Starting phenix.real_space_refine on Wed Feb 12 18:14:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wz4_32904/02_2025/7wz4_32904.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wz4_32904/02_2025/7wz4_32904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wz4_32904/02_2025/7wz4_32904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wz4_32904/02_2025/7wz4_32904.map" model { file = "/net/cci-nas-00/data/ceres_data/7wz4_32904/02_2025/7wz4_32904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wz4_32904/02_2025/7wz4_32904.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5185 2.51 5 N 1419 2.21 5 O 1526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8187 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1692 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain breaks: 3 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1715 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2577 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 431 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 3.76, per 1000 atoms: 0.46 Number of scatterers: 8187 At special positions: 0 Unit cell: (90.95, 119.85, 125.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1526 8.00 N 1419 7.00 C 5185 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 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: 2.12 Conformation dependent library (CDL) restraints added in 1.2 seconds 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1994 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 13 sheets defined 37.2% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'R' and resid 34 through 59 removed outlier: 3.512A pdb=" N TYR R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER R 39 " --> pdb=" O SER R 35 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY R 40 " --> pdb=" O LEU R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 63 Processing helix chain 'R' and resid 64 through 88 removed outlier: 3.819A pdb=" N PHE R 69 " --> pdb=" O THR R 65 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET R 85 " --> pdb=" O CYS R 81 " (cutoff:3.500A) Proline residue: R 86 - end of helix Processing helix chain 'R' and resid 116 through 144 removed outlier: 3.591A pdb=" N CYS R 132 " --> pdb=" O LEU R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 153 Processing helix chain 'R' and resid 154 through 175 removed outlier: 3.743A pdb=" N TRP R 166 " --> pdb=" O LEU R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 227 removed outlier: 4.173A pdb=" N LEU R 195 " --> pdb=" O HIS R 191 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU R 196 " --> pdb=" O TYR R 192 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA R 197 " --> pdb=" O PRO R 193 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA R 198 " --> pdb=" O ALA R 194 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL R 216 " --> pdb=" O TYR R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 308 removed outlier: 3.652A pdb=" N LEU R 287 " --> pdb=" O GLY R 283 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 317 through 337 Proline residue: R 333 - end of helix Processing helix chain 'R' and resid 340 through 351 Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.647A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.374A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.831A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.013A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.520A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.583A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.558A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.532A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.135A 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 87 through 91 removed outlier: 3.719A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.737A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.775A 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 removed outlier: 6.746A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.712A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.081A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.609A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.650A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.531A 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: 6.649A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.653A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.975A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.380A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.823A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1152 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: 2.49 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2671 1.34 - 1.46: 1981 1.46 - 1.58: 3611 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 8343 Sorted by residual: bond pdb=" N TRP R 179 " pdb=" CA TRP R 179 " ideal model delta sigma weight residual 1.455 1.481 -0.026 1.25e-02 6.40e+03 4.31e+00 bond pdb=" CA THR B 181 " pdb=" CB THR B 181 " ideal model delta sigma weight residual 1.527 1.562 -0.034 2.48e-02 1.63e+03 1.93e+00 bond pdb=" C TRP R 179 " pdb=" O TRP R 179 " ideal model delta sigma weight residual 1.234 1.244 -0.010 1.22e-02 6.72e+03 7.18e-01 bond pdb=" CA GLY B 41 " pdb=" C GLY B 41 " ideal model delta sigma weight residual 1.523 1.513 0.010 1.19e-02 7.06e+03 6.94e-01 bond pdb=" CB ASP G 26 " pdb=" CG ASP G 26 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.61e-01 ... (remaining 8338 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 11125 1.88 - 3.75: 166 3.75 - 5.63: 16 5.63 - 7.50: 2 7.50 - 9.38: 1 Bond angle restraints: 11310 Sorted by residual: angle pdb=" N THR R 337 " pdb=" CA THR R 337 " pdb=" C THR R 337 " ideal model delta sigma weight residual 110.44 114.15 -3.71 1.20e+00 6.94e-01 9.57e+00 angle pdb=" CA TRP R 179 " pdb=" C TRP R 179 " pdb=" O TRP R 179 " ideal model delta sigma weight residual 120.99 117.82 3.17 1.12e+00 7.97e-01 8.01e+00 angle pdb=" CA LEU R 152 " pdb=" CB LEU R 152 " pdb=" CG LEU R 152 " ideal model delta sigma weight residual 116.30 125.68 -9.38 3.50e+00 8.16e-02 7.18e+00 angle pdb=" N ALA S 92 " pdb=" CA ALA S 92 " pdb=" C ALA S 92 " ideal model delta sigma weight residual 107.88 111.57 -3.69 1.41e+00 5.03e-01 6.85e+00 angle pdb=" C GLY S 197 " pdb=" N THR S 198 " pdb=" CA THR S 198 " ideal model delta sigma weight residual 123.05 126.89 -3.84 1.57e+00 4.06e-01 5.99e+00 ... (remaining 11305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 4544 17.44 - 34.88: 331 34.88 - 52.32: 62 52.32 - 69.76: 8 69.76 - 87.20: 6 Dihedral angle restraints: 4951 sinusoidal: 1858 harmonic: 3093 Sorted by residual: dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 158.53 21.47 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA ARG S 179 " pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta harmonic sigma weight residual 180.00 162.59 17.41 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA LEU R 83 " pdb=" C LEU R 83 " pdb=" N TRP R 84 " pdb=" CA TRP R 84 " ideal model delta harmonic sigma weight residual 180.00 -163.36 -16.64 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 4948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 822 0.032 - 0.065: 323 0.065 - 0.097: 98 0.097 - 0.129: 57 0.129 - 0.161: 5 Chirality restraints: 1305 Sorted by residual: chirality pdb=" CB THR B 181 " pdb=" CA THR B 181 " pdb=" OG1 THR B 181 " pdb=" CG2 THR B 181 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" CA MET R 85 " pdb=" N MET R 85 " pdb=" C MET R 85 " pdb=" CB MET R 85 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.97e-01 ... (remaining 1302 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 338 " 0.010 2.00e-02 2.50e+03 1.01e-02 2.56e+00 pdb=" CG TRP R 338 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP R 338 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP R 338 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 338 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 338 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 338 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 338 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 338 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 338 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " -0.006 2.00e-02 2.50e+03 1.24e-02 1.55e+00 pdb=" C THR B 87 " 0.022 2.00e-02 2.50e+03 pdb=" O THR B 87 " -0.008 2.00e-02 2.50e+03 pdb=" N ASN B 88 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA S 40 " 0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO S 41 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO S 41 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO S 41 " 0.017 5.00e-02 4.00e+02 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 78 2.66 - 3.22: 7228 3.22 - 3.78: 11695 3.78 - 4.34: 16121 4.34 - 4.90: 28264 Nonbonded interactions: 63386 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.096 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.101 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.141 3.040 nonbonded pdb=" OD2 ASP B 83 " pdb=" OG1 THR B 86 " model vdw 2.280 3.040 nonbonded pdb=" NH2 ARG S 190 " pdb=" OD2 ASP S 211 " model vdw 2.282 3.120 ... (remaining 63381 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: 10.320 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 18.180 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:11.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 0.039 8343 Z= 0.222 Angle : 0.590 9.377 11310 Z= 0.347 Chirality : 0.042 0.161 1305 Planarity : 0.003 0.031 1431 Dihedral : 12.942 87.201 2951 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.12 % Allowed : 0.23 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.09 (0.26), residues: 1051 helix: 2.46 (0.28), residues: 349 sheet: 0.58 (0.31), residues: 283 loop : -0.68 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 338 HIS 0.005 0.001 HIS B 142 PHE 0.011 0.001 PHE B 199 TYR 0.008 0.001 TYR B 105 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.930 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 155 ARG cc_start: 0.4093 (mmt180) cc_final: 0.3818 (mmt180) REVERT: R 217 ARG cc_start: 0.6608 (ttm-80) cc_final: 0.6404 (ptm160) REVERT: R 339 ARG cc_start: 0.8284 (mmm160) cc_final: 0.7705 (mmt-90) REVERT: A 26 ASP cc_start: 0.7396 (m-30) cc_final: 0.7170 (m-30) REVERT: A 308 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7592 (mt-10) REVERT: B 19 ARG cc_start: 0.7362 (ttm170) cc_final: 0.7070 (ttm110) REVERT: B 127 LYS cc_start: 0.8971 (mttm) cc_final: 0.8691 (mttt) REVERT: B 134 ARG cc_start: 0.7719 (mtm110) cc_final: 0.7489 (mtp-110) REVERT: G 58 GLU cc_start: 0.7835 (pm20) cc_final: 0.6927 (mm-30) REVERT: S 211 ASP cc_start: 0.8392 (m-30) cc_final: 0.8109 (m-30) outliers start: 1 outliers final: 2 residues processed: 159 average time/residue: 1.3784 time to fit residues: 231.3613 Evaluate side-chains 130 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 128 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 179 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 61 optimal weight: 0.0060 chunk 95 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 67 ASN B 16 ASN B 32 GLN B 340 ASN S 130 GLN S 167 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.163742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.107188 restraints weight = 9341.455| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.90 r_work: 0.3154 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8343 Z= 0.149 Angle : 0.502 8.556 11310 Z= 0.262 Chirality : 0.041 0.132 1305 Planarity : 0.003 0.029 1431 Dihedral : 4.546 50.608 1160 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.85 % Allowed : 10.84 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.36 (0.27), residues: 1051 helix: 2.84 (0.28), residues: 345 sheet: 0.60 (0.30), residues: 290 loop : -0.56 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 338 HIS 0.003 0.001 HIS R 131 PHE 0.012 0.001 PHE B 199 TYR 0.012 0.001 TYR S 178 ARG 0.005 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.910 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 85 MET cc_start: 0.6527 (OUTLIER) cc_final: 0.5638 (mmm) REVERT: R 217 ARG cc_start: 0.6181 (ttm-80) cc_final: 0.5980 (ptm160) REVERT: R 339 ARG cc_start: 0.8414 (mmm160) cc_final: 0.7845 (mmt-90) REVERT: A 22 ASN cc_start: 0.7066 (m-40) cc_final: 0.6726 (m110) REVERT: A 28 GLU cc_start: 0.5787 (mt-10) cc_final: 0.5559 (tt0) REVERT: A 51 LYS cc_start: 0.7977 (ttmm) cc_final: 0.7535 (ttpp) REVERT: A 309 ASP cc_start: 0.7835 (p0) cc_final: 0.7503 (p0) REVERT: A 313 ARG cc_start: 0.7701 (ptp90) cc_final: 0.7459 (ptp90) REVERT: B 19 ARG cc_start: 0.6867 (ttm170) cc_final: 0.6623 (ttm110) REVERT: B 127 LYS cc_start: 0.8751 (mttm) cc_final: 0.8311 (mttt) REVERT: B 134 ARG cc_start: 0.7883 (mtm110) cc_final: 0.7659 (mtp-110) REVERT: B 175 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.6925 (mp10) REVERT: G 58 GLU cc_start: 0.7712 (pm20) cc_final: 0.6892 (mm-30) REVERT: S 3 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7625 (pt0) outliers start: 16 outliers final: 6 residues processed: 140 average time/residue: 1.4492 time to fit residues: 213.4658 Evaluate side-chains 130 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 337 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 71 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 32 GLN B 340 ASN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.158608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.101650 restraints weight = 9513.226| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.94 r_work: 0.3074 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8343 Z= 0.307 Angle : 0.565 8.253 11310 Z= 0.297 Chirality : 0.043 0.140 1305 Planarity : 0.004 0.030 1431 Dihedral : 4.833 56.976 1160 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.58 % Allowed : 11.42 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.24 (0.26), residues: 1051 helix: 2.86 (0.28), residues: 345 sheet: 0.48 (0.30), residues: 292 loop : -0.69 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 47 HIS 0.007 0.001 HIS B 142 PHE 0.018 0.002 PHE A 196 TYR 0.015 0.001 TYR B 105 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.941 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 85 MET cc_start: 0.6385 (OUTLIER) cc_final: 0.6153 (mpp) REVERT: R 179 TRP cc_start: 0.7157 (OUTLIER) cc_final: 0.6659 (m-10) REVERT: R 344 ARG cc_start: 0.5967 (OUTLIER) cc_final: 0.5688 (mtt180) REVERT: A 22 ASN cc_start: 0.7154 (m-40) cc_final: 0.6841 (m110) REVERT: A 26 ASP cc_start: 0.7013 (m-30) cc_final: 0.6748 (m-30) REVERT: A 28 GLU cc_start: 0.6138 (mt-10) cc_final: 0.5881 (tt0) REVERT: A 251 ASP cc_start: 0.7526 (t0) cc_final: 0.7117 (t0) REVERT: A 309 ASP cc_start: 0.7578 (p0) cc_final: 0.7238 (p0) REVERT: A 313 ARG cc_start: 0.7734 (ptp90) cc_final: 0.7400 (ptp-170) REVERT: B 46 ARG cc_start: 0.7385 (mtm-85) cc_final: 0.6711 (mtp85) REVERT: B 127 LYS cc_start: 0.8925 (mttm) cc_final: 0.8468 (mttt) REVERT: B 134 ARG cc_start: 0.7931 (mtm110) cc_final: 0.7676 (mtp-110) REVERT: B 175 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7135 (mp10) REVERT: B 291 ASP cc_start: 0.7588 (m-30) cc_final: 0.7339 (m-30) REVERT: G 58 GLU cc_start: 0.7726 (pm20) cc_final: 0.6893 (mm-30) REVERT: S 3 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7674 (pt0) REVERT: S 154 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8396 (tt) REVERT: S 211 ASP cc_start: 0.8252 (m-30) cc_final: 0.7974 (m-30) outliers start: 31 outliers final: 14 residues processed: 140 average time/residue: 1.4323 time to fit residues: 211.1951 Evaluate side-chains 138 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 221 VAL Chi-restraints excluded: chain R residue 337 THR Chi-restraints excluded: chain R residue 344 ARG Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 24 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 2 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 16 ASN B 32 GLN B 340 ASN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.160023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.103274 restraints weight = 9461.767| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.95 r_work: 0.3097 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8343 Z= 0.214 Angle : 0.519 7.788 11310 Z= 0.271 Chirality : 0.041 0.133 1305 Planarity : 0.003 0.031 1431 Dihedral : 4.636 52.728 1160 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.34 % Allowed : 13.26 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.29 (0.26), residues: 1051 helix: 2.93 (0.28), residues: 345 sheet: 0.51 (0.30), residues: 290 loop : -0.69 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.005 0.001 HIS B 142 PHE 0.014 0.001 PHE B 199 TYR 0.011 0.001 TYR S 178 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.865 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 344 ARG cc_start: 0.5947 (OUTLIER) cc_final: 0.5685 (mtt180) REVERT: A 22 ASN cc_start: 0.7182 (m-40) cc_final: 0.6842 (m110) REVERT: A 25 GLU cc_start: 0.6721 (tm-30) cc_final: 0.6517 (tm-30) REVERT: A 26 ASP cc_start: 0.7161 (m-30) cc_final: 0.6828 (m-30) REVERT: A 28 GLU cc_start: 0.6010 (mt-10) cc_final: 0.5804 (tt0) REVERT: A 51 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7569 (ttpm) REVERT: A 251 ASP cc_start: 0.7516 (t0) cc_final: 0.7143 (t0) REVERT: A 309 ASP cc_start: 0.7493 (p0) cc_final: 0.7109 (p0) REVERT: A 313 ARG cc_start: 0.7755 (ptp90) cc_final: 0.7356 (ptp-170) REVERT: B 46 ARG cc_start: 0.7339 (mtm-85) cc_final: 0.6643 (mtp85) REVERT: B 127 LYS cc_start: 0.8869 (mttm) cc_final: 0.8421 (mttt) REVERT: B 134 ARG cc_start: 0.7861 (mtm110) cc_final: 0.7573 (mtp-110) REVERT: B 175 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7113 (mp10) REVERT: B 215 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7592 (mt-10) REVERT: B 219 ARG cc_start: 0.7629 (mmt180) cc_final: 0.7068 (mmt180) REVERT: B 291 ASP cc_start: 0.7524 (m-30) cc_final: 0.7305 (m-30) REVERT: G 58 GLU cc_start: 0.7756 (pm20) cc_final: 0.6917 (mm-30) REVERT: S 211 ASP cc_start: 0.8275 (m-30) cc_final: 0.8032 (m-30) outliers start: 29 outliers final: 16 residues processed: 141 average time/residue: 1.4475 time to fit residues: 214.8484 Evaluate side-chains 142 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 221 VAL Chi-restraints excluded: chain R residue 337 THR Chi-restraints excluded: chain R residue 344 ARG Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 30 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 16 ASN B 32 GLN B 340 ASN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.160773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.104419 restraints weight = 9356.700| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.89 r_work: 0.3115 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8343 Z= 0.188 Angle : 0.491 6.713 11310 Z= 0.259 Chirality : 0.041 0.201 1305 Planarity : 0.003 0.034 1431 Dihedral : 4.194 47.318 1157 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.81 % Allowed : 13.73 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.35 (0.27), residues: 1051 helix: 3.03 (0.28), residues: 345 sheet: 0.48 (0.30), residues: 292 loop : -0.65 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.004 0.001 HIS B 142 PHE 0.013 0.001 PHE B 199 TYR 0.011 0.001 TYR S 178 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.876 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 344 ARG cc_start: 0.5899 (OUTLIER) cc_final: 0.5632 (mtt180) REVERT: A 22 ASN cc_start: 0.7166 (m-40) cc_final: 0.6827 (m110) REVERT: A 25 GLU cc_start: 0.6712 (tm-30) cc_final: 0.6467 (tm-30) REVERT: A 26 ASP cc_start: 0.7175 (m-30) cc_final: 0.6842 (m-30) REVERT: A 28 GLU cc_start: 0.5965 (mt-10) cc_final: 0.5764 (tt0) REVERT: A 51 LYS cc_start: 0.8050 (ttmm) cc_final: 0.7519 (ttpp) REVERT: A 251 ASP cc_start: 0.7459 (t0) cc_final: 0.7184 (t0) REVERT: A 309 ASP cc_start: 0.7396 (p0) cc_final: 0.7022 (p0) REVERT: A 313 ARG cc_start: 0.7729 (ptp90) cc_final: 0.7270 (ptp90) REVERT: B 46 ARG cc_start: 0.7371 (mtm-85) cc_final: 0.6609 (mtp85) REVERT: B 127 LYS cc_start: 0.8815 (mttm) cc_final: 0.8352 (mttt) REVERT: B 134 ARG cc_start: 0.7842 (mtm110) cc_final: 0.7619 (mtp-110) REVERT: B 175 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7095 (mp10) REVERT: B 215 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7648 (mt-10) REVERT: B 254 ASP cc_start: 0.8109 (t0) cc_final: 0.7906 (t0) REVERT: B 291 ASP cc_start: 0.7500 (m-30) cc_final: 0.7285 (m-30) REVERT: G 58 GLU cc_start: 0.7729 (pm20) cc_final: 0.6923 (mm-30) REVERT: S 3 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7588 (pt0) REVERT: S 43 LYS cc_start: 0.8650 (mptt) cc_final: 0.8428 (mmtp) REVERT: S 211 ASP cc_start: 0.8258 (m-30) cc_final: 0.8039 (m-30) outliers start: 33 outliers final: 20 residues processed: 146 average time/residue: 1.4237 time to fit residues: 218.8081 Evaluate side-chains 147 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 221 VAL Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 337 THR Chi-restraints excluded: chain R residue 344 ARG Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 67 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 57 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 32 GLN B 340 ASN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.159944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109280 restraints weight = 9548.743| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.49 r_work: 0.3073 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8343 Z= 0.166 Angle : 0.489 8.833 11310 Z= 0.253 Chirality : 0.041 0.161 1305 Planarity : 0.003 0.036 1431 Dihedral : 4.103 46.365 1157 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.58 % Allowed : 14.99 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.42 (0.27), residues: 1051 helix: 3.10 (0.28), residues: 345 sheet: 0.49 (0.30), residues: 292 loop : -0.61 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 PHE 0.013 0.001 PHE B 199 TYR 0.011 0.001 TYR S 178 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.870 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 344 ARG cc_start: 0.6167 (OUTLIER) cc_final: 0.5881 (mtt180) REVERT: A 22 ASN cc_start: 0.7522 (m-40) cc_final: 0.7197 (m110) REVERT: A 25 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6910 (tm-30) REVERT: A 26 ASP cc_start: 0.7496 (m-30) cc_final: 0.7206 (m-30) REVERT: A 28 GLU cc_start: 0.6294 (mt-10) cc_final: 0.6027 (tt0) REVERT: A 29 LYS cc_start: 0.7163 (ttmm) cc_final: 0.6723 (tptt) REVERT: A 51 LYS cc_start: 0.8033 (ttmm) cc_final: 0.7515 (ttpp) REVERT: A 251 ASP cc_start: 0.7713 (t0) cc_final: 0.7418 (t0) REVERT: A 309 ASP cc_start: 0.7420 (p0) cc_final: 0.7060 (p0) REVERT: A 313 ARG cc_start: 0.7792 (ptp90) cc_final: 0.7498 (ptp-170) REVERT: B 46 ARG cc_start: 0.7703 (mtm-85) cc_final: 0.6888 (mtp85) REVERT: B 127 LYS cc_start: 0.8912 (mttm) cc_final: 0.8526 (mttt) REVERT: B 134 ARG cc_start: 0.8148 (mtm110) cc_final: 0.7947 (mtp-110) REVERT: B 219 ARG cc_start: 0.7820 (mmt180) cc_final: 0.7374 (mmt-90) REVERT: B 234 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.9003 (m-80) REVERT: G 58 GLU cc_start: 0.7832 (pm20) cc_final: 0.6981 (mm-30) REVERT: S 3 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7787 (pt0) REVERT: S 154 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8570 (tt) REVERT: S 211 ASP cc_start: 0.8339 (m-30) cc_final: 0.8109 (m-30) outliers start: 31 outliers final: 17 residues processed: 145 average time/residue: 1.4280 time to fit residues: 218.1053 Evaluate side-chains 143 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 221 VAL Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 337 THR Chi-restraints excluded: chain R residue 344 ARG Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 47 optimal weight: 4.9990 chunk 13 optimal weight: 0.0470 chunk 20 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 32 GLN B 340 ASN S 13 GLN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.159758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.103123 restraints weight = 9368.054| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.90 r_work: 0.3111 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8343 Z= 0.297 Angle : 0.554 7.119 11310 Z= 0.291 Chirality : 0.043 0.142 1305 Planarity : 0.003 0.036 1431 Dihedral : 4.427 46.750 1157 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.46 % Allowed : 16.15 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.24 (0.26), residues: 1051 helix: 2.96 (0.28), residues: 344 sheet: 0.39 (0.30), residues: 290 loop : -0.71 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.006 0.001 HIS B 142 PHE 0.014 0.002 PHE B 199 TYR 0.010 0.001 TYR B 105 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.907 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 344 ARG cc_start: 0.6044 (OUTLIER) cc_final: 0.5755 (mtt-85) REVERT: A 22 ASN cc_start: 0.7318 (m-40) cc_final: 0.6977 (m110) REVERT: A 25 GLU cc_start: 0.6883 (tm-30) cc_final: 0.6632 (tm-30) REVERT: A 26 ASP cc_start: 0.7144 (m-30) cc_final: 0.6794 (m-30) REVERT: A 28 GLU cc_start: 0.6112 (mt-10) cc_final: 0.5882 (tt0) REVERT: A 51 LYS cc_start: 0.8069 (ttmm) cc_final: 0.7542 (ttpp) REVERT: A 186 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8030 (mt-10) REVERT: A 251 ASP cc_start: 0.7545 (t0) cc_final: 0.7245 (t0) REVERT: A 309 ASP cc_start: 0.7382 (p0) cc_final: 0.6997 (p0) REVERT: A 313 ARG cc_start: 0.7773 (ptp90) cc_final: 0.7455 (ptp-170) REVERT: B 46 ARG cc_start: 0.7482 (mtm-85) cc_final: 0.6884 (mtp85) REVERT: B 127 LYS cc_start: 0.8934 (mttm) cc_final: 0.8508 (mttt) REVERT: B 134 ARG cc_start: 0.7890 (mtm110) cc_final: 0.7626 (mtp-110) REVERT: B 219 ARG cc_start: 0.7710 (mmt180) cc_final: 0.7502 (mtt-85) REVERT: B 234 PHE cc_start: 0.9220 (OUTLIER) cc_final: 0.8967 (m-80) REVERT: G 21 MET cc_start: 0.6538 (ttt) cc_final: 0.6213 (mmt) REVERT: G 58 GLU cc_start: 0.7823 (pm20) cc_final: 0.7000 (mm-30) REVERT: S 3 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7639 (pt0) REVERT: S 154 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8428 (tt) REVERT: S 211 ASP cc_start: 0.8269 (m-30) cc_final: 0.8043 (m-30) outliers start: 30 outliers final: 20 residues processed: 144 average time/residue: 1.4594 time to fit residues: 220.8906 Evaluate side-chains 145 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 221 VAL Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 337 THR Chi-restraints excluded: chain R residue 344 ARG Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 32 GLN B 340 ASN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.159178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.108134 restraints weight = 9594.436| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.53 r_work: 0.3054 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8343 Z= 0.164 Angle : 0.489 8.989 11310 Z= 0.254 Chirality : 0.040 0.140 1305 Planarity : 0.003 0.035 1431 Dihedral : 4.174 45.856 1157 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.00 % Allowed : 17.30 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.36 (0.27), residues: 1051 helix: 3.07 (0.28), residues: 345 sheet: 0.45 (0.31), residues: 290 loop : -0.66 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.004 0.001 HIS B 142 PHE 0.013 0.001 PHE B 199 TYR 0.011 0.001 TYR S 178 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.874 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 344 ARG cc_start: 0.6186 (OUTLIER) cc_final: 0.5892 (mtt180) REVERT: A 22 ASN cc_start: 0.7587 (m-40) cc_final: 0.7256 (m110) REVERT: A 25 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6972 (tm-30) REVERT: A 26 ASP cc_start: 0.7469 (m-30) cc_final: 0.7143 (m-30) REVERT: A 28 GLU cc_start: 0.6301 (mt-10) cc_final: 0.6043 (tt0) REVERT: A 29 LYS cc_start: 0.7218 (ttmm) cc_final: 0.6782 (tptt) REVERT: A 51 LYS cc_start: 0.8058 (ttmm) cc_final: 0.7521 (ttpt) REVERT: A 251 ASP cc_start: 0.7759 (t0) cc_final: 0.7482 (t0) REVERT: A 309 ASP cc_start: 0.7390 (p0) cc_final: 0.7011 (p0) REVERT: A 313 ARG cc_start: 0.7787 (ptp90) cc_final: 0.7481 (ptp-170) REVERT: B 46 ARG cc_start: 0.7755 (mtm-85) cc_final: 0.6954 (mtp85) REVERT: B 127 LYS cc_start: 0.8923 (mttm) cc_final: 0.8469 (mttt) REVERT: B 134 ARG cc_start: 0.8153 (mtm110) cc_final: 0.7917 (mtp-110) REVERT: B 234 PHE cc_start: 0.9291 (OUTLIER) cc_final: 0.8975 (m-80) REVERT: G 21 MET cc_start: 0.6692 (ttt) cc_final: 0.6282 (mmt) REVERT: G 58 GLU cc_start: 0.7829 (pm20) cc_final: 0.6989 (mm-30) REVERT: S 154 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8577 (tt) REVERT: S 211 ASP cc_start: 0.8345 (m-30) cc_final: 0.8139 (m-30) outliers start: 26 outliers final: 17 residues processed: 144 average time/residue: 1.4619 time to fit residues: 221.2869 Evaluate side-chains 143 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 VAL Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 337 THR Chi-restraints excluded: chain R residue 344 ARG Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 15 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 32 GLN B 340 ASN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.154471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.104374 restraints weight = 9722.263| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.73 r_work: 0.2992 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8343 Z= 0.274 Angle : 0.539 7.560 11310 Z= 0.283 Chirality : 0.042 0.142 1305 Planarity : 0.003 0.036 1431 Dihedral : 4.160 28.699 1155 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.34 % Allowed : 17.53 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.25 (0.26), residues: 1051 helix: 2.99 (0.28), residues: 344 sheet: 0.39 (0.30), residues: 288 loop : -0.72 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.005 0.001 HIS B 142 PHE 0.014 0.002 PHE B 199 TYR 0.011 0.001 TYR S 178 ARG 0.007 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.939 Fit side-chains REVERT: R 344 ARG cc_start: 0.6156 (OUTLIER) cc_final: 0.5862 (mtt-85) REVERT: A 22 ASN cc_start: 0.7582 (m-40) cc_final: 0.7259 (m110) REVERT: A 25 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6979 (tm-30) REVERT: A 26 ASP cc_start: 0.7424 (m-30) cc_final: 0.7135 (m-30) REVERT: A 28 GLU cc_start: 0.6305 (mt-10) cc_final: 0.6034 (tt0) REVERT: A 51 LYS cc_start: 0.8012 (ttmm) cc_final: 0.7486 (ttpt) REVERT: A 186 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8279 (mt-10) REVERT: A 251 ASP cc_start: 0.7703 (t0) cc_final: 0.7448 (t0) REVERT: A 271 LYS cc_start: 0.7571 (tttt) cc_final: 0.7214 (tttt) REVERT: A 309 ASP cc_start: 0.7392 (p0) cc_final: 0.7000 (p0) REVERT: A 313 ARG cc_start: 0.7797 (ptp90) cc_final: 0.7485 (ptp-170) REVERT: B 46 ARG cc_start: 0.7746 (mtm-85) cc_final: 0.7104 (mtp85) REVERT: B 127 LYS cc_start: 0.8991 (mttm) cc_final: 0.8566 (mttt) REVERT: B 134 ARG cc_start: 0.8142 (mtm110) cc_final: 0.7894 (mtp-110) REVERT: B 234 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.9012 (m-80) REVERT: G 21 MET cc_start: 0.6668 (ttt) cc_final: 0.6259 (mmt) REVERT: G 58 GLU cc_start: 0.7838 (pm20) cc_final: 0.6993 (mm-30) REVERT: S 3 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7722 (pt0) REVERT: S 154 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8543 (tt) REVERT: S 211 ASP cc_start: 0.8296 (m-30) cc_final: 0.8078 (m-30) outliers start: 29 outliers final: 19 residues processed: 140 average time/residue: 1.4688 time to fit residues: 216.1190 Evaluate side-chains 143 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 221 VAL Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 337 THR Chi-restraints excluded: chain R residue 344 ARG Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 29 optimal weight: 0.0050 chunk 5 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 340 ASN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.159543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.107979 restraints weight = 9481.296| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.54 r_work: 0.3061 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8343 Z= 0.149 Angle : 0.483 9.166 11310 Z= 0.251 Chirality : 0.040 0.145 1305 Planarity : 0.003 0.034 1431 Dihedral : 3.914 34.387 1155 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.88 % Allowed : 17.76 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.40 (0.27), residues: 1051 helix: 3.10 (0.28), residues: 345 sheet: 0.42 (0.31), residues: 281 loop : -0.56 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 PHE 0.012 0.001 PHE B 199 TYR 0.011 0.001 TYR S 178 ARG 0.007 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.991 Fit side-chains REVERT: R 344 ARG cc_start: 0.6214 (OUTLIER) cc_final: 0.5891 (mtm180) REVERT: A 22 ASN cc_start: 0.7525 (m-40) cc_final: 0.7186 (m110) REVERT: A 25 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6936 (tm-30) REVERT: A 26 ASP cc_start: 0.7406 (m-30) cc_final: 0.7090 (m-30) REVERT: A 28 GLU cc_start: 0.6253 (mt-10) cc_final: 0.6023 (tt0) REVERT: A 29 LYS cc_start: 0.7169 (ttmm) cc_final: 0.6756 (tptt) REVERT: A 51 LYS cc_start: 0.8058 (ttmm) cc_final: 0.7487 (ttpt) REVERT: A 251 ASP cc_start: 0.7724 (t0) cc_final: 0.7456 (t0) REVERT: A 271 LYS cc_start: 0.7604 (tttt) cc_final: 0.7244 (tttt) REVERT: A 309 ASP cc_start: 0.7229 (p0) cc_final: 0.6861 (p0) REVERT: A 313 ARG cc_start: 0.7797 (ptp90) cc_final: 0.7483 (ptp-170) REVERT: B 46 ARG cc_start: 0.7665 (mtm-85) cc_final: 0.7010 (mtp85) REVERT: B 127 LYS cc_start: 0.8886 (mttm) cc_final: 0.8416 (mttt) REVERT: B 217 MET cc_start: 0.8546 (ptt) cc_final: 0.8265 (pmm) REVERT: B 234 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8939 (m-80) REVERT: G 21 MET cc_start: 0.6689 (ttt) cc_final: 0.6235 (mmt) REVERT: G 58 GLU cc_start: 0.7831 (pm20) cc_final: 0.7004 (mm-30) REVERT: S 3 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7692 (pt0) REVERT: S 154 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8607 (tt) outliers start: 25 outliers final: 17 residues processed: 144 average time/residue: 1.4806 time to fit residues: 224.7529 Evaluate side-chains 143 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 337 THR Chi-restraints excluded: chain R residue 344 ARG Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 30 optimal weight: 0.0670 chunk 60 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 37 optimal weight: 0.0060 overall best weight: 0.4334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 16 ASN B 32 GLN B 340 ASN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.160770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.109037 restraints weight = 9681.078| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.60 r_work: 0.3102 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8343 Z= 0.131 Angle : 0.470 7.245 11310 Z= 0.246 Chirality : 0.040 0.149 1305 Planarity : 0.003 0.036 1431 Dihedral : 3.774 34.238 1155 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.54 % Allowed : 18.80 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.51 (0.27), residues: 1051 helix: 3.14 (0.28), residues: 346 sheet: 0.50 (0.31), residues: 291 loop : -0.50 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.011 0.001 PHE B 199 TYR 0.011 0.001 TYR S 178 ARG 0.007 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6953.19 seconds wall clock time: 123 minutes 27.19 seconds (7407.19 seconds total)