Starting phenix.real_space_refine on Mon May 12 08:28:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbh_38218/05_2025/8xbh_38218.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbh_38218/05_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_38218/05_2025/8xbh_38218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbh_38218/05_2025/8xbh_38218.map" model { file = "/net/cci-nas-00/data/ceres_data/8xbh_38218/05_2025/8xbh_38218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbh_38218/05_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.14, per 1000 atoms: 0.57 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: 2.35 Conformation dependent library (CDL) restraints added in 965.0 milliseconds 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: 0.92 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: 2.46 Time building geometry restraints manager: 2.70 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: 0.080 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: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.540 Find NCS groups from input model: 0.100 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:10.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.330 ------------------------------------------------------------------------------- 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 : 0.895 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: 0.9752 time to fit residues: 236.7614 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 : 0.889 ------------------------------------------------------------------------------- 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 = 10520.752| |-----------------------------------------------------------------------------| 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 : 0.909 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8138 (mp0) cc_final: 0.7547 (mm-30) REVERT: A 248 LYS cc_start: 0.7776 (pttt) cc_final: 0.7345 (pttp) REVERT: A 308 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7000 (tp30) REVERT: A 345 LYS cc_start: 0.8249 (tmtt) cc_final: 0.7882 (tmtp) REVERT: B 47 THR cc_start: 0.8649 (m) cc_final: 0.8428 (m) REVERT: B 76 ASP cc_start: 0.7427 (p0) cc_final: 0.7118 (p0) REVERT: B 155 ASN cc_start: 0.8068 (t0) cc_final: 0.7567 (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: 0.7731 (tpt) REVERT: B 280 LYS cc_start: 0.8254 (tttm) cc_final: 0.7981 (tttp) REVERT: R 51 LYS cc_start: 0.6460 (mppt) cc_final: 0.6115 (mtpp) REVERT: R 91 ILE cc_start: 0.6575 (OUTLIER) cc_final: 0.6031 (mp) REVERT: S 157 ASN cc_start: 0.7252 (m-40) cc_final: 0.7036 (m110) REVERT: S 189 ASP cc_start: 0.7708 (p0) cc_final: 0.7065 (t0) outliers start: 16 outliers final: 6 residues processed: 210 average time/residue: 1.0932 time to fit residues: 247.8062 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 : 1.004 ------------------------------------------------------------------------------- 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: 8.9990 chunk 66 optimal weight: 30.0000 chunk 79 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 ** 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 = 0.4271 r_free = 0.4271 target = 0.210580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.171268 restraints weight = 10492.078| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.12 r_work: 0.3688 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.119 9134 Z= 0.276 Angle : 0.744 10.235 12356 Z= 0.394 Chirality : 0.048 0.281 1402 Planarity : 0.005 0.052 1548 Dihedral : 10.015 133.058 1268 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.01 % Favored : 95.90 % Rotamer: Outliers : 3.49 % Allowed : 15.31 % Favored : 81.19 % 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: 0.06 (0.25), residues: 1121 helix: 1.49 (0.26), residues: 389 sheet: -0.14 (0.30), residues: 297 loop : -1.12 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 99 HIS 0.007 0.002 HIS B 62 PHE 0.035 0.003 PHE B 151 TYR 0.026 0.002 TYR B 264 ARG 0.006 0.001 ARG R 286 Details of bonding type rmsd hydrogen bonds : bond 0.05206 ( 466) hydrogen bonds : angle 4.94019 ( 1326) SS BOND : bond 0.01407 ( 5) SS BOND : angle 2.76058 ( 10) covalent geometry : bond 0.00656 ( 9129) covalent geometry : angle 0.73967 (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 214 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7714 (tt0) REVERT: A 248 LYS cc_start: 0.7978 (pttt) cc_final: 0.7508 (ptmm) REVERT: B 175 GLN cc_start: 0.8467 (mm-40) cc_final: 0.8234 (mm110) REVERT: B 220 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7061 (mp10) REVERT: B 280 LYS cc_start: 0.8575 (tttm) cc_final: 0.8271 (tttp) REVERT: R 76 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7275 (mp) REVERT: R 169 LYS cc_start: 0.6195 (tttm) cc_final: 0.5670 (ttpt) REVERT: R 189 MET cc_start: 0.5824 (tpp) cc_final: 0.5442 (mmp) REVERT: R 192 LEU cc_start: 0.6671 (tp) cc_final: 0.6465 (tt) REVERT: S 179 ARG cc_start: 0.7252 (mmt90) cc_final: 0.6773 (tpp-160) REVERT: S 189 ASP cc_start: 0.7748 (p0) cc_final: 0.7182 (t0) outliers start: 34 outliers final: 13 residues processed: 202 average time/residue: 0.9864 time to fit residues: 215.0903 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 : 1.010 ------------------------------------------------------------------------------- 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: 0.0270 chunk 41 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- 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 ** 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 = 0.4299 r_free = 0.4299 target = 0.213695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.175617 restraints weight = 10451.491| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 1.91 r_work: 0.3765 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9134 Z= 0.139 Angle : 0.618 9.592 12356 Z= 0.324 Chirality : 0.043 0.235 1402 Planarity : 0.004 0.047 1548 Dihedral : 9.580 133.185 1268 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.48 % Favored : 96.43 % Rotamer: Outliers : 2.26 % Allowed : 18.71 % Favored : 79.03 % 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: 0.27 (0.25), residues: 1121 helix: 1.76 (0.26), residues: 389 sheet: 0.02 (0.30), residues: 284 loop : -1.12 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.005 0.001 HIS S 220 PHE 0.022 0.002 PHE S 29 TYR 0.021 0.002 TYR S 178 ARG 0.004 0.000 ARG S 179 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 466) hydrogen bonds : angle 4.63237 ( 1326) SS BOND : bond 0.01198 ( 5) SS BOND : angle 2.96460 ( 10) covalent geometry : bond 0.00314 ( 9129) covalent geometry : angle 0.61285 (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 212 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: A 248 LYS cc_start: 0.7801 (pttt) cc_final: 0.7354 (ptmm) REVERT: B 175 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8193 (mm110) REVERT: B 220 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7074 (mp10) REVERT: R 66 ILE cc_start: 0.8208 (tp) cc_final: 0.7910 (mp) REVERT: R 169 LYS cc_start: 0.5905 (tttm) cc_final: 0.5517 (ttpt) REVERT: R 183 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6833 (tm) REVERT: R 189 MET cc_start: 0.5714 (tpp) cc_final: 0.5322 (mmp) REVERT: R 302 LYS cc_start: 0.7293 (tmmt) cc_final: 0.6264 (mtpt) REVERT: R 303 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6492 (tp30) REVERT: S 20 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7391 (mp) REVERT: S 148 ARG cc_start: 0.6523 (ptp-110) cc_final: 0.6102 (ttp-110) REVERT: S 189 ASP cc_start: 0.7733 (p0) cc_final: 0.7131 (t0) outliers start: 22 outliers final: 10 residues processed: 202 average time/residue: 1.0336 time to fit residues: 224.1871 Evaluate side-chains 193 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 13 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 220 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.209569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.171946 restraints weight = 10395.327| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.07 r_work: 0.3703 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2351 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= 0.226 Angle : 0.714 13.085 12356 Z= 0.375 Chirality : 0.047 0.317 1402 Planarity : 0.004 0.052 1548 Dihedral : 9.741 126.305 1268 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.73 % Favored : 95.18 % Rotamer: Outliers : 3.91 % Allowed : 18.91 % 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: 0.10 (0.25), residues: 1121 helix: 1.51 (0.26), residues: 392 sheet: -0.05 (0.30), residues: 286 loop : -1.13 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 99 HIS 0.005 0.001 HIS S 220 PHE 0.029 0.002 PHE B 151 TYR 0.028 0.002 TYR B 264 ARG 0.006 0.001 ARG R 86 Details of bonding type rmsd hydrogen bonds : bond 0.04845 ( 466) hydrogen bonds : angle 4.87467 ( 1326) SS BOND : bond 0.01236 ( 5) SS BOND : angle 3.72232 ( 10) covalent geometry : bond 0.00537 ( 9129) covalent geometry : angle 0.70596 (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 221 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: A 248 LYS cc_start: 0.7866 (pttt) cc_final: 0.7417 (ptmm) REVERT: B 220 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7130 (mp10) REVERT: R 189 MET cc_start: 0.5771 (tpp) cc_final: 0.5384 (mmp) REVERT: S 189 ASP cc_start: 0.7724 (p0) cc_final: 0.7096 (t0) outliers start: 38 outliers final: 21 residues processed: 205 average time/residue: 0.9825 time to fit residues: 217.3390 Evaluate side-chains 198 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 164 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 331 SER 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 R residue 303 GLU Chi-restraints excluded: chain R residue 334 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 0.0020 chunk 67 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.214922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.177498 restraints weight = 10456.476| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 1.96 r_work: 0.3785 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9134 Z= 0.126 Angle : 0.649 18.039 12356 Z= 0.334 Chirality : 0.044 0.246 1402 Planarity : 0.004 0.047 1548 Dihedral : 9.232 122.180 1268 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.03 % Favored : 96.88 % Rotamer: Outliers : 2.16 % Allowed : 22.40 % Favored : 75.44 % 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 (0.25), residues: 1121 helix: 1.78 (0.26), residues: 389 sheet: 0.11 (0.30), residues: 272 loop : -1.09 (0.29), residues: 460 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 0.018 0.001 PHE B 151 TYR 0.020 0.001 TYR S 178 ARG 0.006 0.000 ARG R 86 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 466) hydrogen bonds : angle 4.61042 ( 1326) SS BOND : bond 0.00714 ( 5) SS BOND : angle 4.23696 ( 10) covalent geometry : bond 0.00280 ( 9129) covalent geometry : angle 0.63837 (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 211 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7581 (tt0) REVERT: A 317 LYS cc_start: 0.8243 (ptpp) cc_final: 0.8041 (ptpt) REVERT: B 220 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7264 (mp10) REVERT: R 169 LYS cc_start: 0.5926 (tttm) cc_final: 0.5570 (ttpt) REVERT: R 183 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6750 (tm) REVERT: R 189 MET cc_start: 0.5527 (tpp) cc_final: 0.5132 (mmp) REVERT: R 302 LYS cc_start: 0.7457 (tmmt) cc_final: 0.6202 (mtpt) REVERT: S 2 VAL cc_start: 0.7892 (t) cc_final: 0.7688 (m) REVERT: S 20 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7503 (mp) REVERT: S 157 ASN cc_start: 0.7482 (m-40) cc_final: 0.7279 (m110) REVERT: S 189 ASP cc_start: 0.7657 (p0) cc_final: 0.7061 (t0) REVERT: S 200 PHE cc_start: 0.7106 (m-80) cc_final: 0.6854 (m-80) outliers start: 21 outliers final: 13 residues processed: 201 average time/residue: 0.9780 time to fit residues: 211.6236 Evaluate side-chains 194 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 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 336 LEU Chi-restraints excluded: chain R residue 69 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 220 GLN B 340 ASN R 293 GLN S 39 GLN S 220 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.208106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.169118 restraints weight = 10492.433| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.96 r_work: 0.3686 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 9134 Z= 0.283 Angle : 0.827 23.195 12356 Z= 0.426 Chirality : 0.050 0.386 1402 Planarity : 0.005 0.055 1548 Dihedral : 9.695 118.339 1268 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.73 % Favored : 95.18 % Rotamer: Outliers : 4.11 % Allowed : 21.79 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.04 (0.25), residues: 1121 helix: 1.34 (0.26), residues: 391 sheet: -0.07 (0.30), residues: 280 loop : -1.19 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 99 HIS 0.011 0.002 HIS S 220 PHE 0.033 0.003 PHE B 151 TYR 0.033 0.003 TYR B 264 ARG 0.008 0.001 ARG R 86 Details of bonding type rmsd hydrogen bonds : bond 0.05262 ( 466) hydrogen bonds : angle 5.09460 ( 1326) SS BOND : bond 0.01546 ( 5) SS BOND : angle 5.25862 ( 10) covalent geometry : bond 0.00671 ( 9129) covalent geometry : angle 0.81326 (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 218 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: A 248 LYS cc_start: 0.7837 (pttm) cc_final: 0.7318 (ptmm) REVERT: A 333 GLN cc_start: 0.8037 (tp40) cc_final: 0.7836 (tp-100) REVERT: R 76 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7247 (mp) REVERT: R 189 MET cc_start: 0.5817 (tpp) cc_final: 0.5413 (mmp) REVERT: S 189 ASP cc_start: 0.7699 (p0) cc_final: 0.7056 (t0) outliers start: 40 outliers final: 28 residues processed: 204 average time/residue: 1.0157 time to fit residues: 223.3382 Evaluate side-chains 201 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 332 VAL Chi-restraints excluded: chain B residue 65 THR 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 211 TRP Chi-restraints excluded: chain B residue 274 THR 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 69 LEU Chi-restraints excluded: chain R residue 76 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 303 GLU Chi-restraints excluded: chain R residue 311 ILE Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 334 ILE 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: 3.9990 chunk 3 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.213629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.176142 restraints weight = 10571.580| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 1.99 r_work: 0.3756 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9134 Z= 0.135 Angle : 0.687 16.684 12356 Z= 0.351 Chirality : 0.045 0.326 1402 Planarity : 0.004 0.048 1548 Dihedral : 9.180 114.177 1268 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.03 % Favored : 96.88 % Rotamer: Outliers : 2.88 % Allowed : 23.43 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.22 (0.25), residues: 1121 helix: 1.64 (0.26), residues: 392 sheet: 0.11 (0.30), residues: 273 loop : -1.14 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 301 HIS 0.005 0.001 HIS S 220 PHE 0.030 0.002 PHE S 29 TYR 0.021 0.002 TYR S 178 ARG 0.009 0.001 ARG S 67 Details of bonding type rmsd hydrogen bonds : bond 0.03966 ( 466) hydrogen bonds : angle 4.76292 ( 1326) SS BOND : bond 0.00805 ( 5) SS BOND : angle 4.96011 ( 10) covalent geometry : bond 0.00304 ( 9129) covalent geometry : angle 0.67244 (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 210 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 0.973 Fit side-chains REVERT: A 207 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7589 (tt0) REVERT: R 66 ILE cc_start: 0.8170 (tp) cc_final: 0.7896 (mp) REVERT: R 169 LYS cc_start: 0.5916 (tttm) cc_final: 0.5542 (ttpt) REVERT: R 183 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6661 (tm) REVERT: R 191 ILE cc_start: 0.6609 (OUTLIER) cc_final: 0.6342 (mp) REVERT: R 302 LYS cc_start: 0.7782 (tmmt) cc_final: 0.7559 (tmmt) REVERT: S 20 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7544 (mp) REVERT: S 157 ASN cc_start: 0.7521 (m-40) cc_final: 0.7298 (m110) REVERT: S 189 ASP cc_start: 0.7776 (p0) cc_final: 0.7126 (t0) outliers start: 28 outliers final: 14 residues processed: 202 average time/residue: 1.0408 time to fit residues: 226.0477 Evaluate side-chains 194 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 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 147 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR 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 69 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 S residue 20 LEU Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 87 optimal weight: 0.0570 chunk 54 optimal weight: 40.0000 chunk 100 optimal weight: 0.0570 chunk 62 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 93 optimal weight: 0.0060 overall best weight: 1.0236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.216811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.178984 restraints weight = 10404.810| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 1.96 r_work: 0.3788 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9134 Z= 0.129 Angle : 0.700 21.651 12356 Z= 0.354 Chirality : 0.044 0.268 1402 Planarity : 0.004 0.054 1548 Dihedral : 8.970 111.099 1268 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.01 % Favored : 95.90 % Rotamer: Outliers : 2.26 % Allowed : 24.36 % Favored : 73.38 % 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: 0.24 (0.25), residues: 1121 helix: 1.66 (0.26), residues: 392 sheet: 0.20 (0.30), residues: 271 loop : -1.20 (0.29), residues: 458 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 0.028 0.001 PHE S 29 TYR 0.020 0.001 TYR S 178 ARG 0.014 0.001 ARG R 86 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 466) hydrogen bonds : angle 4.67659 ( 1326) SS BOND : bond 0.00827 ( 5) SS BOND : angle 5.40113 ( 10) covalent geometry : bond 0.00286 ( 9129) covalent geometry : angle 0.68297 (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 199 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.958 Fit side-chains REVERT: A 207 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7563 (tt0) REVERT: B 262 MET cc_start: 0.7418 (tpt) cc_final: 0.7214 (tpp) REVERT: R 66 ILE cc_start: 0.8355 (tp) cc_final: 0.8047 (mp) REVERT: R 85 LYS cc_start: 0.6713 (tptt) cc_final: 0.5846 (pttp) REVERT: R 86 ARG cc_start: 0.6695 (ptp-110) cc_final: 0.6446 (ptp-110) REVERT: R 169 LYS cc_start: 0.5917 (tttm) cc_final: 0.5586 (ttpt) REVERT: R 183 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6743 (tm) REVERT: R 191 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.6627 (mp) REVERT: R 302 LYS cc_start: 0.7523 (tmmt) cc_final: 0.5976 (mttt) REVERT: S 20 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7552 (mp) REVERT: S 157 ASN cc_start: 0.7561 (m-40) cc_final: 0.7323 (m110) REVERT: S 189 ASP cc_start: 0.7788 (p0) cc_final: 0.7174 (t0) outliers start: 22 outliers final: 13 residues processed: 191 average time/residue: 1.0095 time to fit residues: 207.5130 Evaluate side-chains 194 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 69 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 20 LEU 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 81 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN S 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.213493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.174945 restraints weight = 10464.768| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.03 r_work: 0.3736 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9134 Z= 0.167 Angle : 0.742 24.326 12356 Z= 0.376 Chirality : 0.046 0.287 1402 Planarity : 0.004 0.050 1548 Dihedral : 9.141 113.087 1268 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.81 % Rotamer: Outliers : 2.36 % Allowed : 25.08 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.19 (0.25), residues: 1121 helix: 1.61 (0.26), residues: 391 sheet: 0.09 (0.30), residues: 275 loop : -1.16 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 99 HIS 0.007 0.001 HIS S 220 PHE 0.030 0.002 PHE S 29 TYR 0.020 0.002 TYR S 178 ARG 0.014 0.001 ARG R 86 Details of bonding type rmsd hydrogen bonds : bond 0.04261 ( 466) hydrogen bonds : angle 4.75633 ( 1326) SS BOND : bond 0.01197 ( 5) SS BOND : angle 5.73464 ( 10) covalent geometry : bond 0.00390 ( 9129) covalent geometry : angle 0.72384 (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 195 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.926 Fit side-chains REVERT: A 207 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: R 183 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6674 (tm) REVERT: R 191 ILE cc_start: 0.6889 (OUTLIER) cc_final: 0.6637 (mp) REVERT: S 157 ASN cc_start: 0.7606 (m-40) cc_final: 0.7377 (m110) REVERT: S 189 ASP cc_start: 0.7766 (p0) cc_final: 0.7144 (t0) outliers start: 23 outliers final: 16 residues processed: 188 average time/residue: 1.0550 time to fit residues: 212.8272 Evaluate side-chains 188 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 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 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 69 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 185 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 4.9990 chunk 46 optimal weight: 0.0060 chunk 69 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 89 optimal weight: 0.0030 chunk 54 optimal weight: 40.0000 chunk 5 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.4010 ------------------------------------------------------------------------------- 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 = 0.4316 r_free = 0.4316 target = 0.215651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.177761 restraints weight = 10524.798| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.02 r_work: 0.3768 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3658 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9134 Z= 0.136 Angle : 0.704 22.073 12356 Z= 0.356 Chirality : 0.044 0.267 1402 Planarity : 0.004 0.044 1548 Dihedral : 8.982 115.695 1268 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.01 % Favored : 95.90 % Rotamer: Outliers : 2.67 % Allowed : 24.87 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.20 (0.25), residues: 1121 helix: 1.63 (0.26), residues: 392 sheet: 0.16 (0.30), residues: 273 loop : -1.21 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.006 0.001 HIS S 220 PHE 0.028 0.002 PHE S 29 TYR 0.020 0.001 TYR S 178 ARG 0.007 0.000 ARG S 67 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 466) hydrogen bonds : angle 4.64964 ( 1326) SS BOND : bond 0.00978 ( 5) SS BOND : angle 5.42688 ( 10) covalent geometry : bond 0.00310 ( 9129) covalent geometry : angle 0.68754 (12346) =============================================================================== Job complete usr+sys time: 7797.20 seconds wall clock time: 134 minutes 45.31 seconds (8085.31 seconds total)