 2.3464 time to fit residues: 661.3100 Evaluate side-chains 271 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 251 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 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 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 G residue 18 LEU Chi-restraints excluded: chain G residue 20 MET 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 57 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 B 225 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.133571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.117969 restraints weight = 36950.992| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.94 r_work: 0.3473 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9428 Z= 0.197 Angle : 0.543 5.290 12775 Z= 0.290 Chirality : 0.041 0.175 1434 Planarity : 0.005 0.050 1622 Dihedral : 4.747 24.069 1271 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.18 % Allowed : 20.99 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1148 helix: 2.12 (0.25), residues: 414 sheet: -0.84 (0.29), residues: 265 loop : -0.37 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 297 HIS 0.010 0.001 HIS R 43 PHE 0.021 0.002 PHE R 45 TYR 0.018 0.002 TYR E 235 ARG 0.007 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 488) hydrogen bonds : angle 4.75795 ( 1365) SS BOND : bond 0.00147 ( 1) SS BOND : angle 0.50441 ( 2) covalent geometry : bond 0.00440 ( 9427) covalent geometry : angle 0.54300 (12773) *********************** 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 282 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 260 time to evaluate : 1.296 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: 0.7361 (t80) cc_final: 0.7041 (t80) REVERT: A 192 ASP cc_start: 0.8024 (m-30) cc_final: 0.7752 (m-30) REVERT: A 284 ARG cc_start: 0.7838 (ptp-170) cc_final: 0.7580 (ptp-110) REVERT: A 309 ARG cc_start: 0.7980 (tmm-80) cc_final: 0.7747 (ttt-90) REVERT: A 356 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7716 (mtp-110) REVERT: B 27 ARG cc_start: 0.7623 (mtt180) cc_final: 0.7385 (mtt180) REVERT: B 135 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7674 (mt-10) REVERT: B 195 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7510 (mp) REVERT: B 273 ASN cc_start: 0.7463 (m110) cc_final: 0.7104 (m110) REVERT: B 282 SER cc_start: 0.8557 (t) cc_final: 0.8199 (m) REVERT: B 319 ARG cc_start: 0.8087 (ttt-90) cc_final: 0.7859 (ttt180) REVERT: E 22 SER cc_start: 0.8375 (OUTLIER) cc_final: 0.7980 (p) REVERT: G 29 VAL cc_start: 0.8910 (t) cc_final: 0.8697 (t) REVERT: R 96 LEU cc_start: 0.7787 (mp) cc_final: 0.7545 (mm) outliers start: 22 outliers final: 20 residues processed: 267 average time/residue: 2.3487 time to fit residues: 675.7489 Evaluate side-chains 279 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 256 time to evaluate : 1.357 ------------------------------------------------------------------------------- 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 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 G residue 20 MET 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 63 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 B 225 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.134325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.118566 restraints weight = 36776.761| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.94 r_work: 0.3478 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9428 Z= 0.174 Angle : 0.539 5.025 12775 Z= 0.287 Chirality : 0.041 0.171 1434 Planarity : 0.005 0.053 1622 Dihedral : 4.727 22.563 1271 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.48 % Allowed : 21.29 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1148 helix: 2.13 (0.25), residues: 414 sheet: -0.84 (0.30), residues: 265 loop : -0.36 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 174 HIS 0.010 0.001 HIS R 43 PHE 0.020 0.002 PHE R 45 TYR 0.018 0.001 TYR E 235 ARG 0.009 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 488) hydrogen bonds : angle 4.74809 ( 1365) SS BOND : bond 0.00185 ( 1) SS BOND : angle 0.53509 ( 2) covalent geometry : bond 0.00388 ( 9427) covalent geometry : angle 0.53855 (12773) ********************** 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: 25 poor density : 252 time to evaluate : 1.414 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: 0.7324 (t80) cc_final: 0.7010 (t80) REVERT: A 186 GLU cc_start: 0.7314 (mt-10) cc_final: 0.7099 (tt0) REVERT: A 192 ASP cc_start: 0.7974 (m-30) cc_final: 0.7674 (m-30) REVERT: A 284 ARG cc_start: 0.7831 (ptp-170) cc_final: 0.7571 (ptp-110) REVERT: A 309 ARG cc_start: 0.7973 (tmm-80) cc_final: 0.7743 (ttt-90) REVERT: A 356 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7722 (mtp-110) REVERT: B 27 ARG cc_start: 0.7615 (mtt180) cc_final: 0.7376 (mtt180) REVERT: B 135 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7680 (mt-10) REVERT: B 195 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7467 (mp) REVERT: B 224 ARG cc_start: 0.7787 (mtp180) cc_final: 0.7340 (ttm110) REVERT: B 273 ASN cc_start: 0.7468 (m110) cc_final: 0.7105 (m110) REVERT: B 282 SER cc_start: 0.8567 (t) cc_final: 0.8194 (m) REVERT: B 319 ARG cc_start: 0.8081 (ttt-90) cc_final: 0.7848 (ttt180) REVERT: E 22 SER cc_start: 0.8366 (OUTLIER) cc_final: 0.7972 (p) REVERT: G 29 VAL cc_start: 0.8911 (t) cc_final: 0.8699 (t) REVERT: R 96 LEU cc_start: 0.7783 (mp) cc_final: 0.7538 (mm) REVERT: R 192 PHE cc_start: 0.2656 (OUTLIER) cc_final: 0.1972 (p90) outliers start: 25 outliers final: 22 residues processed: 264 average time/residue: 2.3017 time to fit residues: 654.8672 Evaluate side-chains 276 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 250 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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 142 ARG 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 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 6 SER Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain R residue 192 PHE Chi-restraints excluded: chain R residue 287 ASP 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 64 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN A 245 ASN B 41 ASN B 80 GLN B 225 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.135019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.119427 restraints weight = 36809.647| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.92 r_work: 0.3489 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3613 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= 0.133 Angle : 0.523 4.815 12775 Z= 0.276 Chirality : 0.040 0.153 1434 Planarity : 0.004 0.044 1622 Dihedral : 4.624 22.022 1271 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.08 % Allowed : 21.88 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1148 helix: 2.25 (0.25), residues: 413 sheet: -0.80 (0.30), residues: 265 loop : -0.32 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 174 HIS 0.010 0.001 HIS R 43 PHE 0.021 0.001 PHE R 45 TYR 0.017 0.001 TYR E 235 ARG 0.007 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 488) hydrogen bonds : angle 4.67869 ( 1365) SS BOND : bond 0.00195 ( 1) SS BOND : angle 0.54989 ( 2) covalent geometry : bond 0.00293 ( 9427) covalent geometry : angle 0.52273 (12773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17569.83 seconds wall clock time: 303 minutes 0.17 seconds (18180.17 seconds total)