Starting phenix.real_space_refine on Sat Aug 23 00:58:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gur_34277/08_2025/8gur_34277_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gur_34277/08_2025/8gur_34277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gur_34277/08_2025/8gur_34277_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gur_34277/08_2025/8gur_34277_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gur_34277/08_2025/8gur_34277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gur_34277/08_2025/8gur_34277.map" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5656 2.51 5 N 1505 2.21 5 O 1661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8888 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1827 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 2, 'TRANS': 224} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2188 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 11, 'TRANS': 270} Chain breaks: 1 Chain: "S" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1794 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'9GF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.96, per 1000 atoms: 0.22 Number of scatterers: 8888 At special positions: 0 Unit cell: (93.6, 115.44, 126.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1661 8.00 N 1505 7.00 C 5656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 179 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 339.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 38.8% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.916A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 205 removed outlier: 4.284A pdb=" N ARG A 205 " --> pdb=" O GLY A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.224A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.790A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.860A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.666A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.545A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.701A pdb=" N ARG C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'R' and resid 22 through 27 Processing helix chain 'R' and resid 31 through 62 removed outlier: 4.295A pdb=" N ALA R 35 " --> pdb=" O PRO R 31 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N HIS R 62 " --> pdb=" O ILE R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 66 Processing helix chain 'R' and resid 67 through 95 Processing helix chain 'R' and resid 102 through 137 removed outlier: 4.073A pdb=" N LEU R 107 " --> pdb=" O LYS R 103 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU R 135 " --> pdb=" O ARG R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 172 removed outlier: 3.840A pdb=" N LEU R 151 " --> pdb=" O ARG R 147 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL R 152 " --> pdb=" O GLY R 148 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 187 through 225 removed outlier: 3.502A pdb=" N LEU R 192 " --> pdb=" O ASN R 188 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR R 209 " --> pdb=" O ILE R 205 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY R 210 " --> pdb=" O ILE R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 258 Processing helix chain 'R' and resid 258 through 269 removed outlier: 3.700A pdb=" N LEU R 269 " --> pdb=" O MET R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 276 through 285 Processing helix chain 'R' and resid 285 through 300 removed outlier: 4.137A pdb=" N LEU R 289 " --> pdb=" O SER R 285 " (cutoff:3.500A) Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 303 through 312 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.879A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.946A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.005A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.555A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.693A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.297A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.207A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.409A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.080A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.848A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.014A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 137 removed outlier: 5.800A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN S 182 " --> pdb=" O TYR S 178 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1320 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2858 1.34 - 1.46: 2129 1.46 - 1.58: 3988 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 9071 Sorted by residual: bond pdb=" CAV 9GF R 401 " pdb=" CAW 9GF R 401 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.00e-02 2.50e+03 1.09e+00 bond pdb=" CAD 9GF R 401 " pdb=" CAE 9GF R 401 " ideal model delta sigma weight residual 1.531 1.510 0.021 2.00e-02 2.50e+03 1.06e+00 bond pdb=" CAB 9GF R 401 " pdb=" CAC 9GF R 401 " ideal model delta sigma weight residual 1.527 1.507 0.020 2.00e-02 2.50e+03 9.82e-01 bond pdb=" CAC 9GF R 401 " pdb=" CAD 9GF R 401 " ideal model delta sigma weight residual 1.528 1.509 0.019 2.00e-02 2.50e+03 9.07e-01 bond pdb=" CAA 9GF R 401 " pdb=" CAB 9GF R 401 " ideal model delta sigma weight residual 1.526 1.508 0.018 2.00e-02 2.50e+03 8.10e-01 ... (remaining 9066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 12035 1.45 - 2.91: 195 2.91 - 4.36: 34 4.36 - 5.82: 11 5.82 - 7.27: 6 Bond angle restraints: 12281 Sorted by residual: angle pdb=" C CYS A 3 " pdb=" N THR A 4 " pdb=" CA THR A 4 " ideal model delta sigma weight residual 121.54 126.07 -4.53 1.91e+00 2.74e-01 5.63e+00 angle pdb=" CA TYR S 178 " pdb=" CB TYR S 178 " pdb=" CG TYR S 178 " ideal model delta sigma weight residual 113.90 117.82 -3.92 1.80e+00 3.09e-01 4.73e+00 angle pdb=" CA LEU R 46 " pdb=" CB LEU R 46 " pdb=" CG LEU R 46 " ideal model delta sigma weight residual 116.30 123.57 -7.27 3.50e+00 8.16e-02 4.31e+00 angle pdb=" C MET S 180 " pdb=" N SER S 181 " pdb=" CA SER S 181 " ideal model delta sigma weight residual 123.47 126.58 -3.11 1.53e+00 4.27e-01 4.13e+00 angle pdb=" CA LEU R 71 " pdb=" CB LEU R 71 " pdb=" CG LEU R 71 " ideal model delta sigma weight residual 116.30 123.38 -7.08 3.50e+00 8.16e-02 4.09e+00 ... (remaining 12276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.23: 5282 30.23 - 60.46: 115 60.46 - 90.69: 11 90.69 - 120.92: 3 120.92 - 151.15: 3 Dihedral angle restraints: 5414 sinusoidal: 2117 harmonic: 3297 Sorted by residual: dihedral pdb=" CB CYS R 174 " pdb=" SG CYS R 174 " pdb=" SG CYS R 179 " pdb=" CB CYS R 179 " ideal model delta sinusoidal sigma weight residual -86.00 -144.62 58.62 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CA ARG S 179 " pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta harmonic sigma weight residual -180.00 -147.40 -32.60 0 5.00e+00 4.00e-02 4.25e+01 dihedral pdb=" CAD 9GF R 401 " pdb=" CAE 9GF R 401 " pdb=" CAF 9GF R 401 " pdb=" CAG 9GF R 401 " ideal model delta sinusoidal sigma weight residual -62.05 89.10 -151.15 1 3.00e+01 1.11e-03 2.00e+01 ... (remaining 5411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 929 0.033 - 0.066: 330 0.066 - 0.100: 88 0.100 - 0.133: 50 0.133 - 0.166: 3 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" CG LEU R 43 " pdb=" CB LEU R 43 " pdb=" CD1 LEU R 43 " pdb=" CD2 LEU R 43 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CB THR S 160 " pdb=" CA THR S 160 " pdb=" OG1 THR S 160 " pdb=" CG2 THR S 160 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 1397 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR S 178 " -0.011 2.00e-02 2.50e+03 9.22e-03 1.70e+00 pdb=" CG TYR S 178 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR S 178 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR S 178 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR S 178 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR S 178 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR S 178 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR S 178 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR R 137 " 0.021 5.00e-02 4.00e+02 3.21e-02 1.64e+00 pdb=" N PRO R 138 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO R 138 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 138 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 295 " 0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO R 296 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO R 296 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 296 " 0.017 5.00e-02 4.00e+02 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 168 2.69 - 3.24: 8522 3.24 - 3.79: 14083 3.79 - 4.35: 19070 4.35 - 4.90: 31751 Nonbonded interactions: 73594 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.131 3.040 nonbonded pdb=" OH TYR R 70 " pdb=" OG SER R 303 " model vdw 2.139 3.040 nonbonded pdb=" NH1 ARG B 49 " pdb=" O TYR B 85 " model vdw 2.211 3.120 nonbonded pdb=" O CYS A 254 " pdb=" NZ LYS A 317 " model vdw 2.232 3.120 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.235 3.040 ... (remaining 73589 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.970 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 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 : 0.002 0.027 9074 Z= 0.114 Angle : 0.502 7.270 12287 Z= 0.253 Chirality : 0.040 0.166 1400 Planarity : 0.003 0.038 1544 Dihedral : 13.745 151.154 3279 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.25), residues: 1123 helix: 1.29 (0.26), residues: 391 sheet: -0.19 (0.30), residues: 296 loop : -0.37 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 214 TYR 0.023 0.001 TYR S 178 PHE 0.014 0.001 PHE R 117 TRP 0.007 0.001 TRP B 211 HIS 0.003 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9071) covalent geometry : angle 0.50181 (12281) SS BOND : bond 0.00172 ( 3) SS BOND : angle 0.60283 ( 6) hydrogen bonds : bond 0.20520 ( 459) hydrogen bonds : angle 7.39162 ( 1320) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.405 Fit side-chains REVERT: A 209 LYS cc_start: 0.7656 (pttm) cc_final: 0.7435 (pttm) REVERT: A 309 ASP cc_start: 0.7071 (t70) cc_final: 0.6684 (t0) REVERT: B 6 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7847 (tm-30) REVERT: B 13 GLN cc_start: 0.7721 (tm-30) cc_final: 0.7155 (tm-30) REVERT: B 14 LEU cc_start: 0.8239 (mt) cc_final: 0.7867 (mt) REVERT: B 254 ASP cc_start: 0.7318 (p0) cc_final: 0.7051 (p0) REVERT: R 132 TYR cc_start: 0.7584 (t80) cc_final: 0.7239 (t80) REVERT: R 157 MET cc_start: 0.7218 (tmm) cc_final: 0.6792 (tmm) REVERT: R 237 MET cc_start: 0.4133 (ppp) cc_final: 0.3902 (ppp) REVERT: S 43 LYS cc_start: 0.8370 (mmpt) cc_final: 0.8017 (mmpt) outliers start: 0 outliers final: 1 residues processed: 200 average time/residue: 0.4821 time to fit residues: 103.9656 Evaluate side-chains 184 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 75 GLN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.141991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.124629 restraints weight = 12756.934| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.13 r_work: 0.3530 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9074 Z= 0.166 Angle : 0.577 9.644 12287 Z= 0.298 Chirality : 0.042 0.147 1400 Planarity : 0.004 0.033 1544 Dihedral : 10.372 151.016 1263 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.65 % Allowed : 10.41 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.25), residues: 1123 helix: 1.41 (0.25), residues: 400 sheet: -0.11 (0.30), residues: 281 loop : -0.27 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 149 TYR 0.028 0.002 TYR S 178 PHE 0.012 0.001 PHE B 199 TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 9071) covalent geometry : angle 0.57686 (12281) SS BOND : bond 0.00266 ( 3) SS BOND : angle 1.03479 ( 6) hydrogen bonds : bond 0.04620 ( 459) hydrogen bonds : angle 5.22634 ( 1320) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 209 time to evaluate : 0.354 Fit side-chains REVERT: A 209 LYS cc_start: 0.8246 (pttm) cc_final: 0.8043 (pttm) REVERT: A 309 ASP cc_start: 0.7693 (t70) cc_final: 0.7306 (t0) REVERT: B 4 LEU cc_start: 0.8447 (tt) cc_final: 0.8200 (tm) REVERT: B 6 GLN cc_start: 0.8400 (tm-30) cc_final: 0.7989 (tm-30) REVERT: B 13 GLN cc_start: 0.7964 (tm-30) cc_final: 0.7377 (tm-30) REVERT: B 14 LEU cc_start: 0.8414 (mt) cc_final: 0.8052 (mt) REVERT: B 17 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7926 (tm-30) REVERT: B 254 ASP cc_start: 0.7884 (p0) cc_final: 0.7622 (p0) REVERT: R 132 TYR cc_start: 0.8072 (t80) cc_final: 0.7748 (t80) REVERT: R 157 MET cc_start: 0.7558 (tmm) cc_final: 0.7216 (tmm) REVERT: R 237 MET cc_start: 0.4873 (ppp) cc_final: 0.4636 (ppp) REVERT: S 43 LYS cc_start: 0.8677 (mmpt) cc_final: 0.8306 (mmpt) REVERT: S 148 ARG cc_start: 0.7707 (mtp-110) cc_final: 0.7394 (mtp-110) REVERT: S 201 THR cc_start: 0.8344 (p) cc_final: 0.8128 (t) outliers start: 16 outliers final: 3 residues processed: 213 average time/residue: 0.5234 time to fit residues: 119.0700 Evaluate side-chains 198 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 195 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain R residue 306 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 16 optimal weight: 0.0670 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 75 GLN B 220 GLN R 291 ASN S 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.142832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.125198 restraints weight = 12666.199| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.17 r_work: 0.3531 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9074 Z= 0.142 Angle : 0.533 9.757 12287 Z= 0.276 Chirality : 0.041 0.134 1400 Planarity : 0.003 0.035 1544 Dihedral : 10.318 151.603 1261 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.47 % Allowed : 12.89 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.25), residues: 1123 helix: 1.55 (0.26), residues: 399 sheet: -0.11 (0.29), residues: 283 loop : -0.38 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 168 TYR 0.023 0.001 TYR S 178 PHE 0.015 0.001 PHE R 117 TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9071) covalent geometry : angle 0.53239 (12281) SS BOND : bond 0.00237 ( 3) SS BOND : angle 0.83749 ( 6) hydrogen bonds : bond 0.04076 ( 459) hydrogen bonds : angle 4.98178 ( 1320) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.241 Fit side-chains REVERT: A 197 LYS cc_start: 0.8240 (mmmt) cc_final: 0.7958 (mmmt) REVERT: A 309 ASP cc_start: 0.7693 (t70) cc_final: 0.7312 (t0) REVERT: B 6 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8032 (tm-30) REVERT: B 13 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7373 (tm-30) REVERT: B 14 LEU cc_start: 0.8460 (mt) cc_final: 0.8093 (mt) REVERT: B 17 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7875 (tm-30) REVERT: B 146 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8081 (mt) REVERT: B 254 ASP cc_start: 0.7927 (p0) cc_final: 0.7664 (p0) REVERT: R 132 TYR cc_start: 0.8101 (t80) cc_final: 0.7798 (t80) REVERT: R 157 MET cc_start: 0.7568 (tmm) cc_final: 0.7297 (tmm) REVERT: R 237 MET cc_start: 0.4896 (ppp) cc_final: 0.4650 (ppp) REVERT: S 43 LYS cc_start: 0.8689 (mmpt) cc_final: 0.8302 (mmpt) REVERT: S 83 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8097 (mtm) REVERT: S 148 ARG cc_start: 0.7753 (mtp-110) cc_final: 0.7462 (mtp-110) outliers start: 24 outliers final: 12 residues processed: 205 average time/residue: 0.4976 time to fit residues: 109.3346 Evaluate side-chains 211 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 30 optimal weight: 0.0970 chunk 61 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 42 optimal weight: 0.0000 chunk 91 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 75 GLN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.141767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.124123 restraints weight = 12817.285| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.18 r_work: 0.3531 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9074 Z= 0.134 Angle : 0.534 10.045 12287 Z= 0.272 Chirality : 0.041 0.134 1400 Planarity : 0.003 0.032 1544 Dihedral : 10.303 151.821 1261 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.40 % Allowed : 14.54 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.25), residues: 1123 helix: 1.61 (0.26), residues: 399 sheet: -0.07 (0.30), residues: 285 loop : -0.41 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 168 TYR 0.025 0.001 TYR S 178 PHE 0.022 0.001 PHE R 281 TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9071) covalent geometry : angle 0.53428 (12281) SS BOND : bond 0.00229 ( 3) SS BOND : angle 0.74205 ( 6) hydrogen bonds : bond 0.03771 ( 459) hydrogen bonds : angle 4.81121 ( 1320) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 0.344 Fit side-chains REVERT: A 9 ASP cc_start: 0.7503 (m-30) cc_final: 0.7152 (m-30) REVERT: A 197 LYS cc_start: 0.8286 (mmmt) cc_final: 0.8014 (mmmt) REVERT: A 309 ASP cc_start: 0.7713 (t70) cc_final: 0.7329 (t0) REVERT: B 6 GLN cc_start: 0.8395 (tm-30) cc_final: 0.8031 (tm-30) REVERT: B 13 GLN cc_start: 0.7972 (tm-30) cc_final: 0.7407 (tm-30) REVERT: B 14 LEU cc_start: 0.8477 (mt) cc_final: 0.8100 (mt) REVERT: B 17 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7881 (tm-30) REVERT: B 190 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8184 (OUTLIER) REVERT: B 239 ASN cc_start: 0.8416 (m110) cc_final: 0.7930 (m110) REVERT: B 254 ASP cc_start: 0.7913 (p0) cc_final: 0.7651 (p0) REVERT: R 132 TYR cc_start: 0.8107 (t80) cc_final: 0.7761 (t80) REVERT: R 157 MET cc_start: 0.7567 (tmm) cc_final: 0.7293 (tmm) REVERT: R 237 MET cc_start: 0.4895 (ppp) cc_final: 0.4676 (ppp) REVERT: R 285 SER cc_start: 0.8156 (m) cc_final: 0.7893 (p) REVERT: S 43 LYS cc_start: 0.8691 (mmpt) cc_final: 0.8288 (mmpt) REVERT: S 83 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8156 (mtm) outliers start: 33 outliers final: 20 residues processed: 221 average time/residue: 0.5030 time to fit residues: 119.0443 Evaluate side-chains 215 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 96 optimal weight: 0.0570 chunk 16 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 75 GLN B 119 ASN B 125 ASN B 155 ASN B 220 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.140797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.123268 restraints weight = 12839.411| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.15 r_work: 0.3522 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9074 Z= 0.166 Angle : 0.548 10.169 12287 Z= 0.279 Chirality : 0.041 0.136 1400 Planarity : 0.003 0.031 1544 Dihedral : 10.319 152.116 1261 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.30 % Allowed : 15.88 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.25), residues: 1123 helix: 1.53 (0.26), residues: 399 sheet: -0.09 (0.30), residues: 286 loop : -0.44 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 168 TYR 0.024 0.001 TYR S 178 PHE 0.022 0.002 PHE R 281 TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 9071) covalent geometry : angle 0.54805 (12281) SS BOND : bond 0.00244 ( 3) SS BOND : angle 0.79166 ( 6) hydrogen bonds : bond 0.03800 ( 459) hydrogen bonds : angle 4.78228 ( 1320) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.275 Fit side-chains REVERT: A 8 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7448 (mt-10) REVERT: A 197 LYS cc_start: 0.8302 (mmmt) cc_final: 0.8064 (mmmt) REVERT: A 309 ASP cc_start: 0.7775 (t70) cc_final: 0.7395 (t0) REVERT: B 6 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8016 (tm-30) REVERT: B 13 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7387 (tm-30) REVERT: B 14 LEU cc_start: 0.8513 (mt) cc_final: 0.8098 (mt) REVERT: B 17 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7904 (tm-30) REVERT: B 147 SER cc_start: 0.8107 (p) cc_final: 0.7900 (p) REVERT: B 190 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8144 (pt) REVERT: B 227 SER cc_start: 0.8669 (t) cc_final: 0.8389 (m) REVERT: B 254 ASP cc_start: 0.7860 (p0) cc_final: 0.7595 (p0) REVERT: R 132 TYR cc_start: 0.8166 (t80) cc_final: 0.7832 (t80) REVERT: R 157 MET cc_start: 0.7585 (tmm) cc_final: 0.7293 (tmm) REVERT: R 285 SER cc_start: 0.8155 (m) cc_final: 0.7927 (p) REVERT: R 306 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7761 (tp) REVERT: S 43 LYS cc_start: 0.8698 (mmpt) cc_final: 0.8289 (mmpt) REVERT: S 83 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8183 (mtm) outliers start: 32 outliers final: 18 residues processed: 209 average time/residue: 0.4857 time to fit residues: 108.8261 Evaluate side-chains 217 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 55 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 10 optimal weight: 0.0270 chunk 87 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 75 GLN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.141888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.124198 restraints weight = 12769.526| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.17 r_work: 0.3522 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9074 Z= 0.154 Angle : 0.558 10.209 12287 Z= 0.282 Chirality : 0.041 0.135 1400 Planarity : 0.003 0.038 1544 Dihedral : 10.297 151.375 1261 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.40 % Allowed : 16.60 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.25), residues: 1123 helix: 1.51 (0.26), residues: 399 sheet: -0.09 (0.30), residues: 282 loop : -0.44 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 168 TYR 0.024 0.001 TYR S 178 PHE 0.026 0.001 PHE R 281 TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9071) covalent geometry : angle 0.55743 (12281) SS BOND : bond 0.00244 ( 3) SS BOND : angle 0.71608 ( 6) hydrogen bonds : bond 0.03767 ( 459) hydrogen bonds : angle 4.73119 ( 1320) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.363 Fit side-chains REVERT: A 197 LYS cc_start: 0.8320 (mmmt) cc_final: 0.8085 (mtmt) REVERT: A 209 LYS cc_start: 0.8170 (pttm) cc_final: 0.7928 (pttm) REVERT: A 309 ASP cc_start: 0.7768 (t70) cc_final: 0.7388 (t0) REVERT: B 6 GLN cc_start: 0.8377 (tm-30) cc_final: 0.7965 (tm-30) REVERT: B 13 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7400 (tm-30) REVERT: B 14 LEU cc_start: 0.8494 (mt) cc_final: 0.8114 (mt) REVERT: B 17 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7941 (tm-30) REVERT: B 147 SER cc_start: 0.8102 (p) cc_final: 0.7879 (p) REVERT: B 190 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8144 (pt) REVERT: B 227 SER cc_start: 0.8687 (t) cc_final: 0.8403 (m) REVERT: B 254 ASP cc_start: 0.7862 (p0) cc_final: 0.7594 (p0) REVERT: R 132 TYR cc_start: 0.8171 (t80) cc_final: 0.7845 (t80) REVERT: R 157 MET cc_start: 0.7596 (tmm) cc_final: 0.7277 (tmm) REVERT: R 306 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7718 (tp) REVERT: S 12 VAL cc_start: 0.8121 (t) cc_final: 0.7910 (t) REVERT: S 38 ARG cc_start: 0.8507 (mtp85) cc_final: 0.8148 (ptp-170) REVERT: S 43 LYS cc_start: 0.8694 (mmpt) cc_final: 0.8275 (mmpt) REVERT: S 83 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8136 (ptp) REVERT: S 178 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7199 (p90) outliers start: 33 outliers final: 17 residues processed: 214 average time/residue: 0.5020 time to fit residues: 115.3996 Evaluate side-chains 219 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 178 TYR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 91 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 61 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 75 GLN B 220 GLN R 267 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.141549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.123925 restraints weight = 12848.703| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.15 r_work: 0.3517 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9074 Z= 0.169 Angle : 0.557 10.240 12287 Z= 0.284 Chirality : 0.041 0.153 1400 Planarity : 0.003 0.040 1544 Dihedral : 10.342 148.959 1261 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.61 % Allowed : 17.11 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.25), residues: 1123 helix: 1.48 (0.26), residues: 399 sheet: -0.11 (0.30), residues: 281 loop : -0.48 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 168 TYR 0.024 0.001 TYR S 178 PHE 0.026 0.001 PHE R 281 TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9071) covalent geometry : angle 0.55658 (12281) SS BOND : bond 0.00225 ( 3) SS BOND : angle 0.76055 ( 6) hydrogen bonds : bond 0.03785 ( 459) hydrogen bonds : angle 4.73498 ( 1320) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 0.352 Fit side-chains REVERT: A 197 LYS cc_start: 0.8339 (mmmt) cc_final: 0.8104 (mtmt) REVERT: A 309 ASP cc_start: 0.7775 (t70) cc_final: 0.7397 (t0) REVERT: B 4 LEU cc_start: 0.8438 (tt) cc_final: 0.8198 (tm) REVERT: B 6 GLN cc_start: 0.8384 (tm-30) cc_final: 0.7975 (tm-30) REVERT: B 13 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7415 (tm-30) REVERT: B 14 LEU cc_start: 0.8508 (mt) cc_final: 0.8121 (mt) REVERT: B 17 GLN cc_start: 0.8258 (tm-30) cc_final: 0.7924 (tm-30) REVERT: B 147 SER cc_start: 0.8105 (p) cc_final: 0.7898 (p) REVERT: B 227 SER cc_start: 0.8677 (t) cc_final: 0.8385 (m) REVERT: B 254 ASP cc_start: 0.7862 (p0) cc_final: 0.7594 (p0) REVERT: R 132 TYR cc_start: 0.8172 (t80) cc_final: 0.7845 (t80) REVERT: R 157 MET cc_start: 0.7600 (tmm) cc_final: 0.7281 (tmm) REVERT: R 306 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7747 (tp) REVERT: S 12 VAL cc_start: 0.8116 (t) cc_final: 0.7901 (t) REVERT: S 38 ARG cc_start: 0.8509 (mtp85) cc_final: 0.8166 (ptp-170) REVERT: S 43 LYS cc_start: 0.8704 (mmpt) cc_final: 0.8286 (mmpt) REVERT: S 60 TYR cc_start: 0.8677 (m-80) cc_final: 0.8474 (m-80) REVERT: S 83 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8087 (ptp) REVERT: S 178 TYR cc_start: 0.7991 (OUTLIER) cc_final: 0.7225 (p90) outliers start: 35 outliers final: 18 residues processed: 215 average time/residue: 0.4789 time to fit residues: 110.5334 Evaluate side-chains 219 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 178 TYR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 74 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 0.0050 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 0.0570 chunk 31 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.3512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 75 GLN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.143246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.125641 restraints weight = 12763.034| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.16 r_work: 0.3539 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9074 Z= 0.119 Angle : 0.554 10.030 12287 Z= 0.277 Chirality : 0.041 0.134 1400 Planarity : 0.003 0.045 1544 Dihedral : 10.341 149.644 1261 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.78 % Allowed : 18.14 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.25), residues: 1123 helix: 1.62 (0.26), residues: 404 sheet: -0.10 (0.30), residues: 270 loop : -0.45 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 168 TYR 0.024 0.001 TYR S 178 PHE 0.029 0.001 PHE R 281 TRP 0.010 0.001 TRP B 297 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9071) covalent geometry : angle 0.55351 (12281) SS BOND : bond 0.00223 ( 3) SS BOND : angle 0.54314 ( 6) hydrogen bonds : bond 0.03477 ( 459) hydrogen bonds : angle 4.63741 ( 1320) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.348 Fit side-chains REVERT: A 197 LYS cc_start: 0.8333 (mmmt) cc_final: 0.8101 (mtmt) REVERT: A 309 ASP cc_start: 0.7702 (t70) cc_final: 0.7315 (t0) REVERT: B 4 LEU cc_start: 0.8401 (tt) cc_final: 0.8191 (tm) REVERT: B 6 GLN cc_start: 0.8399 (tm-30) cc_final: 0.7997 (tm-30) REVERT: B 13 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7403 (tm-30) REVERT: B 14 LEU cc_start: 0.8480 (mt) cc_final: 0.8094 (mt) REVERT: B 17 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7869 (tm-30) REVERT: B 147 SER cc_start: 0.8141 (p) cc_final: 0.7907 (p) REVERT: B 239 ASN cc_start: 0.8436 (m110) cc_final: 0.8062 (m110) REVERT: B 254 ASP cc_start: 0.7907 (p0) cc_final: 0.7634 (p0) REVERT: R 132 TYR cc_start: 0.8119 (t80) cc_final: 0.7790 (t80) REVERT: R 157 MET cc_start: 0.7595 (tmm) cc_final: 0.7269 (tmm) REVERT: R 306 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7744 (tp) REVERT: S 43 LYS cc_start: 0.8690 (mmpt) cc_final: 0.8264 (mmpt) REVERT: S 83 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8068 (ptp) REVERT: S 178 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.7164 (p90) outliers start: 27 outliers final: 16 residues processed: 205 average time/residue: 0.4451 time to fit residues: 98.7140 Evaluate side-chains 202 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 178 TYR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 106 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 101 optimal weight: 0.0570 chunk 30 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 75 GLN B 110 ASN B 119 ASN B 125 ASN B 155 ASN B 176 GLN B 220 GLN B 230 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.142794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.125208 restraints weight = 12735.476| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.15 r_work: 0.3536 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9074 Z= 0.130 Angle : 0.551 10.245 12287 Z= 0.279 Chirality : 0.041 0.138 1400 Planarity : 0.003 0.044 1544 Dihedral : 10.360 150.371 1261 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.99 % Allowed : 18.14 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.25), residues: 1123 helix: 1.62 (0.26), residues: 404 sheet: -0.04 (0.30), residues: 268 loop : -0.50 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 168 TYR 0.023 0.001 TYR S 178 PHE 0.027 0.001 PHE R 281 TRP 0.009 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9071) covalent geometry : angle 0.55143 (12281) SS BOND : bond 0.00220 ( 3) SS BOND : angle 0.55086 ( 6) hydrogen bonds : bond 0.03492 ( 459) hydrogen bonds : angle 4.62401 ( 1320) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.346 Fit side-chains REVERT: A 197 LYS cc_start: 0.8338 (mmmt) cc_final: 0.8121 (mtmt) REVERT: A 309 ASP cc_start: 0.7631 (t70) cc_final: 0.7245 (t0) REVERT: B 6 GLN cc_start: 0.8393 (tm-30) cc_final: 0.7984 (tm-30) REVERT: B 13 GLN cc_start: 0.7931 (tm-30) cc_final: 0.7371 (tm-30) REVERT: B 14 LEU cc_start: 0.8492 (mt) cc_final: 0.8110 (mt) REVERT: B 17 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7868 (tm-30) REVERT: B 147 SER cc_start: 0.8114 (p) cc_final: 0.7876 (p) REVERT: B 239 ASN cc_start: 0.8446 (m110) cc_final: 0.8097 (m110) REVERT: B 254 ASP cc_start: 0.7919 (p0) cc_final: 0.7653 (p0) REVERT: R 132 TYR cc_start: 0.8123 (t80) cc_final: 0.7797 (t80) REVERT: R 157 MET cc_start: 0.7629 (tmm) cc_final: 0.7296 (tmm) REVERT: R 306 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7473 (tt) REVERT: S 43 LYS cc_start: 0.8681 (mmpt) cc_final: 0.8253 (mmpt) REVERT: S 83 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8027 (ptp) REVERT: S 178 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.7205 (p90) outliers start: 29 outliers final: 18 residues processed: 203 average time/residue: 0.4524 time to fit residues: 99.2649 Evaluate side-chains 201 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 178 TYR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 75 GLN B 119 ASN B 125 ASN B 155 ASN B 176 GLN B 220 GLN B 230 ASN S 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.142563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.124866 restraints weight = 12683.970| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.17 r_work: 0.3530 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9074 Z= 0.153 Angle : 0.583 10.860 12287 Z= 0.291 Chirality : 0.041 0.144 1400 Planarity : 0.003 0.044 1544 Dihedral : 10.396 150.141 1261 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.37 % Allowed : 18.97 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.25), residues: 1123 helix: 1.58 (0.26), residues: 404 sheet: -0.08 (0.30), residues: 269 loop : -0.51 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 168 TYR 0.025 0.001 TYR S 178 PHE 0.026 0.001 PHE R 281 TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9071) covalent geometry : angle 0.58303 (12281) SS BOND : bond 0.00215 ( 3) SS BOND : angle 0.62303 ( 6) hydrogen bonds : bond 0.03589 ( 459) hydrogen bonds : angle 4.64907 ( 1320) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.348 Fit side-chains REVERT: A 197 LYS cc_start: 0.8330 (mmmt) cc_final: 0.8097 (mtmt) REVERT: A 309 ASP cc_start: 0.7724 (t70) cc_final: 0.7342 (t0) REVERT: B 4 LEU cc_start: 0.8367 (tt) cc_final: 0.8139 (tm) REVERT: B 6 GLN cc_start: 0.8400 (tm-30) cc_final: 0.7985 (tm-30) REVERT: B 13 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7372 (tm-30) REVERT: B 14 LEU cc_start: 0.8449 (mt) cc_final: 0.8024 (mt) REVERT: B 17 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7863 (tm-30) REVERT: B 147 SER cc_start: 0.8106 (p) cc_final: 0.7878 (p) REVERT: B 227 SER cc_start: 0.8709 (OUTLIER) cc_final: 0.8399 (m) REVERT: B 239 ASN cc_start: 0.8464 (m110) cc_final: 0.8102 (m110) REVERT: B 254 ASP cc_start: 0.7928 (p0) cc_final: 0.7642 (p0) REVERT: R 132 TYR cc_start: 0.8138 (t80) cc_final: 0.7805 (t80) REVERT: R 157 MET cc_start: 0.7657 (tmm) cc_final: 0.7332 (tmm) REVERT: R 306 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7462 (tt) REVERT: S 43 LYS cc_start: 0.8685 (mmpt) cc_final: 0.8247 (mmpt) REVERT: S 83 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8079 (ptp) REVERT: S 178 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.7206 (p90) outliers start: 23 outliers final: 15 residues processed: 192 average time/residue: 0.4861 time to fit residues: 100.4280 Evaluate side-chains 200 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 178 TYR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 57 optimal weight: 0.0370 chunk 59 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 75 GLN B 110 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 220 GLN B 230 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.142313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.124655 restraints weight = 12648.789| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.14 r_work: 0.3527 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9074 Z= 0.167 Angle : 0.585 11.365 12287 Z= 0.294 Chirality : 0.042 0.140 1400 Planarity : 0.003 0.042 1544 Dihedral : 10.440 150.122 1261 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.37 % Allowed : 19.28 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.25), residues: 1123 helix: 1.52 (0.26), residues: 404 sheet: -0.19 (0.30), residues: 270 loop : -0.41 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 168 TYR 0.023 0.001 TYR S 178 PHE 0.025 0.001 PHE R 281 TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 9071) covalent geometry : angle 0.58448 (12281) SS BOND : bond 0.00215 ( 3) SS BOND : angle 0.66205 ( 6) hydrogen bonds : bond 0.03667 ( 459) hydrogen bonds : angle 4.68859 ( 1320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3420.74 seconds wall clock time: 59 minutes 5.43 seconds (3545.43 seconds total)