Starting phenix.real_space_refine on Sat Jul 26 21:05:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbh_38218/07_2025/8xbh_38218.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbh_38218/07_2025/8xbh_38218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xbh_38218/07_2025/8xbh_38218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbh_38218/07_2025/8xbh_38218.map" model { file = "/net/cci-nas-00/data/ceres_data/8xbh_38218/07_2025/8xbh_38218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbh_38218/07_2025/8xbh_38218.cif" } resolution = 2.83 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 ------------------------------------------------------------------------------- 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= -0.004 sd= 0.523 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 67 5.16 5 C 5709 2.51 5 N 1514 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8947 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1706 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "R" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2424 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 5, 'TRANS': 292} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'KW3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.46, per 1000 atoms: 0.61 Number of scatterers: 8947 At special positions: 0 Unit cell: (90.37, 120.063, 135.555, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 67 16.00 P 1 15.00 O 1656 8.00 N 1514 7.00 C 5709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 114 " distance=2.05 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 299 " distance=2.03 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 204 " 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=2.04 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: 2.53 Conformation dependent library (CDL) restraints added in 1.1 seconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 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: 24 helices and 13 sheets defined 38.6% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.698A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.865A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.167A 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 removed outlier: 3.524A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.689A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.568A pdb=" N GLY A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.765A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 22 Processing helix chain 'G' and resid 29 through 44 removed outlier: 4.047A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 81 Processing helix chain 'R' and resid 87 through 117 Proline residue: R 108 - end of helix removed outlier: 4.161A pdb=" N GLN R 117 " --> pdb=" O TYR R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 157 removed outlier: 3.635A pdb=" N CYS R 127 " --> pdb=" O GLY R 123 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR R 135 " --> pdb=" O GLY R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 197 removed outlier: 3.675A pdb=" N LYS R 195 " --> pdb=" O ILE R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 252 removed outlier: 4.038A pdb=" N ALA R 217 " --> pdb=" O ALA R 213 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG R 252 " --> pdb=" O ILE R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 294 removed outlier: 4.117A pdb=" N TYR R 261 " --> pdb=" O ASN R 257 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA R 262 " --> pdb=" O SER R 258 " (cutoff:3.500A) Proline residue: R 281 - end of helix removed outlier: 4.046A pdb=" N PHE R 287 " --> pdb=" O HIS R 283 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE R 288 " --> pdb=" O ALA R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 331 removed outlier: 3.994A pdb=" N LYS R 302 " --> pdb=" O SER R 298 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE R 304 " --> pdb=" O TYR R 300 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN R 319 " --> pdb=" O LEU R 315 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS R 321 " --> pdb=" O SER R 317 " (cutoff:3.500A) Proline residue: R 324 - end of helix removed outlier: 3.548A pdb=" N TYR R 327 " --> pdb=" O ASP R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 331 through 342 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.949A 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 helix chain 'S' and resid 208 through 212 removed outlier: 3.807A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 191 removed outlier: 7.353A pdb=" N GLY A 183 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLY A 202 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N GLY A 203 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.526A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.419A 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: 7.463A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.952A 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 153 removed outlier: 5.075A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.016A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.849A 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: 6.860A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.538A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.646A 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 10 through 12 removed outlier: 6.280A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.272A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.272A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN S 219 " --> pdb=" O THR S 226 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1326 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: 2.64 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1572 1.33 - 1.45: 2425 1.45 - 1.57: 5032 1.57 - 1.69: 2 1.69 - 1.82: 98 Bond restraints: 9129 Sorted by residual: bond pdb=" C4 KW3 R 401 " pdb=" O6 KW3 R 401 " ideal model delta sigma weight residual 1.414 1.469 -0.055 2.00e-02 2.50e+03 7.65e+00 bond pdb=" C1 KW3 R 401 " pdb=" C2 KW3 R 401 " ideal model delta sigma weight residual 1.519 1.469 0.050 2.00e-02 2.50e+03 6.20e+00 bond pdb=" O6 KW3 R 401 " pdb=" P1 KW3 R 401 " ideal model delta sigma weight residual 1.652 1.605 0.047 2.00e-02 2.50e+03 5.47e+00 bond pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " ideal model delta sigma weight residual 1.808 1.751 0.057 3.30e-02 9.18e+02 2.96e+00 bond pdb=" CA ASP B 312 " pdb=" C ASP B 312 " ideal model delta sigma weight residual 1.523 1.546 -0.023 1.34e-02 5.57e+03 2.94e+00 ... (remaining 9124 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 12267 2.98 - 5.95: 71 5.95 - 8.93: 6 8.93 - 11.90: 0 11.90 - 14.88: 2 Bond angle restraints: 12346 Sorted by residual: angle pdb=" CA CYS B 103 " pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " ideal model delta sigma weight residual 114.40 129.28 -14.88 2.30e+00 1.89e-01 4.19e+01 angle pdb=" N GLY B 115 " pdb=" CA GLY B 115 " pdb=" C GLY B 115 " ideal model delta sigma weight residual 110.80 117.25 -6.45 1.41e+00 5.03e-01 2.09e+01 angle pdb=" N VAL S 64 " pdb=" CA VAL S 64 " pdb=" C VAL S 64 " ideal model delta sigma weight residual 113.20 109.00 4.20 9.60e-01 1.09e+00 1.92e+01 angle pdb=" N CYS B 103 " pdb=" CA CYS B 103 " pdb=" C CYS B 103 " ideal model delta sigma weight residual 107.73 113.98 -6.25 1.61e+00 3.86e-01 1.51e+01 angle pdb=" CA CYS B 114 " pdb=" CB CYS B 114 " pdb=" SG CYS B 114 " ideal model delta sigma weight residual 114.40 122.61 -8.21 2.30e+00 1.89e-01 1.28e+01 ... (remaining 12341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.77: 5165 24.77 - 49.54: 245 49.54 - 74.32: 18 74.32 - 99.09: 11 99.09 - 123.86: 3 Dihedral angle restraints: 5442 sinusoidal: 2143 harmonic: 3299 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 145.80 -52.80 1 1.00e+01 1.00e-02 3.80e+01 dihedral pdb=" CA PHE B 292 " pdb=" C PHE B 292 " pdb=" N ASN B 293 " pdb=" CA ASN B 293 " ideal model delta harmonic sigma weight residual -180.00 -155.11 -24.89 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA CYS B 103 " pdb=" C CYS B 103 " pdb=" N ALA B 104 " pdb=" CA ALA B 104 " ideal model delta harmonic sigma weight residual 180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 5439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1095 0.050 - 0.099: 251 0.099 - 0.149: 51 0.149 - 0.198: 3 0.198 - 0.248: 2 Chirality restraints: 1402 Sorted by residual: chirality pdb=" CA CYS B 103 " pdb=" N CYS B 103 " pdb=" C CYS B 103 " pdb=" CB CYS B 103 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA TYR S 178 " pdb=" N TYR S 178 " pdb=" C TYR S 178 " pdb=" CB TYR S 178 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB VAL R 280 " pdb=" CA VAL R 280 " pdb=" CG1 VAL R 280 " pdb=" CG2 VAL R 280 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.39e-01 ... (remaining 1399 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 318 " 0.013 2.00e-02 2.50e+03 1.29e-02 2.93e+00 pdb=" CG PHE R 318 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE R 318 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE R 318 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 318 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 318 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE R 318 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 247 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C ASP B 247 " -0.029 2.00e-02 2.50e+03 pdb=" O ASP B 247 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA B 248 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.71e+00 pdb=" N PRO G 55 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.023 5.00e-02 4.00e+02 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 236 2.70 - 3.25: 8761 3.25 - 3.80: 14331 3.80 - 4.35: 18834 4.35 - 4.90: 31715 Nonbonded interactions: 73877 Sorted by model distance: nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.151 3.040 nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.192 3.120 nonbonded pdb=" NH1 ARG S 67 " pdb=" O SER S 85 " model vdw 2.199 3.120 nonbonded pdb=" OG SER R 54 " pdb=" O HIS R 114 " model vdw 2.218 3.040 nonbonded pdb=" OG SER R 331 " pdb=" OD1 ASN R 333 " model vdw 2.238 3.040 ... (remaining 73872 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: 0.090 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 23.870 Find NCS groups from input model: 0.120 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:14.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 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 : 0.003 0.057 9134 Z= 0.161 Angle : 0.684 14.881 12356 Z= 0.380 Chirality : 0.044 0.248 1402 Planarity : 0.004 0.041 1548 Dihedral : 14.311 123.859 3301 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.84 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1121 helix: 1.85 (0.26), residues: 396 sheet: -0.26 (0.30), residues: 297 loop : -0.98 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS R 206 PHE 0.030 0.002 PHE R 318 TYR 0.020 0.002 TYR A 320 ARG 0.004 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.12014 ( 466) hydrogen bonds : angle 5.43975 ( 1326) SS BOND : bond 0.00977 ( 5) SS BOND : angle 3.56743 ( 10) covalent geometry : bond 0.00329 ( 9129) covalent geometry : angle 0.67632 (12346) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.6957 (ttp80) cc_final: 0.6637 (mtp-110) REVERT: A 209 LYS cc_start: 0.7908 (tttt) cc_final: 0.7678 (tttm) REVERT: A 345 LYS cc_start: 0.8008 (tmtt) cc_final: 0.7756 (tmtp) REVERT: B 155 ASN cc_start: 0.7936 (t0) cc_final: 0.7604 (t0) REVERT: B 220 GLN cc_start: 0.7390 (mm-40) cc_final: 0.7125 (mp10) REVERT: B 280 LYS cc_start: 0.7968 (tttm) cc_final: 0.7742 (tttp) REVERT: B 301 LYS cc_start: 0.8072 (mtpp) cc_final: 0.7860 (mttm) REVERT: B 325 MET cc_start: 0.7818 (mmm) cc_final: 0.7597 (mmm) REVERT: S 189 ASP cc_start: 0.7363 (p0) cc_final: 0.6965 (t0) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 1.0416 time to fit residues: 252.4847 Evaluate side-chains 190 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.0070 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 333 GLN B 88 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN R 293 GLN S 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.220790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.183831 restraints weight = 10520.750| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 1.94 r_work: 0.3842 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9134 Z= 0.113 Angle : 0.583 10.839 12356 Z= 0.304 Chirality : 0.042 0.186 1402 Planarity : 0.004 0.039 1548 Dihedral : 9.692 134.644 1268 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.21 % Favored : 96.70 % Rotamer: Outliers : 1.64 % Allowed : 11.51 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.26), residues: 1121 helix: 1.85 (0.26), residues: 403 sheet: -0.07 (0.31), residues: 285 loop : -1.16 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.003 0.001 HIS S 220 PHE 0.014 0.001 PHE B 151 TYR 0.018 0.001 TYR S 178 ARG 0.007 0.000 ARG R 86 Details of bonding type rmsd hydrogen bonds : bond 0.03684 ( 466) hydrogen bonds : angle 4.56652 ( 1326) SS BOND : bond 0.00547 ( 5) SS BOND : angle 2.23668 ( 10) covalent geometry : bond 0.00242 ( 9129) covalent geometry : angle 0.57941 (12346) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 1.354 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8136 (mp0) cc_final: 0.7547 (mm-30) REVERT: A 248 LYS cc_start: 0.7780 (pttt) cc_final: 0.7350 (pttp) REVERT: A 308 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7003 (tp30) REVERT: A 345 LYS cc_start: 0.8249 (tmtt) cc_final: 0.7883 (tmtp) REVERT: B 47 THR cc_start: 0.8645 (m) cc_final: 0.8424 (m) REVERT: B 76 ASP cc_start: 0.7425 (p0) cc_final: 0.7119 (p0) REVERT: B 155 ASN cc_start: 0.8070 (t0) cc_final: 0.7569 (t0) REVERT: B 175 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7825 (mm110) REVERT: B 188 MET cc_start: 0.7951 (mmm) cc_final: 0.7732 (tpt) REVERT: B 280 LYS cc_start: 0.8257 (tttm) cc_final: 0.7983 (tttp) REVERT: R 51 LYS cc_start: 0.6454 (mppt) cc_final: 0.6110 (mtpp) REVERT: R 91 ILE cc_start: 0.6581 (OUTLIER) cc_final: 0.6035 (mp) REVERT: S 157 ASN cc_start: 0.7249 (m-40) cc_final: 0.7041 (m110) REVERT: S 189 ASP cc_start: 0.7711 (p0) cc_final: 0.7068 (t0) outliers start: 16 outliers final: 6 residues processed: 210 average time/residue: 1.2097 time to fit residues: 273.4866 Evaluate side-chains 185 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 178 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain R residue 87 ASN Chi-restraints excluded: chain R residue 91 ILE Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 74 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 66 optimal weight: 30.0000 chunk 79 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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** A 333 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 244 ASN R 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.210049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.171517 restraints weight = 10571.251| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.05 r_work: 0.3702 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 9134 Z= 0.259 Angle : 0.729 10.522 12356 Z= 0.386 Chirality : 0.048 0.285 1402 Planarity : 0.005 0.051 1548 Dihedral : 9.979 133.041 1268 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.81 % Rotamer: Outliers : 3.49 % Allowed : 15.01 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.25), residues: 1121 helix: 1.55 (0.26), residues: 389 sheet: -0.13 (0.30), residues: 297 loop : -1.11 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 99 HIS 0.007 0.002 HIS B 62 PHE 0.034 0.003 PHE B 151 TYR 0.023 0.002 TYR B 264 ARG 0.006 0.001 ARG R 286 Details of bonding type rmsd hydrogen bonds : bond 0.05104 ( 466) hydrogen bonds : angle 4.90253 ( 1326) SS BOND : bond 0.01160 ( 5) SS BOND : angle 2.79456 ( 10) covalent geometry : bond 0.00613 ( 9129) covalent geometry : angle 0.72464 (12346) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: A 243 MET cc_start: 0.8743 (tpt) cc_final: 0.8540 (tpt) REVERT: A 248 LYS cc_start: 0.7940 (pttt) cc_final: 0.7464 (ptmm) REVERT: B 175 GLN cc_start: 0.8338 (mm-40) cc_final: 0.8080 (mm110) REVERT: B 220 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7019 (mp10) REVERT: B 269 ILE cc_start: 0.8074 (mp) cc_final: 0.7802 (mp) REVERT: B 280 LYS cc_start: 0.8573 (tttm) cc_final: 0.8254 (tttp) REVERT: R 76 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7347 (mp) REVERT: R 169 LYS cc_start: 0.6181 (tttm) cc_final: 0.5656 (ttpt) REVERT: R 189 MET cc_start: 0.5773 (tpp) cc_final: 0.5391 (mmp) REVERT: S 148 ARG cc_start: 0.6465 (ptp-110) cc_final: 0.5900 (ptp90) REVERT: S 179 ARG cc_start: 0.7272 (mmt90) cc_final: 0.6846 (tpp-160) REVERT: S 189 ASP cc_start: 0.7731 (p0) cc_final: 0.7168 (t0) outliers start: 34 outliers final: 13 residues processed: 205 average time/residue: 0.9962 time to fit residues: 220.0225 Evaluate side-chains 184 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 303 GLU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 23 optimal weight: 0.0040 chunk 3 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 0.3980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 333 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 212 ASN R 293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.217171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.180850 restraints weight = 10508.469| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.01 r_work: 0.3809 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 9134 Z= 0.112 Angle : 0.586 9.143 12356 Z= 0.305 Chirality : 0.042 0.213 1402 Planarity : 0.004 0.043 1548 Dihedral : 9.348 132.830 1268 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.03 % Favored : 96.88 % Rotamer: Outliers : 2.36 % Allowed : 18.81 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.25), residues: 1121 helix: 1.89 (0.26), residues: 390 sheet: -0.02 (0.30), residues: 277 loop : -1.08 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.004 0.001 HIS S 220 PHE 0.021 0.001 PHE S 29 TYR 0.035 0.001 TYR A 320 ARG 0.004 0.000 ARG S 179 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 466) hydrogen bonds : angle 4.50122 ( 1326) SS BOND : bond 0.00850 ( 5) SS BOND : angle 2.79208 ( 10) covalent geometry : bond 0.00239 ( 9129) covalent geometry : angle 0.58114 (12346) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: B 175 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8089 (mm110) REVERT: B 220 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.6984 (mp10) REVERT: B 268 ASN cc_start: 0.7524 (OUTLIER) cc_final: 0.7301 (t0) REVERT: R 48 MET cc_start: 0.3902 (ttp) cc_final: 0.3397 (mpp) REVERT: R 169 LYS cc_start: 0.5934 (tttm) cc_final: 0.5573 (ttpt) REVERT: R 183 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6831 (tm) REVERT: S 148 ARG cc_start: 0.6345 (ptp-110) cc_final: 0.5936 (ttp-110) REVERT: S 189 ASP cc_start: 0.7762 (p0) cc_final: 0.7128 (t0) REVERT: S 200 PHE cc_start: 0.7125 (m-80) cc_final: 0.6898 (m-80) outliers start: 23 outliers final: 9 residues processed: 205 average time/residue: 1.0457 time to fit residues: 230.0856 Evaluate side-chains 188 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 303 GLU Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 13 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 79 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 62 optimal weight: 0.0050 overall best weight: 2.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN R 137 ASN R 293 GLN S 39 GLN S 157 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.214223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.175625 restraints weight = 10412.964| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 1.97 r_work: 0.3753 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9134 Z= 0.150 Angle : 0.632 12.314 12356 Z= 0.330 Chirality : 0.044 0.307 1402 Planarity : 0.004 0.041 1548 Dihedral : 9.330 125.571 1268 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.01 % Favored : 95.90 % Rotamer: Outliers : 2.67 % Allowed : 20.14 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.25), residues: 1121 helix: 1.85 (0.26), residues: 389 sheet: 0.09 (0.30), residues: 287 loop : -1.06 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.005 0.001 HIS S 220 PHE 0.021 0.002 PHE B 151 TYR 0.021 0.002 TYR A 320 ARG 0.007 0.001 ARG S 67 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 466) hydrogen bonds : angle 4.57348 ( 1326) SS BOND : bond 0.01180 ( 5) SS BOND : angle 3.73686 ( 10) covalent geometry : bond 0.00349 ( 9129) covalent geometry : angle 0.62317 (12346) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: B 175 GLN cc_start: 0.8513 (mm-40) cc_final: 0.8236 (mm110) REVERT: B 220 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7049 (mp10) REVERT: R 169 LYS cc_start: 0.5959 (tttm) cc_final: 0.5577 (ttpt) REVERT: R 183 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6769 (tm) REVERT: R 189 MET cc_start: 0.5403 (tpp) cc_final: 0.4951 (mmp) REVERT: S 189 ASP cc_start: 0.7728 (p0) cc_final: 0.7141 (t0) outliers start: 26 outliers final: 15 residues processed: 197 average time/residue: 1.0521 time to fit residues: 223.0468 Evaluate side-chains 201 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 303 GLU Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 0.3980 chunk 92 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 30 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN R 293 GLN S 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.218632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.181783 restraints weight = 10561.118| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 1.96 r_work: 0.3826 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3718 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9134 Z= 0.111 Angle : 0.608 13.292 12356 Z= 0.312 Chirality : 0.042 0.218 1402 Planarity : 0.003 0.040 1548 Dihedral : 8.955 119.395 1268 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.03 % Favored : 96.88 % Rotamer: Outliers : 2.67 % Allowed : 21.48 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1121 helix: 1.95 (0.26), residues: 392 sheet: 0.12 (0.30), residues: 270 loop : -1.06 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.004 0.001 HIS S 220 PHE 0.015 0.001 PHE S 29 TYR 0.021 0.001 TYR A 320 ARG 0.006 0.000 ARG R 86 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 466) hydrogen bonds : angle 4.45387 ( 1326) SS BOND : bond 0.00969 ( 5) SS BOND : angle 3.85391 ( 10) covalent geometry : bond 0.00241 ( 9129) covalent geometry : angle 0.59852 (12346) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 1.004 Fit side-chains REVERT: A 207 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7556 (tt0) REVERT: B 175 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8208 (mm110) REVERT: B 268 ASN cc_start: 0.7589 (OUTLIER) cc_final: 0.7335 (t0) REVERT: R 85 LYS cc_start: 0.6697 (tptt) cc_final: 0.5818 (pttp) REVERT: R 169 LYS cc_start: 0.5911 (tttm) cc_final: 0.5571 (ttpt) REVERT: R 183 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6636 (tm) REVERT: R 191 ILE cc_start: 0.6994 (OUTLIER) cc_final: 0.6772 (mp) REVERT: R 302 LYS cc_start: 0.7614 (tmmt) cc_final: 0.6183 (mtpt) REVERT: S 185 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8583 (p) REVERT: S 189 ASP cc_start: 0.7693 (p0) cc_final: 0.7110 (t0) outliers start: 26 outliers final: 13 residues processed: 206 average time/residue: 0.9927 time to fit residues: 220.4305 Evaluate side-chains 198 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 62 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 108 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 340 ASN S 39 GLN S 157 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.212790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.174572 restraints weight = 10435.777| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.09 r_work: 0.3697 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 9134 Z= 0.208 Angle : 0.717 14.658 12356 Z= 0.371 Chirality : 0.046 0.340 1402 Planarity : 0.004 0.045 1548 Dihedral : 9.317 117.061 1268 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.55 % Favored : 95.36 % Rotamer: Outliers : 3.60 % Allowed : 21.07 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.25), residues: 1121 helix: 1.63 (0.26), residues: 392 sheet: 0.11 (0.30), residues: 285 loop : -1.05 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 99 HIS 0.009 0.001 HIS S 220 PHE 0.026 0.002 PHE B 151 TYR 0.024 0.002 TYR B 264 ARG 0.012 0.001 ARG R 86 Details of bonding type rmsd hydrogen bonds : bond 0.04629 ( 466) hydrogen bonds : angle 4.75452 ( 1326) SS BOND : bond 0.01325 ( 5) SS BOND : angle 4.49800 ( 10) covalent geometry : bond 0.00495 ( 9129) covalent geometry : angle 0.70596 (12346) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.953 Fit side-chains REVERT: A 207 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: A 248 LYS cc_start: 0.7788 (pttm) cc_final: 0.7280 (ptmm) REVERT: B 220 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7112 (mp10) REVERT: B 234 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.7072 (t80) REVERT: R 76 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7404 (mp) REVERT: R 183 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6550 (tm) REVERT: R 191 ILE cc_start: 0.6685 (OUTLIER) cc_final: 0.6401 (mp) REVERT: S 179 ARG cc_start: 0.7089 (mmt90) cc_final: 0.6727 (mmt90) REVERT: S 189 ASP cc_start: 0.7642 (p0) cc_final: 0.7031 (t0) outliers start: 35 outliers final: 18 residues processed: 196 average time/residue: 1.0463 time to fit residues: 220.5300 Evaluate side-chains 194 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 83 HIS Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 311 ILE Chi-restraints excluded: chain R residue 334 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 86 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 68 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN R 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.213176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.175518 restraints weight = 10530.814| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.04 r_work: 0.3732 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 9134 Z= 0.161 Angle : 0.676 12.914 12356 Z= 0.348 Chirality : 0.044 0.297 1402 Planarity : 0.004 0.049 1548 Dihedral : 9.155 115.274 1268 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.84 % Favored : 96.07 % Rotamer: Outliers : 2.98 % Allowed : 22.30 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1121 helix: 1.67 (0.26), residues: 391 sheet: 0.12 (0.30), residues: 285 loop : -1.06 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.006 0.001 HIS S 220 PHE 0.031 0.002 PHE S 29 TYR 0.021 0.002 TYR B 264 ARG 0.014 0.001 ARG R 86 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 466) hydrogen bonds : angle 4.65801 ( 1326) SS BOND : bond 0.01145 ( 5) SS BOND : angle 4.11990 ( 10) covalent geometry : bond 0.00376 ( 9129) covalent geometry : angle 0.66596 (12346) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 1.090 Fit side-chains REVERT: A 207 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7589 (tt0) REVERT: A 248 LYS cc_start: 0.7722 (pttm) cc_final: 0.7218 (ptmm) REVERT: B 220 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7169 (mp10) REVERT: R 183 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6689 (tm) REVERT: R 191 ILE cc_start: 0.6909 (OUTLIER) cc_final: 0.6651 (mp) REVERT: S 179 ARG cc_start: 0.6950 (mmt90) cc_final: 0.6622 (mmt90) REVERT: S 189 ASP cc_start: 0.7636 (p0) cc_final: 0.7022 (t0) outliers start: 29 outliers final: 19 residues processed: 193 average time/residue: 1.0718 time to fit residues: 222.3781 Evaluate side-chains 193 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 220 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 54 optimal weight: 50.0000 chunk 100 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN R 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.212226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.173402 restraints weight = 10355.700| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.01 r_work: 0.3699 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 9134 Z= 0.211 Angle : 0.791 25.922 12356 Z= 0.401 Chirality : 0.047 0.352 1402 Planarity : 0.004 0.050 1548 Dihedral : 9.330 113.823 1268 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.27 % Rotamer: Outliers : 3.08 % Allowed : 22.51 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1121 helix: 1.49 (0.26), residues: 390 sheet: -0.01 (0.30), residues: 280 loop : -1.15 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.007 0.001 HIS S 220 PHE 0.031 0.002 PHE S 29 TYR 0.026 0.002 TYR B 264 ARG 0.015 0.001 ARG R 86 Details of bonding type rmsd hydrogen bonds : bond 0.04714 ( 466) hydrogen bonds : angle 4.87658 ( 1326) SS BOND : bond 0.01543 ( 5) SS BOND : angle 5.91235 ( 10) covalent geometry : bond 0.00501 ( 9129) covalent geometry : angle 0.77327 (12346) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.942 Fit side-chains REVERT: A 207 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: A 248 LYS cc_start: 0.7803 (pttm) cc_final: 0.7303 (ptmm) REVERT: B 220 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7153 (mp10) REVERT: B 304 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.6243 (mtp-110) REVERT: R 183 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6538 (tm) REVERT: R 191 ILE cc_start: 0.6617 (OUTLIER) cc_final: 0.6305 (mp) REVERT: S 189 ASP cc_start: 0.7740 (p0) cc_final: 0.7122 (t0) outliers start: 30 outliers final: 20 residues processed: 191 average time/residue: 1.0473 time to fit residues: 214.9001 Evaluate side-chains 195 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 83 HIS Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 311 ILE Chi-restraints excluded: chain R residue 334 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 220 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 67 optimal weight: 0.0000 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN R 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.214419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.176958 restraints weight = 10478.285| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.00 r_work: 0.3757 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9134 Z= 0.140 Angle : 0.726 23.271 12356 Z= 0.363 Chirality : 0.044 0.292 1402 Planarity : 0.004 0.043 1548 Dihedral : 9.011 115.884 1268 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.84 % Favored : 96.07 % Rotamer: Outliers : 2.36 % Allowed : 22.82 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1121 helix: 1.63 (0.26), residues: 391 sheet: 0.05 (0.31), residues: 266 loop : -1.07 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.005 0.001 HIS S 220 PHE 0.028 0.002 PHE S 29 TYR 0.018 0.002 TYR B 264 ARG 0.009 0.001 ARG R 86 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 466) hydrogen bonds : angle 4.69113 ( 1326) SS BOND : bond 0.01162 ( 5) SS BOND : angle 5.84239 ( 10) covalent geometry : bond 0.00319 ( 9129) covalent geometry : angle 0.70670 (12346) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 1.010 Fit side-chains REVERT: A 207 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: B 217 MET cc_start: 0.6240 (mmp) cc_final: 0.6030 (mpm) REVERT: B 220 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7162 (mp10) REVERT: R 169 LYS cc_start: 0.5928 (tttm) cc_final: 0.5561 (ttpt) REVERT: R 183 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6658 (tm) REVERT: R 191 ILE cc_start: 0.6973 (OUTLIER) cc_final: 0.6748 (mp) REVERT: S 159 ASN cc_start: 0.6273 (m-40) cc_final: 0.5979 (p0) REVERT: S 189 ASP cc_start: 0.7685 (p0) cc_final: 0.7042 (t0) outliers start: 23 outliers final: 14 residues processed: 192 average time/residue: 1.0563 time to fit residues: 218.0138 Evaluate side-chains 195 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 0.9990 chunk 46 optimal weight: 0.0000 chunk 69 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 74 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN R 212 ASN R 309 ASN S 157 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.219318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.182252 restraints weight = 10547.662| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.99 r_work: 0.3826 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3718 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9134 Z= 0.116 Angle : 0.678 19.127 12356 Z= 0.341 Chirality : 0.043 0.263 1402 Planarity : 0.004 0.056 1548 Dihedral : 8.769 118.268 1268 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.01 % Favored : 95.90 % Rotamer: Outliers : 1.95 % Allowed : 24.05 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1121 helix: 1.76 (0.26), residues: 390 sheet: 0.10 (0.30), residues: 266 loop : -1.09 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 99 HIS 0.005 0.001 HIS S 220 PHE 0.027 0.001 PHE S 29 TYR 0.018 0.001 TYR S 178 ARG 0.013 0.001 ARG R 86 Details of bonding type rmsd hydrogen bonds : bond 0.03608 ( 466) hydrogen bonds : angle 4.52724 ( 1326) SS BOND : bond 0.00797 ( 5) SS BOND : angle 5.41511 ( 10) covalent geometry : bond 0.00254 ( 9129) covalent geometry : angle 0.66065 (12346) =============================================================================== Job complete usr+sys time: 8166.40 seconds wall clock time: 141 minutes 52.01 seconds (8512.01 seconds total)