Starting phenix.real_space_refine on Wed Aug 5 03:15:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25ik_80137/08_2026/25ik_80137.cif Found real_map, /net/cci-nas-00/data/ceres_data/25ik_80137/08_2026/25ik_80137.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/25ik_80137/08_2026/25ik_80137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25ik_80137/08_2026/25ik_80137.map" model { file = "/net/cci-nas-00/data/ceres_data/25ik_80137/08_2026/25ik_80137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25ik_80137/08_2026/25ik_80137.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.101 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 53 5.16 5 C 5345 2.51 5 N 1401 2.21 5 O 1539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8338 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 2010 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1700 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 6, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 5, 'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2492 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 6, 'GLN:plan1': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 82 Chain: "C" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 397 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "S" Number of atoms: 1739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1739 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 1.38, per 1000 atoms: 0.17 Number of scatterers: 8338 At special positions: 0 Unit cell: (84.48, 118.08, 121.92, 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 53 16.00 O 1539 8.00 N 1401 7.00 C 5345 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 171 " - pdb=" SG CYS R 184 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 384.8 milliseconds 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2062 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 12 sheets defined 37.6% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'R' and resid 34 through 60 removed outlier: 3.618A pdb=" N ILE R 39 " --> pdb=" O VAL R 35 " (cutoff:3.500A) Proline residue: R 44 - end of helix Processing helix chain 'R' and resid 66 through 92 Processing helix chain 'R' and resid 93 through 95 No H-bonds generated for 'chain 'R' and resid 93 through 95' Processing helix chain 'R' and resid 101 through 136 removed outlier: 3.746A pdb=" N THR R 107 " --> pdb=" O TYR R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 142 Processing helix chain 'R' and resid 147 through 171 removed outlier: 3.610A pdb=" N MET R 170 " --> pdb=" O MET R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 196 removed outlier: 3.507A pdb=" N ALA R 186 " --> pdb=" O ASN R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 216 Processing helix chain 'R' and resid 227 through 241 removed outlier: 3.573A pdb=" N ILE R 234 " --> pdb=" O ILE R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 242 through 254 removed outlier: 3.532A pdb=" N LEU R 250 " --> pdb=" O LEU R 246 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 281 removed outlier: 4.242A pdb=" N HIS R 263 " --> pdb=" O GLY R 259 " (cutoff:3.500A) Proline residue: R 277 - end of helix Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.740A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 49 removed outlier: 4.394A pdb=" N GLY A 45 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LYS A 46 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N SER A 47 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 101 removed outlier: 3.536A pdb=" N ILE A 97 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN A 98 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 145 through 155 Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.387A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 removed outlier: 4.083A pdb=" N ALA A 168 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 164 through 169' Processing helix chain 'A' and resid 183 through 204 removed outlier: 3.916A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.866A 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 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 76 removed outlier: 4.662A pdb=" N VAL A 86 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 105 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.524A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.577A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.078A 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: 6.188A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.479A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.244A 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: 6.611A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.014A 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: 6.239A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.402A 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: 3.688A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 6 removed outlier: 3.606A pdb=" N MET S 83 " --> pdb=" O ARG S 18 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.996A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N CYS S 96 " --> pdb=" O GLY S 112 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY S 114 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TYR S 94 " --> pdb=" O GLY S 114 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 137 removed outlier: 3.595A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1254 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 0.76 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: 2668 1.34 - 1.46: 2104 1.46 - 1.58: 3675 1.58 - 1.70: 0 1.70 - 1.81: 75 Bond restraints: 8522 Sorted by residual: bond pdb=" CB GLU A 166 " pdb=" CG GLU A 166 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.49e+00 bond pdb=" CA GLY B 244 " pdb=" C GLY B 244 " ideal model delta sigma weight residual 1.520 1.513 0.007 7.30e-03 1.88e+04 9.95e-01 bond pdb=" CA ASP B 247 " pdb=" CB ASP B 247 " ideal model delta sigma weight residual 1.530 1.546 -0.017 1.69e-02 3.50e+03 9.57e-01 bond pdb=" CA ASP B 247 " pdb=" C ASP B 247 " ideal model delta sigma weight residual 1.522 1.538 -0.016 1.72e-02 3.38e+03 9.09e-01 bond pdb=" CB ASP B 247 " pdb=" CG ASP B 247 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 8.96e-01 ... (remaining 8517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 11400 1.51 - 3.01: 163 3.01 - 4.52: 28 4.52 - 6.03: 9 6.03 - 7.54: 2 Bond angle restraints: 11602 Sorted by residual: angle pdb=" N MET R 242 " pdb=" CA MET R 242 " pdb=" C MET R 242 " ideal model delta sigma weight residual 109.81 116.30 -6.49 2.21e+00 2.05e-01 8.62e+00 angle pdb=" CA GLU A 166 " pdb=" CB GLU A 166 " pdb=" CG GLU A 166 " ideal model delta sigma weight residual 114.10 119.89 -5.79 2.00e+00 2.50e-01 8.39e+00 angle pdb=" N GLY S 114 " pdb=" CA GLY S 114 " pdb=" C GLY S 114 " ideal model delta sigma weight residual 111.38 115.94 -4.56 1.63e+00 3.76e-01 7.84e+00 angle pdb=" C GLN S 113 " pdb=" N GLY S 114 " pdb=" CA GLY S 114 " ideal model delta sigma weight residual 121.61 119.48 2.13 7.70e-01 1.69e+00 7.62e+00 angle pdb=" CB GLU A 166 " pdb=" CG GLU A 166 " pdb=" CD GLU A 166 " ideal model delta sigma weight residual 112.60 117.11 -4.51 1.70e+00 3.46e-01 7.05e+00 ... (remaining 11597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4250 17.95 - 35.91: 534 35.91 - 53.86: 170 53.86 - 71.82: 15 71.82 - 89.77: 11 Dihedral angle restraints: 4980 sinusoidal: 1784 harmonic: 3196 Sorted by residual: dihedral pdb=" CB CYS R 171 " pdb=" SG CYS R 171 " pdb=" SG CYS R 184 " pdb=" CB CYS R 184 " ideal model delta sinusoidal sigma weight residual 93.00 175.22 -82.22 1 1.00e+01 1.00e-02 8.30e+01 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 60.16 32.84 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" CA THR R 11 " pdb=" C THR R 11 " pdb=" N SER R 12 " pdb=" CA SER R 12 " ideal model delta harmonic sigma weight residual 180.00 161.21 18.79 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 4977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 802 0.028 - 0.055: 342 0.055 - 0.083: 113 0.083 - 0.111: 74 0.111 - 0.138: 20 Chirality restraints: 1351 Sorted by residual: chirality pdb=" CA THR B 196 " pdb=" N THR B 196 " pdb=" C THR B 196 " pdb=" CB THR B 196 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA PRO R 243 " pdb=" N PRO R 243 " pdb=" C PRO R 243 " pdb=" CB PRO R 243 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 1348 not shown) Planarity restraints: 1459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 166 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" CD GLU A 166 " 0.038 2.00e-02 2.50e+03 pdb=" OE1 GLU A 166 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU A 166 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET R 242 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO R 243 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO R 243 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 243 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 48 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.86e+00 pdb=" C THR A 48 " 0.024 2.00e-02 2.50e+03 pdb=" O THR A 48 " -0.009 2.00e-02 2.50e+03 pdb=" N ILE A 49 " -0.008 2.00e-02 2.50e+03 ... (remaining 1456 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 207 2.68 - 3.24: 7927 3.24 - 3.79: 13449 3.79 - 4.35: 18567 4.35 - 4.90: 31164 Nonbonded interactions: 71314 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.129 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.186 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.221 3.040 nonbonded pdb=" O VAL A 198 " pdb=" OG1 THR A 202 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.239 3.040 ... (remaining 71309 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: 0.330 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.980 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 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 0.037 8525 Z= 0.120 Angle : 0.502 7.537 11608 Z= 0.273 Chirality : 0.040 0.138 1351 Planarity : 0.003 0.054 1459 Dihedral : 17.484 89.774 2909 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.20 % Allowed : 32.10 % Favored : 62.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.25), residues: 1077 helix: 1.05 (0.27), residues: 357 sheet: 0.28 (0.29), residues: 282 loop : -0.46 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 49 TYR 0.021 0.001 TYR R 102 PHE 0.020 0.001 PHE S 68 TRP 0.009 0.001 TRP S 111 HIS 0.009 0.001 HIS S 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8522) covalent geometry : angle 0.50174 / 0.27 (11602) SS BOND : bond 0.00168 / 0.08 ( 3) SS BOND : angle 0.94555 / 0.59 ( 6) hydrogen bonds : bond 0.24451 / 16.17 ( 442) hydrogen bonds : angle 7.91196 / 5.66 ( 1254) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 127 time to evaluate : 0.251 Fit side-chains REVERT: B 264 TYR cc_start: 0.8181 (m-80) cc_final: 0.7869 (m-80) outliers start: 45 outliers final: 37 residues processed: 163 average time/residue: 0.3212 time to fit residues: 57.5740 Evaluate side-chains 156 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 74 SER Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 161 CYS Chi-restraints excluded: chain R residue 170 MET Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 248 TYR Chi-restraints excluded: chain R residue 274 SER Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 152 SER Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 50.0000 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 101 ASN A 123 ASN B 268 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.155304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.121151 restraints weight = 9646.011| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.83 r_work: 0.3200 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8525 Z= 0.174 Angle : 0.562 6.888 11608 Z= 0.304 Chirality : 0.043 0.161 1351 Planarity : 0.004 0.060 1459 Dihedral : 6.825 53.153 1235 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 6.81 % Allowed : 26.67 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.25), residues: 1077 helix: 1.86 (0.26), residues: 359 sheet: 0.02 (0.28), residues: 286 loop : -0.31 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 49 TYR 0.021 0.001 TYR R 102 PHE 0.016 0.001 PHE S 68 TRP 0.020 0.002 TRP B 169 HIS 0.007 0.001 HIS S 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 8522) covalent geometry : angle 0.56220 / 0.30 (11602) SS BOND : bond 0.00279 / 0.14 ( 3) SS BOND : angle 0.80267 / 0.48 ( 6) hydrogen bonds : bond 0.05151 / 3.40 ( 442) hydrogen bonds : angle 5.08333 / 3.68 ( 1254) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 133 time to evaluate : 0.231 Fit side-chains REVERT: A 26 ASP cc_start: 0.8144 (p0) cc_final: 0.7842 (p0) REVERT: A 73 LYS cc_start: 0.7718 (mptt) cc_final: 0.7395 (mptt) REVERT: B 57 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8405 (ptpp) REVERT: B 127 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8315 (mttp) REVERT: B 175 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7485 (pm20) REVERT: B 212 ASP cc_start: 0.8195 (t0) cc_final: 0.7919 (t0) REVERT: S 223 TYR cc_start: 0.7949 (m-80) cc_final: 0.7109 (m-80) outliers start: 59 outliers final: 26 residues processed: 171 average time/residue: 0.3409 time to fit residues: 63.6504 Evaluate side-chains 150 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 244 MET Chi-restraints excluded: chain R residue 248 TYR Chi-restraints excluded: chain R residue 263 HIS Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 113 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 24 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 101 ASN B 239 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.158166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123843 restraints weight = 9582.548| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.88 r_work: 0.3228 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8525 Z= 0.123 Angle : 0.505 7.432 11608 Z= 0.272 Chirality : 0.042 0.139 1351 Planarity : 0.004 0.058 1459 Dihedral : 5.213 55.808 1197 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 6.81 % Allowed : 26.56 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.25), residues: 1077 helix: 2.18 (0.26), residues: 360 sheet: -0.09 (0.28), residues: 287 loop : -0.26 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.019 0.001 TYR R 102 PHE 0.015 0.001 PHE R 114 TRP 0.017 0.001 TRP B 169 HIS 0.007 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 8522) covalent geometry : angle 0.50454 / 0.27 (11602) SS BOND : bond 0.00312 / 0.16 ( 3) SS BOND : angle 1.08917 / 0.68 ( 6) hydrogen bonds : bond 0.04254 / 2.78 ( 442) hydrogen bonds : angle 4.65913 / 3.35 ( 1254) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 136 time to evaluate : 0.322 Fit side-chains REVERT: R 106 VAL cc_start: 0.8580 (t) cc_final: 0.8307 (m) REVERT: R 203 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.7183 (tpt) REVERT: A 9 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.7206 (m-30) REVERT: B 130 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: B 142 HIS cc_start: 0.8802 (OUTLIER) cc_final: 0.8407 (m170) REVERT: B 175 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7454 (pm20) REVERT: S 212 VAL cc_start: 0.8504 (m) cc_final: 0.8299 (p) REVERT: S 223 TYR cc_start: 0.8107 (m-80) cc_final: 0.7362 (m-80) outliers start: 59 outliers final: 25 residues processed: 176 average time/residue: 0.3910 time to fit residues: 74.9401 Evaluate side-chains 153 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 236 ILE Chi-restraints excluded: chain R residue 244 MET Chi-restraints excluded: chain R residue 248 TYR Chi-restraints excluded: chain R residue 263 HIS Chi-restraints excluded: chain R residue 274 SER Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 23 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN B 237 ASN B 239 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.156292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.122506 restraints weight = 9835.264| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.82 r_work: 0.3229 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8525 Z= 0.146 Angle : 0.533 8.613 11608 Z= 0.283 Chirality : 0.043 0.152 1351 Planarity : 0.004 0.057 1459 Dihedral : 5.057 55.310 1192 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 7.04 % Allowed : 27.02 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.26), residues: 1077 helix: 2.25 (0.26), residues: 364 sheet: -0.17 (0.28), residues: 292 loop : -0.29 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 49 TYR 0.016 0.001 TYR R 102 PHE 0.016 0.001 PHE A 74 TRP 0.015 0.001 TRP B 169 HIS 0.015 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 8522) covalent geometry : angle 0.53233 / 0.28 (11602) SS BOND : bond 0.00262 / 0.13 ( 3) SS BOND : angle 0.84101 / 0.54 ( 6) hydrogen bonds : bond 0.04173 / 2.70 ( 442) hydrogen bonds : angle 4.59845 / 3.30 ( 1254) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 129 time to evaluate : 0.205 Fit side-chains REVERT: R 106 VAL cc_start: 0.8487 (t) cc_final: 0.8206 (m) REVERT: R 203 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.6983 (tpt) REVERT: B 127 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8294 (mttp) REVERT: B 130 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: B 142 HIS cc_start: 0.8788 (OUTLIER) cc_final: 0.8407 (m170) REVERT: B 175 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7478 (pm20) REVERT: C 37 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7193 (mp) REVERT: S 212 VAL cc_start: 0.8509 (m) cc_final: 0.8295 (p) REVERT: S 223 TYR cc_start: 0.8133 (m-80) cc_final: 0.7505 (m-80) outliers start: 61 outliers final: 36 residues processed: 167 average time/residue: 0.3594 time to fit residues: 65.1430 Evaluate side-chains 161 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 119 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 236 ILE Chi-restraints excluded: chain R residue 244 MET Chi-restraints excluded: chain R residue 248 TYR Chi-restraints excluded: chain R residue 263 HIS Chi-restraints excluded: chain R residue 274 SER Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 18 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN B 88 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.153736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.119637 restraints weight = 9784.389| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.82 r_work: 0.3165 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8525 Z= 0.189 Angle : 0.561 8.583 11608 Z= 0.299 Chirality : 0.044 0.164 1351 Planarity : 0.004 0.058 1459 Dihedral : 5.260 55.194 1192 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 6.70 % Allowed : 27.25 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.25), residues: 1077 helix: 2.19 (0.26), residues: 364 sheet: -0.36 (0.29), residues: 281 loop : -0.31 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 49 TYR 0.015 0.001 TYR R 102 PHE 0.016 0.002 PHE A 74 TRP 0.016 0.002 TRP B 169 HIS 0.023 0.002 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 ( 8522) covalent geometry : angle 0.56054 / 0.30 (11602) SS BOND : bond 0.00229 / 0.12 ( 3) SS BOND : angle 0.96197 / 0.57 ( 6) hydrogen bonds : bond 0.04347 / 2.81 ( 442) hydrogen bonds : angle 4.68512 / 3.37 ( 1254) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 129 time to evaluate : 0.209 Fit side-chains REVERT: R 203 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8303 (tmt) REVERT: A 242 GLU cc_start: 0.7995 (tt0) cc_final: 0.7779 (pt0) REVERT: B 52 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7747 (mtp180) REVERT: B 127 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8296 (mttp) REVERT: B 130 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7262 (tt0) REVERT: B 142 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8463 (m170) REVERT: B 175 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7530 (pm20) REVERT: C 37 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7213 (mp) REVERT: S 212 VAL cc_start: 0.8442 (m) cc_final: 0.8229 (p) REVERT: S 223 TYR cc_start: 0.8173 (m-80) cc_final: 0.7587 (m-80) outliers start: 58 outliers final: 34 residues processed: 163 average time/residue: 0.4181 time to fit residues: 73.9630 Evaluate side-chains 158 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 236 ILE Chi-restraints excluded: chain R residue 244 MET Chi-restraints excluded: chain R residue 248 TYR Chi-restraints excluded: chain R residue 263 HIS Chi-restraints excluded: chain R residue 274 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 98 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN S 155 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.158466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.125046 restraints weight = 9697.357| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.80 r_work: 0.3262 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8525 Z= 0.108 Angle : 0.500 8.333 11608 Z= 0.268 Chirality : 0.042 0.176 1351 Planarity : 0.004 0.056 1459 Dihedral : 5.010 56.231 1192 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.97 % Allowed : 29.21 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.26), residues: 1077 helix: 2.56 (0.27), residues: 358 sheet: -0.21 (0.28), residues: 291 loop : -0.30 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 49 TYR 0.015 0.001 TYR R 102 PHE 0.017 0.001 PHE A 74 TRP 0.018 0.001 TRP B 82 HIS 0.017 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 8522) covalent geometry : angle 0.49965 / 0.27 (11602) SS BOND : bond 0.00281 / 0.14 ( 3) SS BOND : angle 0.85984 / 0.58 ( 6) hydrogen bonds : bond 0.03713 / 2.39 ( 442) hydrogen bonds : angle 4.44699 / 3.17 ( 1254) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 0.314 Fit side-chains REVERT: R 13 PHE cc_start: 0.7054 (OUTLIER) cc_final: 0.5760 (m-10) REVERT: R 203 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.6925 (tpt) REVERT: A 9 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.7235 (m-30) REVERT: A 220 ASP cc_start: 0.6534 (OUTLIER) cc_final: 0.6042 (t0) REVERT: B 52 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7660 (mtp180) REVERT: B 127 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8243 (mttp) REVERT: B 130 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7367 (tt0) REVERT: B 175 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7345 (pm20) REVERT: S 69 THR cc_start: 0.7642 (OUTLIER) cc_final: 0.7330 (p) REVERT: S 83 MET cc_start: 0.8548 (mtp) cc_final: 0.8242 (mtm) REVERT: S 148 ARG cc_start: 0.7930 (mtp85) cc_final: 0.7696 (mtp85) REVERT: S 212 VAL cc_start: 0.8483 (m) cc_final: 0.8249 (p) REVERT: S 223 TYR cc_start: 0.8121 (m-80) cc_final: 0.7584 (m-80) outliers start: 43 outliers final: 17 residues processed: 155 average time/residue: 0.4557 time to fit residues: 76.4095 Evaluate side-chains 147 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 244 MET Chi-restraints excluded: chain R residue 248 TYR Chi-restraints excluded: chain R residue 263 HIS Chi-restraints excluded: chain R residue 274 SER Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 192 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 82 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 59 optimal weight: 0.0770 chunk 13 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.155825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.121870 restraints weight = 9753.685| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.82 r_work: 0.3202 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8525 Z= 0.145 Angle : 0.529 6.167 11608 Z= 0.282 Chirality : 0.043 0.170 1351 Planarity : 0.004 0.057 1459 Dihedral : 4.703 55.755 1187 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 5.66 % Allowed : 28.75 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.26), residues: 1077 helix: 2.54 (0.26), residues: 358 sheet: -0.30 (0.29), residues: 284 loop : -0.32 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 49 TYR 0.014 0.001 TYR R 102 PHE 0.016 0.001 PHE A 74 TRP 0.014 0.001 TRP B 169 HIS 0.012 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 8522) covalent geometry : angle 0.52831 / 0.28 (11602) SS BOND : bond 0.00261 / 0.13 ( 3) SS BOND : angle 0.84399 / 0.53 ( 6) hydrogen bonds : bond 0.03926 / 2.53 ( 442) hydrogen bonds : angle 4.48860 / 3.21 ( 1254) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 126 time to evaluate : 0.311 Fit side-chains REVERT: R 13 PHE cc_start: 0.7031 (OUTLIER) cc_final: 0.5767 (m-10) REVERT: R 174 ARG cc_start: 0.5399 (OUTLIER) cc_final: 0.5096 (mpt180) REVERT: R 203 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8207 (tmt) REVERT: B 52 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7692 (mtp180) REVERT: B 127 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8283 (mttp) REVERT: B 130 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7283 (tt0) REVERT: B 175 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7477 (pm20) REVERT: S 69 THR cc_start: 0.7652 (OUTLIER) cc_final: 0.7332 (p) REVERT: S 212 VAL cc_start: 0.8454 (m) cc_final: 0.8222 (p) REVERT: S 223 TYR cc_start: 0.8082 (m-80) cc_final: 0.7618 (m-80) outliers start: 49 outliers final: 26 residues processed: 157 average time/residue: 0.4368 time to fit residues: 74.2741 Evaluate side-chains 154 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 170 MET Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 244 MET Chi-restraints excluded: chain R residue 248 TYR Chi-restraints excluded: chain R residue 263 HIS Chi-restraints excluded: chain R residue 274 SER Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 192 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 64 optimal weight: 0.5980 chunk 93 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.157991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.124437 restraints weight = 9681.025| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.81 r_work: 0.3229 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8525 Z= 0.119 Angle : 0.516 9.180 11608 Z= 0.275 Chirality : 0.042 0.167 1351 Planarity : 0.004 0.057 1459 Dihedral : 4.648 55.913 1187 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.50 % Allowed : 30.37 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.26), residues: 1077 helix: 2.62 (0.27), residues: 358 sheet: -0.25 (0.29), residues: 280 loop : -0.31 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 49 TYR 0.017 0.001 TYR R 168 PHE 0.016 0.001 PHE A 74 TRP 0.016 0.001 TRP B 169 HIS 0.011 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 8522) covalent geometry : angle 0.51555 / 0.27 (11602) SS BOND : bond 0.00267 / 0.13 ( 3) SS BOND : angle 1.33105 / 0.82 ( 6) hydrogen bonds : bond 0.03739 / 2.40 ( 442) hydrogen bonds : angle 4.44553 / 3.17 ( 1254) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.348 Fit side-chains REVERT: R 13 PHE cc_start: 0.6936 (OUTLIER) cc_final: 0.5716 (m-10) REVERT: R 106 VAL cc_start: 0.8429 (t) cc_final: 0.8218 (m) REVERT: R 174 ARG cc_start: 0.5511 (OUTLIER) cc_final: 0.5145 (mpt180) REVERT: R 203 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8185 (tmt) REVERT: A 9 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7225 (m-30) REVERT: B 127 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8256 (mttp) REVERT: B 130 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7300 (tt0) REVERT: B 175 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7372 (pm20) REVERT: S 69 THR cc_start: 0.7696 (OUTLIER) cc_final: 0.7383 (p) REVERT: S 83 MET cc_start: 0.8615 (mtp) cc_final: 0.8269 (mtm) REVERT: S 212 VAL cc_start: 0.8454 (m) cc_final: 0.8222 (p) REVERT: S 223 TYR cc_start: 0.8071 (m-80) cc_final: 0.7611 (m-80) outliers start: 39 outliers final: 25 residues processed: 154 average time/residue: 0.4553 time to fit residues: 75.7833 Evaluate side-chains 158 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 236 ILE Chi-restraints excluded: chain R residue 244 MET Chi-restraints excluded: chain R residue 248 TYR Chi-restraints excluded: chain R residue 263 HIS Chi-restraints excluded: chain R residue 274 SER Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 192 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 55 optimal weight: 0.0370 chunk 64 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 56 optimal weight: 0.1980 chunk 25 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.160636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.127455 restraints weight = 9665.585| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.81 r_work: 0.3272 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8525 Z= 0.100 Angle : 0.501 6.686 11608 Z= 0.268 Chirality : 0.041 0.181 1351 Planarity : 0.004 0.057 1459 Dihedral : 4.566 56.719 1187 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.62 % Allowed : 30.60 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.26), residues: 1077 helix: 2.73 (0.27), residues: 358 sheet: -0.15 (0.28), residues: 288 loop : -0.25 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 49 TYR 0.015 0.001 TYR R 168 PHE 0.016 0.001 PHE R 114 TRP 0.016 0.001 TRP B 169 HIS 0.007 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 8522) covalent geometry : angle 0.50006 / 0.27 (11602) SS BOND : bond 0.00310 / 0.15 ( 3) SS BOND : angle 1.13630 / 0.73 ( 6) hydrogen bonds : bond 0.03469 / 2.24 ( 442) hydrogen bonds : angle 4.32678 / 3.07 ( 1254) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.314 Fit side-chains REVERT: R 13 PHE cc_start: 0.6773 (OUTLIER) cc_final: 0.5659 (m-10) REVERT: R 106 VAL cc_start: 0.8546 (t) cc_final: 0.8344 (m) REVERT: R 174 ARG cc_start: 0.5401 (OUTLIER) cc_final: 0.4912 (mpt180) REVERT: R 203 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.7190 (tpt) REVERT: A 25 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7991 (mt-10) REVERT: A 220 ASP cc_start: 0.6504 (OUTLIER) cc_final: 0.6050 (t0) REVERT: B 52 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7677 (mtt180) REVERT: B 127 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8212 (mttp) REVERT: B 130 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7393 (tt0) REVERT: B 175 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7381 (pm20) REVERT: B 325 MET cc_start: 0.8649 (tpp) cc_final: 0.8445 (tpp) REVERT: S 69 THR cc_start: 0.7650 (m) cc_final: 0.7352 (p) REVERT: S 83 MET cc_start: 0.8611 (mtp) cc_final: 0.8239 (mtm) REVERT: S 203 THR cc_start: 0.7762 (OUTLIER) cc_final: 0.7468 (p) REVERT: S 212 VAL cc_start: 0.8458 (m) cc_final: 0.8221 (p) REVERT: S 223 TYR cc_start: 0.8096 (m-80) cc_final: 0.7633 (m-80) outliers start: 40 outliers final: 19 residues processed: 157 average time/residue: 0.4544 time to fit residues: 77.0058 Evaluate side-chains 150 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 248 TYR Chi-restraints excluded: chain R residue 263 HIS Chi-restraints excluded: chain R residue 274 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 69 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 36 HIS B 259 GLN S 155 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.156613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.122618 restraints weight = 9740.462| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.82 r_work: 0.3222 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8525 Z= 0.159 Angle : 0.553 8.077 11608 Z= 0.294 Chirality : 0.043 0.178 1351 Planarity : 0.004 0.056 1459 Dihedral : 4.757 56.456 1187 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.04 % Allowed : 31.29 % Favored : 64.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.26), residues: 1077 helix: 2.60 (0.27), residues: 358 sheet: -0.26 (0.29), residues: 282 loop : -0.29 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 49 TYR 0.017 0.001 TYR R 168 PHE 0.018 0.002 PHE A 74 TRP 0.014 0.001 TRP B 169 HIS 0.009 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 8522) covalent geometry : angle 0.55281 / 0.29 (11602) SS BOND : bond 0.00419 / 0.22 ( 3) SS BOND : angle 1.09098 / 0.63 ( 6) hydrogen bonds : bond 0.03932 / 2.52 ( 442) hydrogen bonds : angle 4.47708 / 3.20 ( 1254) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: R 13 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.5715 (m-10) REVERT: R 106 VAL cc_start: 0.8528 (t) cc_final: 0.8310 (m) REVERT: R 174 ARG cc_start: 0.5451 (OUTLIER) cc_final: 0.5014 (mpt180) REVERT: R 203 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8218 (tmt) REVERT: R 247 LEU cc_start: 0.7939 (mt) cc_final: 0.7686 (mp) REVERT: A 25 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8067 (mt-10) REVERT: A 220 ASP cc_start: 0.6541 (OUTLIER) cc_final: 0.6057 (t0) REVERT: B 52 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7729 (mtp180) REVERT: B 127 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8274 (mttp) REVERT: B 130 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7292 (tt0) REVERT: B 175 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7488 (pm20) REVERT: S 69 THR cc_start: 0.7730 (m) cc_final: 0.7421 (p) REVERT: S 212 VAL cc_start: 0.8484 (m) cc_final: 0.8253 (p) REVERT: S 223 TYR cc_start: 0.8093 (m-80) cc_final: 0.7621 (m-80) outliers start: 35 outliers final: 19 residues processed: 151 average time/residue: 0.4781 time to fit residues: 77.8770 Evaluate side-chains 145 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 248 TYR Chi-restraints excluded: chain R residue 263 HIS Chi-restraints excluded: chain R residue 274 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 97 optimal weight: 0.1980 chunk 38 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 36 HIS A 101 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.158209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124741 restraints weight = 9649.164| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.80 r_work: 0.3231 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8525 Z= 0.120 Angle : 0.531 7.942 11608 Z= 0.282 Chirality : 0.042 0.191 1351 Planarity : 0.004 0.055 1459 Dihedral : 4.716 57.442 1187 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.46 % Allowed : 32.68 % Favored : 63.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.26), residues: 1077 helix: 2.65 (0.27), residues: 357 sheet: -0.23 (0.29), residues: 282 loop : -0.26 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 49 TYR 0.015 0.001 TYR R 168 PHE 0.017 0.001 PHE A 74 TRP 0.015 0.001 TRP B 169 HIS 0.006 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 8522) covalent geometry : angle 0.53100 / 0.28 (11602) SS BOND : bond 0.00251 / 0.13 ( 3) SS BOND : angle 1.02522 / 0.65 ( 6) hydrogen bonds : bond 0.03671 / 2.36 ( 442) hydrogen bonds : angle 4.43239 / 3.15 ( 1254) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2914.17 seconds wall clock time: 50 minutes 29.09 seconds (3029.09 seconds total)