Starting phenix.real_space_refine on Thu Jul 2 13:58:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vdh_31918/07_2026/7vdh_31918.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vdh_31918/07_2026/7vdh_31918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vdh_31918/07_2026/7vdh_31918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vdh_31918/07_2026/7vdh_31918.map" model { file = "/net/cci-nas-00/data/ceres_data/7vdh_31918/07_2026/7vdh_31918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vdh_31918/07_2026/7vdh_31918.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7vdh_31918/07_2026/7vdh_31918.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vdh_31918/07_2026/7vdh_31918.cif" } resolution = 2.9 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= 0.001 sd= 0.006 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 64 5.16 5 C 5592 2.51 5 N 1457 2.21 5 O 1597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8710 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2131 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 8, 'TRANS': 258} Chain: "A" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1751 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2590 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 415 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1757 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'6IB': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.22, per 1000 atoms: 0.25 Number of scatterers: 8710 At special positions: 0 Unit cell: (119.928, 112.564, 102.044, 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 64 16.00 O 1597 8.00 N 1457 7.00 C 5592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 26 " - pdb=" SG CYS R 258 " distance=2.03 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.02 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.08 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.05 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: 0.65 Conformation dependent library (CDL) restraints added in 433.0 milliseconds 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 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: 28 helices and 13 sheets defined 37.6% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'R' and resid 27 through 29 No H-bonds generated for 'chain 'R' and resid 27 through 29' Processing helix chain 'R' and resid 30 through 57 Processing helix chain 'R' and resid 62 through 94 removed outlier: 3.834A pdb=" N VAL R 66 " --> pdb=" O ASN R 62 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 133 removed outlier: 4.224A pdb=" N THR R 107 " --> pdb=" O SER R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 139 Processing helix chain 'R' and resid 144 through 167 Processing helix chain 'R' and resid 176 through 213 removed outlier: 4.135A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 235 Processing helix chain 'R' and resid 236 through 245 removed outlier: 3.938A pdb=" N GLY R 240 " --> pdb=" O GLY R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 250 Processing helix chain 'R' and resid 256 through 280 Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 280 through 285 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.777A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.874A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.162A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.173A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.880A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.093A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.810A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.758A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.706A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.076A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.679A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.513A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.589A 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: 3.849A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.654A 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: 6.624A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.685A 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: 3.660A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.558A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.401A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.258A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.252A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.252A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.541A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1269 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: 1.50 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2688 1.34 - 1.47: 2451 1.47 - 1.60: 3676 1.60 - 1.74: 1 1.74 - 1.87: 88 Bond restraints: 8904 Sorted by residual: bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.672 -0.137 2.00e-02 2.50e+03 4.70e+01 bond pdb=" C ALA S 40 " pdb=" N PRO S 41 " ideal model delta sigma weight residual 1.335 1.392 -0.058 1.28e-02 6.10e+03 2.03e+01 bond pdb=" CG1 ILE B 232 " pdb=" CD1 ILE B 232 " ideal model delta sigma weight residual 1.513 1.367 0.146 3.90e-02 6.57e+02 1.41e+01 bond pdb=" N THR B 143 " pdb=" CA THR B 143 " ideal model delta sigma weight residual 1.457 1.500 -0.042 1.29e-02 6.01e+03 1.07e+01 bond pdb=" C31 6IB R 402 " pdb=" N5 6IB R 402 " ideal model delta sigma weight residual 1.447 1.503 -0.056 2.00e-02 2.50e+03 7.87e+00 ... (remaining 8899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 11647 3.30 - 6.60: 353 6.60 - 9.90: 52 9.90 - 13.20: 13 13.20 - 16.50: 5 Bond angle restraints: 12070 Sorted by residual: angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 138.04 -16.50 1.91e+00 2.74e-01 7.46e+01 angle pdb=" CA CYS B 149 " pdb=" CB CYS B 149 " pdb=" SG CYS B 149 " ideal model delta sigma weight residual 114.40 129.91 -15.51 2.30e+00 1.89e-01 4.55e+01 angle pdb=" CA GLY B 144 " pdb=" C GLY B 144 " pdb=" N TYR B 145 " ideal model delta sigma weight residual 114.58 119.87 -5.29 8.60e-01 1.35e+00 3.78e+01 angle pdb=" CA ARG A 208 " pdb=" CB ARG A 208 " pdb=" CG ARG A 208 " ideal model delta sigma weight residual 114.10 125.10 -11.00 2.00e+00 2.50e-01 3.02e+01 angle pdb=" C GLY S 197 " pdb=" N THR S 198 " pdb=" CA THR S 198 " ideal model delta sigma weight residual 124.31 133.10 -8.79 1.67e+00 3.59e-01 2.77e+01 ... (remaining 12065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4768 17.93 - 35.86: 382 35.86 - 53.79: 56 53.79 - 71.72: 17 71.72 - 89.65: 7 Dihedral angle restraints: 5230 sinusoidal: 2032 harmonic: 3198 Sorted by residual: dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " ideal model delta harmonic sigma weight residual 180.00 149.89 30.11 0 5.00e+00 4.00e-02 3.63e+01 dihedral pdb=" CA PHE R 172 " pdb=" C PHE R 172 " pdb=" N SER R 173 " pdb=" CA SER R 173 " ideal model delta harmonic sigma weight residual 180.00 156.15 23.85 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA GLU S 210 " pdb=" C GLU S 210 " pdb=" N ASP S 211 " pdb=" CA ASP S 211 " ideal model delta harmonic sigma weight residual 180.00 156.81 23.19 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 5227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1268 0.131 - 0.261: 91 0.261 - 0.392: 8 0.392 - 0.523: 0 0.523 - 0.653: 3 Chirality restraints: 1370 Sorted by residual: chirality pdb=" CG LEU A 310 " pdb=" CB LEU A 310 " pdb=" CD1 LEU A 310 " pdb=" CD2 LEU A 310 " both_signs ideal model delta sigma weight residual False -2.59 -1.94 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CG LEU S 162 " pdb=" CB LEU S 162 " pdb=" CD1 LEU S 162 " pdb=" CD2 LEU S 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.01 -0.58 2.00e-01 2.50e+01 8.44e+00 chirality pdb=" CG LEU S 117 " pdb=" CB LEU S 117 " pdb=" CD1 LEU S 117 " pdb=" CD2 LEU S 117 " both_signs ideal model delta sigma weight residual False -2.59 -2.01 -0.58 2.00e-01 2.50e+01 8.36e+00 ... (remaining 1367 not shown) Planarity restraints: 1506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 119 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" CG ASN B 119 " -0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN B 119 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN B 119 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.007 2.00e-02 2.50e+03 2.00e-02 7.96e+00 pdb=" CG TYR B 105 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.73e+00 pdb=" N PRO B 194 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.038 5.00e-02 4.00e+02 ... (remaining 1503 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1576 2.77 - 3.30: 7442 3.30 - 3.83: 15232 3.83 - 4.37: 17626 4.37 - 4.90: 30920 Nonbonded interactions: 72796 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.232 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.273 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.291 3.040 nonbonded pdb=" OH TYR R 113 " pdb=" O GLY R 236 " model vdw 2.313 3.040 nonbonded pdb=" O THR R 107 " pdb=" OG SER R 161 " model vdw 2.313 3.040 ... (remaining 72791 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: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.390 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:5.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 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 : 0.011 0.146 8908 Z= 0.489 Angle : 1.392 16.498 12078 Z= 0.737 Chirality : 0.078 0.653 1370 Planarity : 0.008 0.069 1506 Dihedral : 13.796 89.652 3156 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.38 (0.22), residues: 1093 helix: -2.07 (0.20), residues: 365 sheet: -0.54 (0.29), residues: 295 loop : -1.68 (0.26), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.002 ARG A 21 TYR 0.045 0.004 TYR B 59 PHE 0.032 0.004 PHE R 104 TRP 0.024 0.003 TRP B 82 HIS 0.017 0.002 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.01138 / 0.49 ( 8904) covalent geometry : angle 1.38671 / 0.73 (12070) SS BOND : bond 0.02553 / 1.28 ( 4) SS BOND : angle 4.81527 / 1.64 ( 8) hydrogen bonds : bond 0.13147 / 8.77 ( 440) hydrogen bonds : angle 7.13501 / 4.98 ( 1269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.348 Fit side-chains REVERT: R 58 ARG cc_start: 0.6054 (ttm-80) cc_final: 0.4767 (ttt180) REVERT: A 273 LEU cc_start: 0.8839 (mm) cc_final: 0.8545 (mm) REVERT: A 331 ASN cc_start: 0.8399 (m110) cc_final: 0.8179 (m110) REVERT: A 333 GLN cc_start: 0.8664 (tp40) cc_final: 0.8149 (mm-40) REVERT: A 337 ASP cc_start: 0.8492 (m-30) cc_final: 0.8114 (m-30) REVERT: B 12 GLU cc_start: 0.7968 (pp20) cc_final: 0.7759 (pp20) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.6156 time to fit residues: 128.5996 Evaluate side-chains 151 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.0870 chunk 51 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.8964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 ASN B 91 HIS B 119 ASN B 259 GLN S 3 GLN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.142028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.103555 restraints weight = 12199.961| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.31 r_work: 0.3185 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8908 Z= 0.135 Angle : 0.666 8.530 12078 Z= 0.336 Chirality : 0.044 0.229 1370 Planarity : 0.004 0.041 1506 Dihedral : 6.838 74.514 1227 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.34 % Allowed : 10.08 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.79 (0.24), residues: 1093 helix: 0.16 (0.25), residues: 372 sheet: -0.15 (0.31), residues: 275 loop : -1.27 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 21 TYR 0.015 0.001 TYR S 178 PHE 0.013 0.001 PHE A 189 TRP 0.022 0.001 TRP B 82 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 8904) covalent geometry : angle 0.66476 / 0.34 (12070) SS BOND : bond 0.00720 / 0.36 ( 4) SS BOND : angle 1.64202 / 0.56 ( 8) hydrogen bonds : bond 0.04138 / 2.79 ( 440) hydrogen bonds : angle 5.02277 / 3.46 ( 1269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: R 58 ARG cc_start: 0.6032 (ttm-80) cc_final: 0.4789 (ttt180) REVERT: R 234 LEU cc_start: 0.8589 (mt) cc_final: 0.8353 (mm) REVERT: A 276 GLU cc_start: 0.7846 (pp20) cc_final: 0.7630 (pp20) REVERT: A 287 TYR cc_start: 0.9041 (m-80) cc_final: 0.8760 (m-80) REVERT: B 12 GLU cc_start: 0.8080 (pp20) cc_final: 0.7813 (pp20) REVERT: B 23 LYS cc_start: 0.9117 (ttpp) cc_final: 0.8910 (ttpp) REVERT: G 32 LYS cc_start: 0.7999 (mptt) cc_final: 0.7631 (tptt) outliers start: 22 outliers final: 5 residues processed: 179 average time/residue: 0.5006 time to fit residues: 95.6076 Evaluate side-chains 156 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 151 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 84 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 40 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 82 GLN A 304 GLN A 333 GLN B 110 ASN S 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.139288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.100195 restraints weight = 12114.838| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.28 r_work: 0.3136 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8908 Z= 0.186 Angle : 0.664 11.417 12078 Z= 0.332 Chirality : 0.044 0.208 1370 Planarity : 0.004 0.035 1506 Dihedral : 6.476 71.371 1227 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.50 % Allowed : 12.53 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.20 (0.25), residues: 1093 helix: 1.05 (0.27), residues: 373 sheet: -0.15 (0.31), residues: 265 loop : -1.07 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 24 TYR 0.010 0.002 TYR S 163 PHE 0.013 0.001 PHE A 189 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 ( 8904) covalent geometry : angle 0.66198 / 0.33 (12070) SS BOND : bond 0.01068 / 0.53 ( 4) SS BOND : angle 1.88657 / 0.64 ( 8) hydrogen bonds : bond 0.04087 / 2.76 ( 440) hydrogen bonds : angle 4.73061 / 3.25 ( 1269) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 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: 33 poor density : 159 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: R 234 LEU cc_start: 0.8686 (mt) cc_final: 0.8445 (mm) REVERT: A 193 ASP cc_start: 0.7805 (t0) cc_final: 0.7518 (t0) REVERT: A 276 GLU cc_start: 0.7972 (pp20) cc_final: 0.7675 (pp20) REVERT: B 12 GLU cc_start: 0.8106 (pp20) cc_final: 0.7736 (pp20) REVERT: B 23 LYS cc_start: 0.9095 (ttpp) cc_final: 0.8855 (ttpp) REVERT: B 46 ARG cc_start: 0.8744 (mtm-85) cc_final: 0.8311 (mtp-110) REVERT: B 101 MET cc_start: 0.9261 (mtp) cc_final: 0.8942 (mtp) REVERT: B 153 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8064 (p0) REVERT: B 228 ASP cc_start: 0.8073 (p0) cc_final: 0.7842 (p0) REVERT: G 32 LYS cc_start: 0.8035 (mptt) cc_final: 0.7682 (tptt) outliers start: 33 outliers final: 13 residues processed: 171 average time/residue: 0.5159 time to fit residues: 94.2198 Evaluate side-chains 164 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 174 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 4 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN A 333 GLN 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 = 0.137794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.098600 restraints weight = 12311.244| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.29 r_work: 0.3111 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8908 Z= 0.208 Angle : 0.658 9.954 12078 Z= 0.330 Chirality : 0.045 0.200 1370 Planarity : 0.004 0.035 1506 Dihedral : 6.359 68.307 1227 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.14 % Allowed : 14.12 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.02 (0.25), residues: 1093 helix: 1.38 (0.27), residues: 371 sheet: -0.24 (0.31), residues: 267 loop : -0.92 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 24 TYR 0.011 0.002 TYR S 163 PHE 0.014 0.001 PHE A 189 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 ( 8904) covalent geometry : angle 0.65652 / 0.33 (12070) SS BOND : bond 0.01095 / 0.55 ( 4) SS BOND : angle 1.88292 / 0.65 ( 8) hydrogen bonds : bond 0.04092 / 2.77 ( 440) hydrogen bonds : angle 4.60834 / 3.17 ( 1269) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: R 32 ILE cc_start: 0.6777 (OUTLIER) cc_final: 0.6097 (tp) REVERT: R 234 LEU cc_start: 0.8695 (mt) cc_final: 0.8423 (mm) REVERT: A 193 ASP cc_start: 0.7881 (t0) cc_final: 0.7484 (t0) REVERT: A 276 GLU cc_start: 0.8074 (pp20) cc_final: 0.7747 (pp20) REVERT: B 12 GLU cc_start: 0.8102 (pp20) cc_final: 0.7703 (pp20) REVERT: B 23 LYS cc_start: 0.9098 (ttpp) cc_final: 0.8872 (ttpp) REVERT: B 46 ARG cc_start: 0.8737 (mtm-85) cc_final: 0.8292 (mtp-110) REVERT: B 101 MET cc_start: 0.9222 (mtp) cc_final: 0.8936 (mtp) REVERT: B 153 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8084 (p0) REVERT: G 32 LYS cc_start: 0.8097 (mptt) cc_final: 0.7724 (tptt) REVERT: S 46 GLU cc_start: 0.8824 (tt0) cc_final: 0.8551 (pt0) outliers start: 39 outliers final: 14 residues processed: 170 average time/residue: 0.5342 time to fit residues: 96.7557 Evaluate side-chains 162 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 174 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 79 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 38 optimal weight: 0.0000 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN B 44 GLN B 75 GLN S 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.138439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.099433 restraints weight = 12218.801| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.27 r_work: 0.3125 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8908 Z= 0.176 Angle : 0.647 9.835 12078 Z= 0.321 Chirality : 0.044 0.189 1370 Planarity : 0.004 0.035 1506 Dihedral : 6.206 69.013 1227 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.93 % Allowed : 15.82 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.16 (0.26), residues: 1093 helix: 1.45 (0.27), residues: 376 sheet: -0.25 (0.31), residues: 279 loop : -0.76 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 24 TYR 0.010 0.001 TYR S 163 PHE 0.026 0.001 PHE R 35 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 ( 8904) covalent geometry : angle 0.64555 / 0.32 (12070) SS BOND : bond 0.00873 / 0.44 ( 4) SS BOND : angle 1.65890 / 0.57 ( 8) hydrogen bonds : bond 0.03920 / 2.63 ( 440) hydrogen bonds : angle 4.54477 / 3.12 ( 1269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 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: 37 poor density : 155 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: R 32 ILE cc_start: 0.6774 (OUTLIER) cc_final: 0.6237 (tp) REVERT: R 234 LEU cc_start: 0.8675 (mt) cc_final: 0.8391 (mm) REVERT: A 193 ASP cc_start: 0.7912 (t0) cc_final: 0.7480 (t0) REVERT: A 276 GLU cc_start: 0.8102 (pp20) cc_final: 0.7737 (pp20) REVERT: A 308 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: B 12 GLU cc_start: 0.8119 (pp20) cc_final: 0.7711 (pp20) REVERT: B 23 LYS cc_start: 0.9071 (ttpp) cc_final: 0.8832 (ttpp) REVERT: B 46 ARG cc_start: 0.8752 (mtm-85) cc_final: 0.8296 (mtp-110) REVERT: B 101 MET cc_start: 0.9211 (mtp) cc_final: 0.8935 (mtp) REVERT: B 146 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8761 (mp) REVERT: B 153 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8082 (p0) REVERT: S 46 GLU cc_start: 0.8812 (tt0) cc_final: 0.8546 (pt0) REVERT: S 89 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8126 (pm20) outliers start: 37 outliers final: 16 residues processed: 171 average time/residue: 0.4757 time to fit residues: 86.7812 Evaluate side-chains 167 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 174 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 33 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 chunk 73 optimal weight: 0.4980 chunk 30 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN B 142 HIS S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.137332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.098674 restraints weight = 12343.815| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.26 r_work: 0.3122 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8908 Z= 0.201 Angle : 0.669 10.632 12078 Z= 0.333 Chirality : 0.044 0.185 1370 Planarity : 0.004 0.042 1506 Dihedral : 6.207 67.866 1227 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.56 % Allowed : 16.14 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.18 (0.26), residues: 1093 helix: 1.54 (0.27), residues: 378 sheet: -0.31 (0.30), residues: 277 loop : -0.77 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 24 TYR 0.011 0.002 TYR S 163 PHE 0.018 0.001 PHE R 35 TRP 0.015 0.001 TRP B 82 HIS 0.010 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 ( 8904) covalent geometry : angle 0.66805 / 0.33 (12070) SS BOND : bond 0.01051 / 0.53 ( 4) SS BOND : angle 1.82240 / 0.63 ( 8) hydrogen bonds : bond 0.03970 / 2.67 ( 440) hydrogen bonds : angle 4.53577 / 3.12 ( 1269) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: R 32 ILE cc_start: 0.6882 (OUTLIER) cc_final: 0.6286 (tp) REVERT: R 50 PHE cc_start: 0.7621 (t80) cc_final: 0.7416 (t80) REVERT: R 234 LEU cc_start: 0.8695 (mt) cc_final: 0.8419 (mm) REVERT: A 193 ASP cc_start: 0.7911 (t0) cc_final: 0.7457 (t0) REVERT: A 276 GLU cc_start: 0.8194 (pp20) cc_final: 0.7823 (pp20) REVERT: B 12 GLU cc_start: 0.8144 (pp20) cc_final: 0.7736 (pp20) REVERT: B 23 LYS cc_start: 0.9076 (ttpp) cc_final: 0.8838 (ttpp) REVERT: B 46 ARG cc_start: 0.8725 (mtm-85) cc_final: 0.8286 (mtp-110) REVERT: B 101 MET cc_start: 0.9179 (mtp) cc_final: 0.8917 (mtp) REVERT: B 146 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8809 (mp) REVERT: B 153 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8116 (p0) REVERT: S 46 GLU cc_start: 0.8809 (tt0) cc_final: 0.8531 (pt0) REVERT: S 89 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8131 (pm20) outliers start: 43 outliers final: 19 residues processed: 166 average time/residue: 0.5125 time to fit residues: 90.7043 Evaluate side-chains 164 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 174 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 104 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.138170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099526 restraints weight = 12319.699| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.26 r_work: 0.3134 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8908 Z= 0.175 Angle : 0.669 13.623 12078 Z= 0.328 Chirality : 0.044 0.178 1370 Planarity : 0.004 0.048 1506 Dihedral : 6.117 67.971 1227 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.82 % Allowed : 18.05 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.29 (0.26), residues: 1093 helix: 1.61 (0.27), residues: 378 sheet: -0.23 (0.31), residues: 273 loop : -0.71 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 24 TYR 0.009 0.001 TYR S 163 PHE 0.018 0.001 PHE R 35 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 8904) covalent geometry : angle 0.66789 / 0.33 (12070) SS BOND : bond 0.00928 / 0.46 ( 4) SS BOND : angle 1.67769 / 0.59 ( 8) hydrogen bonds : bond 0.03837 / 2.58 ( 440) hydrogen bonds : angle 4.49776 / 3.09 ( 1269) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: R 32 ILE cc_start: 0.6986 (OUTLIER) cc_final: 0.6356 (tp) REVERT: R 50 PHE cc_start: 0.7700 (t80) cc_final: 0.7497 (t80) REVERT: R 58 ARG cc_start: 0.6018 (ttm-80) cc_final: 0.4871 (ttt180) REVERT: R 234 LEU cc_start: 0.8678 (mt) cc_final: 0.8409 (mm) REVERT: R 277 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8767 (tp) REVERT: A 193 ASP cc_start: 0.7986 (t0) cc_final: 0.7549 (t0) REVERT: A 276 GLU cc_start: 0.8201 (pp20) cc_final: 0.7888 (pp20) REVERT: B 12 GLU cc_start: 0.8136 (pp20) cc_final: 0.7718 (pp20) REVERT: B 23 LYS cc_start: 0.9080 (ttpp) cc_final: 0.8839 (ttpp) REVERT: B 46 ARG cc_start: 0.8719 (mtm-85) cc_final: 0.8280 (mtp-110) REVERT: B 101 MET cc_start: 0.9188 (mtp) cc_final: 0.8932 (mtp) REVERT: B 146 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8639 (tp) REVERT: B 153 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8270 (p0) REVERT: B 234 PHE cc_start: 0.9354 (OUTLIER) cc_final: 0.8162 (m-80) REVERT: S 46 GLU cc_start: 0.8799 (tt0) cc_final: 0.8515 (pt0) REVERT: S 89 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8213 (pm20) REVERT: S 93 MET cc_start: 0.8594 (ttm) cc_final: 0.8360 (tpp) outliers start: 36 outliers final: 20 residues processed: 167 average time/residue: 0.4829 time to fit residues: 86.1444 Evaluate side-chains 171 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 174 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN A 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.138122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.099090 restraints weight = 12285.549| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.29 r_work: 0.3122 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8908 Z= 0.189 Angle : 0.690 12.018 12078 Z= 0.337 Chirality : 0.044 0.174 1370 Planarity : 0.004 0.052 1506 Dihedral : 6.087 68.401 1227 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.93 % Allowed : 18.90 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.34 (0.26), residues: 1093 helix: 1.68 (0.27), residues: 378 sheet: -0.20 (0.31), residues: 274 loop : -0.71 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 24 TYR 0.010 0.001 TYR S 163 PHE 0.026 0.001 PHE R 239 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 ( 8904) covalent geometry : angle 0.68905 / 0.34 (12070) SS BOND : bond 0.00977 / 0.49 ( 4) SS BOND : angle 1.83351 / 0.63 ( 8) hydrogen bonds : bond 0.03871 / 2.61 ( 440) hydrogen bonds : angle 4.48612 / 3.08 ( 1269) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 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: 37 poor density : 153 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: R 32 ILE cc_start: 0.6828 (OUTLIER) cc_final: 0.6288 (tp) REVERT: R 50 PHE cc_start: 0.7737 (t80) cc_final: 0.7506 (t80) REVERT: R 234 LEU cc_start: 0.8672 (mt) cc_final: 0.8433 (mm) REVERT: R 277 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8785 (tp) REVERT: A 193 ASP cc_start: 0.8004 (t0) cc_final: 0.7551 (t0) REVERT: A 276 GLU cc_start: 0.8185 (pp20) cc_final: 0.7855 (pp20) REVERT: B 12 GLU cc_start: 0.8134 (pp20) cc_final: 0.7737 (pp20) REVERT: B 23 LYS cc_start: 0.9079 (ttpp) cc_final: 0.8836 (ttpp) REVERT: B 46 ARG cc_start: 0.8736 (mtm-85) cc_final: 0.8275 (mtp-110) REVERT: B 101 MET cc_start: 0.9202 (mtp) cc_final: 0.8918 (mtp) REVERT: B 146 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8639 (tp) REVERT: B 153 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8264 (p0) REVERT: B 228 ASP cc_start: 0.8328 (p0) cc_final: 0.8071 (p0) REVERT: B 234 PHE cc_start: 0.9365 (OUTLIER) cc_final: 0.8215 (m-80) REVERT: S 13 GLN cc_start: 0.8865 (mm110) cc_final: 0.8664 (mm-40) REVERT: S 46 GLU cc_start: 0.8805 (tt0) cc_final: 0.8520 (pt0) REVERT: S 89 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8187 (pm20) outliers start: 37 outliers final: 18 residues processed: 169 average time/residue: 0.5182 time to fit residues: 93.3208 Evaluate side-chains 170 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 174 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 65 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.138036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.099003 restraints weight = 12316.195| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.28 r_work: 0.3117 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8908 Z= 0.188 Angle : 0.687 12.405 12078 Z= 0.336 Chirality : 0.044 0.171 1370 Planarity : 0.004 0.056 1506 Dihedral : 6.086 68.406 1227 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.93 % Allowed : 19.00 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.37 (0.26), residues: 1093 helix: 1.71 (0.27), residues: 378 sheet: -0.15 (0.31), residues: 266 loop : -0.71 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 24 TYR 0.010 0.002 TYR S 163 PHE 0.017 0.001 PHE R 35 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 ( 8904) covalent geometry : angle 0.68523 / 0.34 (12070) SS BOND : bond 0.01034 / 0.52 ( 4) SS BOND : angle 1.77700 / 0.60 ( 8) hydrogen bonds : bond 0.03868 / 2.61 ( 440) hydrogen bonds : angle 4.49505 / 3.09 ( 1269) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 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: 37 poor density : 150 time to evaluate : 0.432 Fit side-chains REVERT: R 32 ILE cc_start: 0.6809 (OUTLIER) cc_final: 0.6295 (tp) REVERT: R 50 PHE cc_start: 0.7708 (t80) cc_final: 0.7500 (t80) REVERT: R 234 LEU cc_start: 0.8688 (mt) cc_final: 0.8453 (mm) REVERT: R 277 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8779 (tp) REVERT: A 193 ASP cc_start: 0.8025 (t0) cc_final: 0.7566 (t0) REVERT: A 276 GLU cc_start: 0.8187 (pp20) cc_final: 0.7859 (pp20) REVERT: B 12 GLU cc_start: 0.8128 (pp20) cc_final: 0.7718 (pp20) REVERT: B 23 LYS cc_start: 0.9076 (ttpp) cc_final: 0.8834 (ttpp) REVERT: B 46 ARG cc_start: 0.8736 (mtm-85) cc_final: 0.8272 (mtp-110) REVERT: B 101 MET cc_start: 0.9198 (mtp) cc_final: 0.8912 (mtp) REVERT: B 146 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8653 (tp) REVERT: B 153 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8254 (p0) REVERT: B 217 MET cc_start: 0.8685 (pp-130) cc_final: 0.8348 (pmm) REVERT: B 228 ASP cc_start: 0.8284 (p0) cc_final: 0.8011 (p0) REVERT: B 234 PHE cc_start: 0.9392 (OUTLIER) cc_final: 0.8229 (m-80) REVERT: S 13 GLN cc_start: 0.8857 (mm110) cc_final: 0.8647 (mm-40) REVERT: S 46 GLU cc_start: 0.8808 (tt0) cc_final: 0.8524 (pt0) REVERT: S 89 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8193 (pm20) REVERT: S 93 MET cc_start: 0.8659 (ttm) cc_final: 0.8399 (tpp) outliers start: 37 outliers final: 20 residues processed: 168 average time/residue: 0.5163 time to fit residues: 92.6170 Evaluate side-chains 172 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 174 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 93 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 0.0980 chunk 104 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN A 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.140377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.101824 restraints weight = 12325.628| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.29 r_work: 0.3162 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8908 Z= 0.134 Angle : 0.670 12.105 12078 Z= 0.326 Chirality : 0.043 0.156 1370 Planarity : 0.004 0.059 1506 Dihedral : 5.908 68.758 1227 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.44 % Allowed : 20.91 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.51 (0.26), residues: 1093 helix: 1.82 (0.27), residues: 379 sheet: -0.07 (0.31), residues: 277 loop : -0.64 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 24 TYR 0.012 0.001 TYR S 178 PHE 0.019 0.001 PHE R 35 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.000 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 8904) covalent geometry : angle 0.66979 / 0.33 (12070) SS BOND : bond 0.00682 / 0.34 ( 4) SS BOND : angle 1.36526 / 0.49 ( 8) hydrogen bonds : bond 0.03569 / 2.41 ( 440) hydrogen bonds : angle 4.45630 / 3.06 ( 1269) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 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: 23 poor density : 152 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: R 32 ILE cc_start: 0.6773 (OUTLIER) cc_final: 0.6273 (tp) REVERT: R 45 LEU cc_start: 0.8305 (mt) cc_final: 0.8000 (mt) REVERT: R 58 ARG cc_start: 0.5748 (ttm-80) cc_final: 0.4672 (ttt180) REVERT: A 193 ASP cc_start: 0.8001 (t0) cc_final: 0.7559 (t0) REVERT: A 276 GLU cc_start: 0.8175 (pp20) cc_final: 0.7827 (pp20) REVERT: B 12 GLU cc_start: 0.8123 (pp20) cc_final: 0.7757 (pp20) REVERT: B 23 LYS cc_start: 0.9036 (ttpp) cc_final: 0.8789 (ttpp) REVERT: B 46 ARG cc_start: 0.8709 (mtm-85) cc_final: 0.8277 (mtp-110) REVERT: B 101 MET cc_start: 0.9173 (mtp) cc_final: 0.8879 (mtp) REVERT: B 228 ASP cc_start: 0.8240 (p0) cc_final: 0.8007 (p0) REVERT: B 234 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.8216 (m-80) REVERT: S 46 GLU cc_start: 0.8792 (tt0) cc_final: 0.8527 (pt0) outliers start: 23 outliers final: 12 residues processed: 163 average time/residue: 0.5354 time to fit residues: 93.0594 Evaluate side-chains 158 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 174 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 73 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN ** S 13 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 = 0.3825 r_free = 0.3825 target = 0.140763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.102478 restraints weight = 12186.701| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.27 r_work: 0.3173 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8908 Z= 0.136 Angle : 0.667 12.828 12078 Z= 0.324 Chirality : 0.043 0.195 1370 Planarity : 0.004 0.061 1506 Dihedral : 5.852 68.073 1227 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.91 % Allowed : 21.87 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.57 (0.26), residues: 1093 helix: 1.86 (0.27), residues: 379 sheet: 0.03 (0.31), residues: 274 loop : -0.66 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 24 TYR 0.012 0.001 TYR S 178 PHE 0.020 0.001 PHE R 35 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.000 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 8904) covalent geometry : angle 0.66593 / 0.32 (12070) SS BOND : bond 0.00731 / 0.37 ( 4) SS BOND : angle 1.65922 / 0.59 ( 8) hydrogen bonds : bond 0.03600 / 2.44 ( 440) hydrogen bonds : angle 4.43652 / 3.04 ( 1269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3343.48 seconds wall clock time: 57 minutes 39.93 seconds (3459.93 seconds total)