Starting phenix.real_space_refine on Thu Feb 13 09:23:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gur_34277/02_2025/8gur_34277_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gur_34277/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gur_34277/02_2025/8gur_34277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gur_34277/02_2025/8gur_34277.map" model { file = "/net/cci-nas-00/data/ceres_data/8gur_34277/02_2025/8gur_34277_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gur_34277/02_2025/8gur_34277_neut.cif" } resolution = 2.84 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= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.26, per 1000 atoms: 0.59 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: 2.17 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.12 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: 2.89 Time building geometry restraints manager: 2.55 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: 1.150 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.900 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.090 ------------------------------------------------------------------------------- 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 9071 Z= 0.160 Angle : 0.502 7.270 12281 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 : 7.78 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 (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: 0.31 (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 TRP 0.007 0.001 TRP B 211 HIS 0.003 0.001 HIS A 195 PHE 0.014 0.001 PHE R 117 TYR 0.023 0.001 TYR S 178 ARG 0.013 0.000 ARG B 214 *********************** 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 : 0.911 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: 1.0519 time to fit residues: 226.8533 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 : 1.035 ------------------------------------------------------------------------------- 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 93 optimal weight: 2.9990 chunk 84 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.141115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.123663 restraints weight = 12601.929| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.14 r_work: 0.3507 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9071 Z= 0.321 Angle : 0.604 9.409 12281 Z= 0.312 Chirality : 0.043 0.164 1400 Planarity : 0.004 0.034 1544 Dihedral : 10.409 150.648 1263 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.96 % Allowed : 10.31 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.36 (0.25), residues: 1123 helix: 1.26 (0.25), residues: 400 sheet: -0.16 (0.30), residues: 282 loop : -0.30 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.005 0.001 HIS A 213 PHE 0.014 0.002 PHE R 202 TYR 0.029 0.002 TYR S 178 ARG 0.009 0.000 ARG R 149 *********************** 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 223 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 204 time to evaluate : 1.265 Fit side-chains REVERT: A 209 LYS cc_start: 0.8251 (pttm) cc_final: 0.8041 (pttm) REVERT: A 309 ASP cc_start: 0.7700 (t70) cc_final: 0.7323 (t0) REVERT: B 4 LEU cc_start: 0.8463 (tt) cc_final: 0.8214 (tm) REVERT: B 6 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7972 (tm-30) REVERT: B 13 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7381 (tm-30) REVERT: B 14 LEU cc_start: 0.8436 (mt) cc_final: 0.8046 (mt) REVERT: B 17 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7925 (tm-30) REVERT: B 118 ASP cc_start: 0.7768 (p0) cc_final: 0.7552 (p0) REVERT: B 146 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8048 (mt) REVERT: B 160 SER cc_start: 0.8219 (p) cc_final: 0.7797 (t) REVERT: B 227 SER cc_start: 0.8699 (t) cc_final: 0.8388 (m) REVERT: B 254 ASP cc_start: 0.7911 (p0) cc_final: 0.7661 (p0) REVERT: R 132 TYR cc_start: 0.8121 (t80) cc_final: 0.7760 (t80) REVERT: R 157 MET cc_start: 0.7625 (tmm) cc_final: 0.7244 (tmm) REVERT: R 237 MET cc_start: 0.4887 (ppp) cc_final: 0.4593 (ppp) REVERT: S 43 LYS cc_start: 0.8702 (mmpt) cc_final: 0.8334 (mmpt) REVERT: S 148 ARG cc_start: 0.7738 (mtp-110) cc_final: 0.7409 (mtp-110) REVERT: S 201 THR cc_start: 0.8370 (p) cc_final: 0.8155 (t) outliers start: 19 outliers final: 7 residues processed: 210 average time/residue: 1.1420 time to fit residues: 256.7529 Evaluate side-chains 204 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 196 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 86 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 0.0050 chunk 42 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.141989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.124390 restraints weight = 12799.891| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.16 r_work: 0.3527 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9071 Z= 0.210 Angle : 0.538 9.780 12281 Z= 0.279 Chirality : 0.041 0.133 1400 Planarity : 0.003 0.034 1544 Dihedral : 10.368 153.471 1261 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.68 % Allowed : 12.37 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.43 (0.25), residues: 1123 helix: 1.44 (0.26), residues: 399 sheet: -0.11 (0.29), residues: 282 loop : -0.40 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.019 0.001 PHE R 94 TYR 0.023 0.001 TYR S 178 ARG 0.007 0.000 ARG S 168 *********************** 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 236 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.968 Fit side-chains REVERT: A 9 ASP cc_start: 0.7512 (m-30) cc_final: 0.7167 (m-30) REVERT: A 197 LYS cc_start: 0.8227 (mmmt) cc_final: 0.7958 (mmmt) REVERT: A 309 ASP cc_start: 0.7716 (t70) cc_final: 0.7323 (t0) REVERT: B 4 LEU cc_start: 0.8418 (tt) cc_final: 0.8181 (tm) REVERT: B 6 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8020 (tm-30) REVERT: B 13 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7366 (tm-30) REVERT: B 14 LEU cc_start: 0.8464 (mt) cc_final: 0.8089 (mt) REVERT: B 17 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7856 (tm-30) REVERT: B 146 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8035 (mt) REVERT: B 160 SER cc_start: 0.8156 (p) cc_final: 0.7926 (t) REVERT: B 190 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8182 (pt) REVERT: B 239 ASN cc_start: 0.8426 (m110) cc_final: 0.7927 (m110) REVERT: B 254 ASP cc_start: 0.7935 (p0) cc_final: 0.7662 (p0) REVERT: R 132 TYR cc_start: 0.8095 (t80) cc_final: 0.7746 (t80) REVERT: R 157 MET cc_start: 0.7614 (tmm) cc_final: 0.7271 (tmm) REVERT: R 237 MET cc_start: 0.4859 (ppp) cc_final: 0.4617 (ppp) REVERT: R 285 SER cc_start: 0.8255 (m) cc_final: 0.7988 (p) REVERT: R 306 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7357 (tt) REVERT: S 43 LYS cc_start: 0.8719 (mmpt) cc_final: 0.8330 (mmpt) outliers start: 26 outliers final: 10 residues processed: 217 average time/residue: 1.0598 time to fit residues: 247.2997 Evaluate side-chains 209 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL 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 146 LEU Chi-restraints excluded: chain B residue 190 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 16 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 82 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 B 293 ASN R 291 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.141441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.123924 restraints weight = 12701.275| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.15 r_work: 0.3524 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9071 Z= 0.208 Angle : 0.558 11.670 12281 Z= 0.281 Chirality : 0.041 0.187 1400 Planarity : 0.003 0.032 1544 Dihedral : 10.324 154.029 1261 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.47 % Allowed : 15.15 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.43 (0.25), residues: 1123 helix: 1.48 (0.26), residues: 399 sheet: -0.13 (0.29), residues: 284 loop : -0.44 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.016 0.001 PHE R 94 TYR 0.025 0.001 TYR S 178 ARG 0.006 0.000 ARG S 168 *********************** 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 229 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.935 Fit side-chains REVERT: A 9 ASP cc_start: 0.7522 (m-30) cc_final: 0.7191 (m-30) REVERT: A 197 LYS cc_start: 0.8283 (mmmt) cc_final: 0.8015 (mmmt) REVERT: A 309 ASP cc_start: 0.7708 (t70) cc_final: 0.7322 (t0) REVERT: B 6 GLN cc_start: 0.8395 (tm-30) cc_final: 0.8024 (tm-30) REVERT: B 13 GLN cc_start: 0.7980 (tm-30) cc_final: 0.7398 (tm-30) REVERT: B 14 LEU cc_start: 0.8484 (mt) cc_final: 0.8094 (mt) REVERT: B 17 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7885 (tm-30) REVERT: B 146 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8044 (mt) REVERT: B 190 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8208 (pt) REVERT: B 254 ASP cc_start: 0.7904 (p0) cc_final: 0.7645 (p0) REVERT: R 132 TYR cc_start: 0.8123 (t80) cc_final: 0.7784 (t80) REVERT: R 157 MET cc_start: 0.7600 (tmm) cc_final: 0.7241 (tmm) REVERT: R 237 MET cc_start: 0.4879 (ppp) cc_final: 0.4657 (ppp) REVERT: R 285 SER cc_start: 0.8391 (m) cc_final: 0.8113 (p) REVERT: R 306 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7389 (tt) REVERT: S 43 LYS cc_start: 0.8704 (mmpt) cc_final: 0.8311 (mmpt) outliers start: 24 outliers final: 9 residues processed: 210 average time/residue: 1.1048 time to fit residues: 248.7804 Evaluate side-chains 208 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 50 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 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 293 MET Chi-restraints excluded: chain R residue 306 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 16 optimal weight: 0.0670 chunk 1 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.142330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.124849 restraints weight = 12501.107| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.12 r_work: 0.3531 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9071 Z= 0.210 Angle : 0.563 13.509 12281 Z= 0.282 Chirality : 0.041 0.145 1400 Planarity : 0.003 0.034 1544 Dihedral : 10.298 155.176 1261 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.68 % Allowed : 16.60 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1123 helix: 1.48 (0.26), residues: 399 sheet: -0.11 (0.30), residues: 282 loop : -0.44 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.017 0.001 PHE R 94 TYR 0.023 0.001 TYR S 178 ARG 0.007 0.000 ARG S 168 *********************** 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 222 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.927 Fit side-chains REVERT: A 197 LYS cc_start: 0.8302 (mmmt) cc_final: 0.8050 (mmmt) REVERT: A 309 ASP cc_start: 0.7697 (t70) cc_final: 0.7311 (t0) REVERT: B 4 LEU cc_start: 0.8411 (tt) cc_final: 0.8178 (tm) REVERT: B 6 GLN cc_start: 0.8381 (tm-30) cc_final: 0.7967 (tm-30) REVERT: B 13 GLN cc_start: 0.7959 (tm-30) cc_final: 0.7382 (tm-30) REVERT: B 14 LEU cc_start: 0.8484 (mt) cc_final: 0.8096 (mt) REVERT: B 17 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7857 (tm-30) REVERT: B 146 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8095 (mt) REVERT: B 147 SER cc_start: 0.8101 (p) cc_final: 0.7875 (p) REVERT: B 190 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8184 (pt) REVERT: B 227 SER cc_start: 0.8661 (t) cc_final: 0.8377 (m) REVERT: B 254 ASP cc_start: 0.7897 (p0) cc_final: 0.7644 (p0) REVERT: R 132 TYR cc_start: 0.8119 (t80) cc_final: 0.7785 (t80) REVERT: R 157 MET cc_start: 0.7573 (tmm) cc_final: 0.7281 (tmm) REVERT: R 237 MET cc_start: 0.4913 (ppp) cc_final: 0.4692 (ppp) REVERT: R 285 SER cc_start: 0.8383 (m) cc_final: 0.8146 (p) REVERT: R 306 ILE cc_start: 0.8049 (mm) cc_final: 0.7433 (tt) REVERT: S 43 LYS cc_start: 0.8685 (mmpt) cc_final: 0.8294 (mmpt) outliers start: 26 outliers final: 14 residues processed: 202 average time/residue: 1.0251 time to fit residues: 224.1962 Evaluate side-chains 205 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 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 S residue 86 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 0.0870 chunk 15 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 76 optimal weight: 4.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.142156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.124573 restraints weight = 12660.560| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.16 r_work: 0.3529 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9071 Z= 0.197 Angle : 0.559 14.370 12281 Z= 0.278 Chirality : 0.041 0.136 1400 Planarity : 0.003 0.031 1544 Dihedral : 10.266 155.386 1261 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.20 % Allowed : 16.39 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.46 (0.25), residues: 1123 helix: 1.55 (0.26), residues: 399 sheet: -0.11 (0.30), residues: 268 loop : -0.46 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.017 0.001 PHE A 259 TYR 0.025 0.001 TYR S 178 ARG 0.006 0.000 ARG B 134 *********************** 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 222 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 0.965 Fit side-chains REVERT: A 197 LYS cc_start: 0.8328 (mmmt) cc_final: 0.8101 (mtmt) REVERT: A 209 LYS cc_start: 0.8176 (pttm) cc_final: 0.7942 (pttm) REVERT: A 309 ASP cc_start: 0.7776 (t70) cc_final: 0.7395 (t0) REVERT: B 4 LEU cc_start: 0.8421 (tt) cc_final: 0.8212 (tm) REVERT: B 6 GLN cc_start: 0.8374 (tm-30) cc_final: 0.7964 (tm-30) REVERT: B 13 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7382 (tm-30) REVERT: B 14 LEU cc_start: 0.8489 (mt) cc_final: 0.8104 (mt) REVERT: B 17 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7926 (tm-30) REVERT: B 147 SER cc_start: 0.8138 (p) cc_final: 0.7926 (p) REVERT: B 227 SER cc_start: 0.8667 (OUTLIER) cc_final: 0.8385 (m) REVERT: B 254 ASP cc_start: 0.7861 (p0) cc_final: 0.7583 (p0) REVERT: R 132 TYR cc_start: 0.8159 (t80) cc_final: 0.7830 (t80) REVERT: R 157 MET cc_start: 0.7576 (tmm) cc_final: 0.7278 (tmm) REVERT: R 237 MET cc_start: 0.4948 (ppp) cc_final: 0.4711 (ppp) REVERT: R 285 SER cc_start: 0.8371 (m) cc_final: 0.8150 (p) REVERT: R 306 ILE cc_start: 0.8054 (mm) cc_final: 0.7441 (tt) REVERT: S 43 LYS cc_start: 0.8689 (mmpt) cc_final: 0.8267 (mmpt) REVERT: S 178 TYR cc_start: 0.7938 (OUTLIER) cc_final: 0.7189 (p90) outliers start: 31 outliers final: 16 residues processed: 199 average time/residue: 1.0310 time to fit residues: 221.3520 Evaluate side-chains 207 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 50 THR 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 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 S residue 86 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 88 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 105 optimal weight: 0.0060 chunk 106 optimal weight: 0.2980 chunk 69 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3905 r_free = 0.3905 target = 0.143019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.125354 restraints weight = 12767.639| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.18 r_work: 0.3536 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9071 Z= 0.180 Angle : 0.547 14.929 12281 Z= 0.273 Chirality : 0.040 0.134 1400 Planarity : 0.003 0.030 1544 Dihedral : 10.279 152.900 1261 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.51 % Allowed : 17.01 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.48 (0.25), residues: 1123 helix: 1.60 (0.26), residues: 404 sheet: -0.12 (0.30), residues: 269 loop : -0.49 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.003 0.001 HIS B 142 PHE 0.015 0.001 PHE R 94 TYR 0.022 0.001 TYR S 178 ARG 0.007 0.000 ARG B 134 *********************** 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: 34 poor density : 203 time to evaluate : 0.900 Fit side-chains REVERT: A 197 LYS cc_start: 0.8345 (mmmt) cc_final: 0.8115 (mtmt) REVERT: A 309 ASP cc_start: 0.7612 (t70) cc_final: 0.7227 (t0) REVERT: B 6 GLN cc_start: 0.8388 (tm-30) cc_final: 0.8021 (tm-30) REVERT: B 13 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7382 (tm-30) REVERT: B 14 LEU cc_start: 0.8482 (mt) cc_final: 0.8111 (mt) REVERT: B 17 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7879 (tm-30) REVERT: B 147 SER cc_start: 0.8117 (p) cc_final: 0.7852 (p) REVERT: B 227 SER cc_start: 0.8696 (OUTLIER) cc_final: 0.8403 (m) REVERT: B 239 ASN cc_start: 0.8408 (m110) cc_final: 0.7910 (m110) REVERT: B 254 ASP cc_start: 0.7900 (p0) cc_final: 0.7630 (p0) REVERT: R 132 TYR cc_start: 0.8124 (t80) cc_final: 0.7790 (t80) REVERT: R 157 MET cc_start: 0.7625 (tmm) cc_final: 0.7314 (tmm) REVERT: R 237 MET cc_start: 0.4933 (ppp) cc_final: 0.4691 (ppp) REVERT: R 285 SER cc_start: 0.8402 (m) cc_final: 0.8179 (p) REVERT: R 306 ILE cc_start: 0.8024 (mm) cc_final: 0.7405 (tt) REVERT: S 12 VAL cc_start: 0.8132 (t) cc_final: 0.7919 (t) REVERT: S 43 LYS cc_start: 0.8681 (mmpt) cc_final: 0.8257 (mmpt) REVERT: S 178 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.7124 (p90) outliers start: 34 outliers final: 19 residues processed: 213 average time/residue: 0.9607 time to fit residues: 221.7890 Evaluate side-chains 208 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU 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 50 THR 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 227 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 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 32 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 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 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 75 GLN B 110 ASN B 119 ASN B 125 ASN B 155 ASN B 220 GLN B 230 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.141987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.124385 restraints weight = 12808.810| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.15 r_work: 0.3525 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9071 Z= 0.246 Angle : 0.587 15.172 12281 Z= 0.290 Chirality : 0.042 0.150 1400 Planarity : 0.003 0.030 1544 Dihedral : 10.336 152.062 1261 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.40 % Allowed : 17.53 % 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 (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: 0.41 (0.25), residues: 1123 helix: 1.52 (0.26), residues: 399 sheet: -0.18 (0.30), residues: 272 loop : -0.46 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.016 0.001 PHE A 259 TYR 0.025 0.001 TYR S 178 ARG 0.007 0.000 ARG B 134 *********************** 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 229 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 1.211 Fit side-chains REVERT: A 197 LYS cc_start: 0.8345 (mmmt) cc_final: 0.8130 (mtmt) REVERT: A 309 ASP cc_start: 0.7600 (t70) cc_final: 0.7228 (t0) REVERT: B 4 LEU cc_start: 0.8401 (tt) cc_final: 0.8195 (tm) REVERT: B 6 GLN cc_start: 0.8394 (tm-30) cc_final: 0.7975 (tm-30) REVERT: B 13 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7406 (tm-30) REVERT: B 14 LEU cc_start: 0.8523 (mt) cc_final: 0.8129 (mt) REVERT: B 17 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7882 (tm-30) REVERT: B 147 SER cc_start: 0.8092 (p) cc_final: 0.7840 (p) REVERT: B 227 SER cc_start: 0.8687 (t) cc_final: 0.8393 (m) REVERT: B 239 ASN cc_start: 0.8409 (m110) cc_final: 0.8094 (m110) REVERT: B 254 ASP cc_start: 0.7877 (p0) cc_final: 0.7603 (p0) REVERT: R 132 TYR cc_start: 0.8138 (t80) cc_final: 0.7802 (t80) REVERT: R 157 MET cc_start: 0.7654 (tmm) cc_final: 0.7347 (tmm) REVERT: R 237 MET cc_start: 0.4914 (ppp) cc_final: 0.4669 (ppp) REVERT: R 285 SER cc_start: 0.8442 (m) cc_final: 0.8229 (p) REVERT: R 306 ILE cc_start: 0.8056 (mm) cc_final: 0.7832 (mt) REVERT: S 43 LYS cc_start: 0.8681 (mmpt) cc_final: 0.8262 (mmpt) REVERT: S 128 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.6976 (mmm) outliers start: 33 outliers final: 18 residues processed: 202 average time/residue: 1.0174 time to fit residues: 221.9422 Evaluate side-chains 205 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 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 228 ASP Chi-restraints excluded: chain R residue 110 ILE 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 S residue 128 MET Chi-restraints excluded: chain S residue 160 THR 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 44 optimal weight: 0.1980 chunk 100 optimal weight: 0.0040 chunk 90 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 75 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN 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 = 0.3901 r_free = 0.3901 target = 0.142711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.125221 restraints weight = 12684.422| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.16 r_work: 0.3536 rms_B_bonded: 2.61 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: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9071 Z= 0.190 Angle : 0.564 15.241 12281 Z= 0.281 Chirality : 0.041 0.138 1400 Planarity : 0.003 0.033 1544 Dihedral : 10.349 151.064 1261 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.27 % Allowed : 18.97 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.49 (0.25), residues: 1123 helix: 1.60 (0.26), residues: 402 sheet: -0.01 (0.30), residues: 265 loop : -0.56 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.005 0.001 HIS B 183 PHE 0.012 0.001 PHE R 94 TYR 0.027 0.001 TYR S 178 ARG 0.007 0.000 ARG B 134 *********************** 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 219 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 0.952 Fit side-chains REVERT: A 197 LYS cc_start: 0.8327 (mmmt) cc_final: 0.8112 (mtmt) REVERT: A 309 ASP cc_start: 0.7626 (t70) cc_final: 0.7241 (t0) REVERT: B 4 LEU cc_start: 0.8402 (tt) cc_final: 0.8194 (tm) REVERT: B 6 GLN cc_start: 0.8391 (tm-30) cc_final: 0.7977 (tm-30) REVERT: B 13 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7370 (tm-30) REVERT: B 14 LEU cc_start: 0.8497 (mt) cc_final: 0.8119 (mt) REVERT: B 17 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7869 (tm-30) REVERT: B 227 SER cc_start: 0.8694 (t) cc_final: 0.8390 (m) REVERT: B 239 ASN cc_start: 0.8464 (m110) cc_final: 0.8088 (m110) REVERT: B 254 ASP cc_start: 0.7913 (p0) cc_final: 0.7638 (p0) REVERT: R 132 TYR cc_start: 0.8136 (t80) cc_final: 0.7803 (t80) REVERT: R 157 MET cc_start: 0.7665 (tmm) cc_final: 0.7342 (tmm) REVERT: R 237 MET cc_start: 0.4934 (ppp) cc_final: 0.4679 (ppp) REVERT: R 285 SER cc_start: 0.8418 (m) cc_final: 0.8176 (p) REVERT: R 306 ILE cc_start: 0.8048 (mm) cc_final: 0.7828 (mt) REVERT: S 12 VAL cc_start: 0.8150 (t) cc_final: 0.7934 (t) REVERT: S 43 LYS cc_start: 0.8690 (mmpt) cc_final: 0.8257 (mmpt) REVERT: S 128 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.6890 (mmm) outliers start: 22 outliers final: 14 residues processed: 201 average time/residue: 0.9875 time to fit residues: 214.3544 Evaluate side-chains 200 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 50 THR 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 223 LEU Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 160 THR 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 22 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 0.0030 chunk 7 optimal weight: 3.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 75 GLN B 155 ASN B 220 GLN B 230 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.140151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.122503 restraints weight = 12833.365| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.14 r_work: 0.3499 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9071 Z= 0.358 Angle : 0.633 14.849 12281 Z= 0.316 Chirality : 0.044 0.156 1400 Planarity : 0.004 0.033 1544 Dihedral : 10.463 148.675 1261 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.16 % Allowed : 18.87 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.24 (0.25), residues: 1123 helix: 1.37 (0.26), residues: 396 sheet: -0.29 (0.30), residues: 274 loop : -0.54 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 211 HIS 0.006 0.001 HIS B 142 PHE 0.015 0.002 PHE A 259 TYR 0.035 0.002 TYR S 178 ARG 0.008 0.000 ARG B 134 ********************** 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 224 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7653 (mt-10) REVERT: A 309 ASP cc_start: 0.7811 (t70) cc_final: 0.7441 (t0) REVERT: B 6 GLN cc_start: 0.8379 (tm-30) cc_final: 0.7955 (tm-30) REVERT: B 13 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7392 (tm-30) REVERT: B 14 LEU cc_start: 0.8537 (mt) cc_final: 0.8129 (mt) REVERT: B 17 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7915 (tm-30) REVERT: B 227 SER cc_start: 0.8718 (t) cc_final: 0.8412 (m) REVERT: B 254 ASP cc_start: 0.7890 (p0) cc_final: 0.7616 (p0) REVERT: R 132 TYR cc_start: 0.8189 (t80) cc_final: 0.7874 (t80) REVERT: R 157 MET cc_start: 0.7654 (tmm) cc_final: 0.7242 (tmm) REVERT: R 237 MET cc_start: 0.4925 (ppp) cc_final: 0.4644 (ppp) REVERT: R 285 SER cc_start: 0.8451 (m) cc_final: 0.8234 (p) REVERT: R 306 ILE cc_start: 0.8109 (mm) cc_final: 0.7908 (mt) REVERT: S 12 VAL cc_start: 0.8140 (t) cc_final: 0.7933 (t) REVERT: S 43 LYS cc_start: 0.8701 (mmpt) cc_final: 0.8304 (mmpt) REVERT: S 128 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.6965 (mmm) outliers start: 21 outliers final: 16 residues processed: 207 average time/residue: 1.1460 time to fit residues: 254.5512 Evaluate side-chains 215 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL 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 50 THR Chi-restraints excluded: chain B residue 112 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 B residue 274 THR 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 S residue 128 MET Chi-restraints excluded: chain S residue 160 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 110 optimal weight: 0.0670 chunk 79 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 0.2980 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 89 optimal weight: 0.0770 chunk 78 optimal weight: 0.6980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3900 r_free = 0.3900 target = 0.142652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.125093 restraints weight = 12694.511| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.17 r_work: 0.3540 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9071 Z= 0.180 Angle : 0.572 15.189 12281 Z= 0.284 Chirality : 0.041 0.146 1400 Planarity : 0.003 0.034 1544 Dihedral : 10.427 148.579 1261 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.86 % Allowed : 19.69 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.48 (0.25), residues: 1123 helix: 1.54 (0.26), residues: 406 sheet: -0.08 (0.30), residues: 278 loop : -0.48 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 297 HIS 0.004 0.001 HIS B 183 PHE 0.019 0.001 PHE A 259 TYR 0.026 0.001 TYR S 178 ARG 0.008 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7009.85 seconds wall clock time: 124 minutes 38.92 seconds (7478.92 seconds total)