Starting phenix.real_space_refine on Thu Jul 2 16:13:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vb6_64917/07_2026/9vb6_64917.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vb6_64917/07_2026/9vb6_64917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vb6_64917/07_2026/9vb6_64917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vb6_64917/07_2026/9vb6_64917.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vb6_64917/07_2026/9vb6_64917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vb6_64917/07_2026/9vb6_64917.map" } resolution = 3.38 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= -0.004 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 61 5.16 5 C 5802 2.51 5 N 1555 2.21 5 O 1708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 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: 9129 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1815 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 226} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2578 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 404 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} 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: "D" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1762 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2485 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 309} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.85, per 1000 atoms: 0.20 Number of scatterers: 9129 At special positions: 0 Unit cell: (98.2167, 124.5, 136.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 61 16.00 P 3 15.00 O 1708 8.00 N 1555 7.00 C 5802 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.11 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.05 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.02 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: 0.51 Conformation dependent library (CDL) restraints added in 373.0 milliseconds 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2208 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 39.3% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.753A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 201 through 204 removed outlier: 3.512A pdb=" N GLN A 204 " --> pdb=" O VAL A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 201 through 204' Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.507A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.311A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.682A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 328 through 351 removed outlier: 3.799A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.520A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.840A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.572A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 45 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'R' and resid 51 through 55 removed outlier: 3.568A pdb=" N LEU R 54 " --> pdb=" O SER R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 91 Processing helix chain 'R' and resid 97 through 128 Proline residue: R 121 - end of helix removed outlier: 3.631A pdb=" N TYR R 125 " --> pdb=" O PRO R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 172 Processing helix chain 'R' and resid 172 through 180 Processing helix chain 'R' and resid 181 through 200 removed outlier: 3.929A pdb=" N ALA R 200 " --> pdb=" O SER R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 207 removed outlier: 4.041A pdb=" N LEU R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 273 removed outlier: 4.723A pdb=" N PHE R 247 " --> pdb=" O MET R 243 " (cutoff:3.500A) Proline residue: R 248 - end of helix removed outlier: 3.773A pdb=" N ILE R 258 " --> pdb=" O VAL R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 329 removed outlier: 3.810A pdb=" N ALA R 297 " --> pdb=" O GLY R 293 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 335 through 366 removed outlier: 4.039A pdb=" N ASP R 340 " --> pdb=" O PRO R 336 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE R 341 " --> pdb=" O PHE R 337 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 368 through 379 Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 removed outlier: 3.739A pdb=" N HIS A 57 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.501A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.575A 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: 3.606A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.737A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 6.849A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.769A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.217A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.414A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.631A pdb=" N GLY D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR D 118 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.631A pdb=" N GLY D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR D 118 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 130 Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.766A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 209 through 211 477 hydrogen bonds defined for protein. 1350 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: 1.34 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 244 1.23 - 1.38: 2893 1.38 - 1.53: 4140 1.53 - 1.68: 1956 1.68 - 1.83: 91 Bond restraints: 9324 Sorted by residual: bond pdb=" CB SER R 52 " pdb=" OG SER R 52 " ideal model delta sigma weight residual 1.417 1.076 0.341 2.00e-02 2.50e+03 2.90e+02 bond pdb=" CG LEU R 71 " pdb=" CD1 LEU R 71 " ideal model delta sigma weight residual 1.521 1.768 -0.247 3.30e-02 9.18e+02 5.62e+01 bond pdb=" CG PHE R 174 " pdb=" CD2 PHE R 174 " ideal model delta sigma weight residual 1.384 1.234 0.150 2.10e-02 2.27e+03 5.09e+01 bond pdb=" CG PHE R 174 " pdb=" CD1 PHE R 174 " ideal model delta sigma weight residual 1.384 1.526 -0.142 2.10e-02 2.27e+03 4.58e+01 bond pdb=" CB ILE R 60 " pdb=" CG2 ILE R 60 " ideal model delta sigma weight residual 1.521 1.340 0.181 3.30e-02 9.18e+02 3.01e+01 ... (remaining 9319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 12330 4.84 - 9.68: 310 9.68 - 14.52: 12 14.52 - 19.36: 3 19.36 - 24.20: 1 Bond angle restraints: 12656 Sorted by residual: angle pdb=" CD ARG R 90 " pdb=" NE ARG R 90 " pdb=" CZ ARG R 90 " ideal model delta sigma weight residual 124.40 100.20 24.20 1.40e+00 5.10e-01 2.99e+02 angle pdb=" NE ARG R 90 " pdb=" CZ ARG R 90 " pdb=" NH2 ARG R 90 " ideal model delta sigma weight residual 119.20 132.50 -13.30 9.00e-01 1.23e+00 2.18e+02 angle pdb=" NE ARG R 90 " pdb=" CZ ARG R 90 " pdb=" NH1 ARG R 90 " ideal model delta sigma weight residual 121.50 106.79 14.71 1.00e+00 1.00e+00 2.16e+02 angle pdb=" N LYS R 234 " pdb=" CA LYS R 234 " pdb=" CB LYS R 234 " ideal model delta sigma weight residual 110.01 123.17 -13.16 1.45e+00 4.76e-01 8.24e+01 angle pdb=" N VAL R 302 " pdb=" CA VAL R 302 " pdb=" CB VAL R 302 " ideal model delta sigma weight residual 110.51 120.36 -9.85 1.11e+00 8.12e-01 7.87e+01 ... (remaining 12651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.71: 5352 34.71 - 69.42: 137 69.42 - 104.13: 12 104.13 - 138.83: 2 138.83 - 173.54: 3 Dihedral angle restraints: 5506 sinusoidal: 2084 harmonic: 3422 Sorted by residual: dihedral pdb=" CB CYS R 141 " pdb=" SG CYS R 141 " pdb=" SG CYS R 224 " pdb=" CB CYS R 224 " ideal model delta sinusoidal sigma weight residual -86.00 -173.14 87.14 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CD ARG R 90 " pdb=" NE ARG R 90 " pdb=" CZ ARG R 90 " pdb=" NH1 ARG R 90 " ideal model delta sinusoidal sigma weight residual 0.00 73.99 -73.99 1 1.00e+01 1.00e-02 6.95e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 166.96 -73.96 1 1.00e+01 1.00e-02 6.95e+01 ... (remaining 5503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.245: 1402 0.245 - 0.489: 44 0.489 - 0.734: 0 0.734 - 0.978: 1 0.978 - 1.223: 1 Chirality restraints: 1448 Sorted by residual: chirality pdb=" CG LEU R 71 " pdb=" CB LEU R 71 " pdb=" CD1 LEU R 71 " pdb=" CD2 LEU R 71 " both_signs ideal model delta sigma weight residual False -2.59 -3.81 1.22 2.00e-01 2.50e+01 3.74e+01 chirality pdb=" CB ILE R 60 " pdb=" CA ILE R 60 " pdb=" CG1 ILE R 60 " pdb=" CG2 ILE R 60 " both_signs ideal model delta sigma weight residual False 2.64 1.76 0.89 2.00e-01 2.50e+01 1.98e+01 chirality pdb=" CA HIS A 244 " pdb=" N HIS A 244 " pdb=" C HIS A 244 " pdb=" CB HIS A 244 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.64e+00 ... (remaining 1445 not shown) Planarity restraints: 1592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 90 " -1.258 9.50e-02 1.11e+02 5.64e-01 1.93e+02 pdb=" NE ARG R 90 " 0.075 2.00e-02 2.50e+03 pdb=" CZ ARG R 90 " -0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG R 90 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG R 90 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 303 " -0.529 9.50e-02 1.11e+02 2.44e-01 7.52e+01 pdb=" NE ARG R 303 " -0.005 2.00e-02 2.50e+03 pdb=" CZ ARG R 303 " 0.117 2.00e-02 2.50e+03 pdb=" NH1 ARG R 303 " -0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG R 303 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 174 " 0.061 2.00e-02 2.50e+03 5.17e-02 4.68e+01 pdb=" CG PHE R 174 " -0.120 2.00e-02 2.50e+03 pdb=" CD1 PHE R 174 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE R 174 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE R 174 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE R 174 " 0.015 2.00e-02 2.50e+03 pdb=" CZ PHE R 174 " 0.010 2.00e-02 2.50e+03 ... (remaining 1589 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1775 2.84 - 3.35: 9187 3.35 - 3.87: 15061 3.87 - 4.38: 17575 4.38 - 4.90: 29908 Nonbonded interactions: 73506 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.320 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.339 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.368 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.376 3.040 nonbonded pdb=" O THR A 48 " pdb=" N LYS A 51 " model vdw 2.383 3.120 ... (remaining 73501 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: 0.100 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.650 Find NCS groups from input model: 0.070 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 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 : 0.012 0.341 9327 Z= 0.732 Angle : 2.044 24.199 12662 Z= 1.389 Chirality : 0.120 1.223 1448 Planarity : 0.019 0.564 1592 Dihedral : 15.935 173.543 3289 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.57 % Favored : 95.34 % Rotamer: Outliers : 6.59 % Allowed : 8.55 % Favored : 84.86 % Cbeta Deviations : 1.09 % Peptide Plane: Cis-proline : 6.25 % 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: -2.24 (0.22), residues: 1159 helix: -1.10 (0.23), residues: 405 sheet: -1.35 (0.30), residues: 258 loop : -1.75 (0.24), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.110 0.006 ARG R 303 TYR 0.050 0.006 TYR A 296 PHE 0.120 0.007 PHE R 174 TRP 0.065 0.009 TRP B 99 HIS 0.046 0.007 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.01226 / 0.73 ( 9324) covalent geometry : angle 2.04172 / 1.39 (12656) SS BOND : bond 0.04691 / 2.45 ( 3) SS BOND : angle 4.65712 / 2.45 ( 6) hydrogen bonds : bond 0.20645 / 13.65 ( 472) hydrogen bonds : angle 8.33954 / 5.92 ( 1350) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 288 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 ASN cc_start: 0.9320 (m-40) cc_final: 0.8848 (m-40) REVERT: A 243 MET cc_start: 0.8787 (tpp) cc_final: 0.7914 (tpp) REVERT: A 244 HIS cc_start: 0.9498 (t70) cc_final: 0.9004 (m90) REVERT: A 246 SER cc_start: 0.9538 (m) cc_final: 0.9266 (p) REVERT: A 247 MET cc_start: 0.9579 (ttm) cc_final: 0.9146 (mtp) REVERT: A 256 ASN cc_start: 0.9262 (t0) cc_final: 0.8848 (t0) REVERT: A 263 SER cc_start: 0.8956 (p) cc_final: 0.8708 (m) REVERT: A 287 TYR cc_start: 0.9022 (m-10) cc_final: 0.8362 (m-80) REVERT: A 344 ILE cc_start: 0.9438 (mt) cc_final: 0.9156 (mm) REVERT: A 347 ASN cc_start: 0.9467 (m-40) cc_final: 0.9246 (m110) REVERT: A 349 LYS cc_start: 0.9472 (OUTLIER) cc_final: 0.9124 (tppp) REVERT: B 169 TRP cc_start: 0.8774 (OUTLIER) cc_final: 0.7649 (m-90) REVERT: B 217 MET cc_start: 0.9125 (pmm) cc_final: 0.8913 (pmm) REVERT: B 280 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8600 (ttpp) REVERT: C 19 LEU cc_start: 0.9609 (mt) cc_final: 0.9387 (mt) REVERT: C 24 ASN cc_start: 0.9492 (p0) cc_final: 0.9251 (p0) REVERT: C 57 SER cc_start: 0.9568 (p) cc_final: 0.9364 (p) REVERT: D 62 ASP cc_start: 0.9215 (m-30) cc_final: 0.8959 (p0) REVERT: D 90 ASP cc_start: 0.8929 (m-30) cc_final: 0.8491 (m-30) REVERT: D 93 MET cc_start: 0.9014 (tpp) cc_final: 0.8684 (tpp) REVERT: D 189 ASP cc_start: 0.8958 (p0) cc_final: 0.8470 (t0) REVERT: R 85 LEU cc_start: 0.9441 (mt) cc_final: 0.9208 (mt) REVERT: R 92 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7948 (pttp) REVERT: R 99 SER cc_start: 0.8923 (OUTLIER) cc_final: 0.8653 (t) REVERT: R 112 ASP cc_start: 0.8805 (m-30) cc_final: 0.8596 (m-30) REVERT: R 134 TRP cc_start: 0.8097 (t-100) cc_final: 0.7627 (t-100) REVERT: R 149 ASP cc_start: 0.8628 (m-30) cc_final: 0.8137 (t0) REVERT: R 165 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8508 (mp0) REVERT: R 171 CYS cc_start: 0.8976 (m) cc_final: 0.8731 (t) REVERT: R 187 LYS cc_start: 0.9149 (tmtt) cc_final: 0.8917 (ptmt) REVERT: R 193 TRP cc_start: 0.8379 (m100) cc_final: 0.7867 (m100) REVERT: R 207 MET cc_start: 0.9448 (mmt) cc_final: 0.9120 (mmm) REVERT: R 210 GLN cc_start: 0.9044 (tt0) cc_final: 0.8763 (tm-30) REVERT: R 249 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8542 (tmm) outliers start: 64 outliers final: 26 residues processed: 337 average time/residue: 0.0926 time to fit residues: 41.1409 Evaluate side-chains 205 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain R residue 92 LYS Chi-restraints excluded: chain R residue 99 SER Chi-restraints excluded: chain R residue 151 CYS Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 241 THR Chi-restraints excluded: chain R residue 249 MET Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 257 THR Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain R residue 365 ASN Chi-restraints excluded: chain R residue 373 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 50.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 57 HIS A 213 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS B 6 GLN B 88 ASN B 91 HIS B 311 HIS B 340 ASN D 130 GLN ** R 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 126 ASN ** R 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 350 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.085296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.063878 restraints weight = 26207.023| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.69 r_work: 0.2868 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9327 Z= 0.177 Angle : 0.723 13.316 12662 Z= 0.372 Chirality : 0.046 0.197 1448 Planarity : 0.004 0.047 1592 Dihedral : 11.961 166.048 1349 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.15 % Allowed : 14.83 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.44 (0.23), residues: 1159 helix: 1.08 (0.24), residues: 414 sheet: -0.79 (0.29), residues: 294 loop : -1.15 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 87 TYR 0.022 0.002 TYR R 354 PHE 0.026 0.002 PHE R 371 TRP 0.017 0.002 TRP B 99 HIS 0.017 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 ( 9324) covalent geometry : angle 0.72209 / 0.37 (12656) SS BOND : bond 0.00593 / 0.28 ( 3) SS BOND : angle 1.61571 / 0.83 ( 6) hydrogen bonds : bond 0.05020 / 3.46 ( 472) hydrogen bonds : angle 5.32745 / 3.82 ( 1350) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 187 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7991 (mmp) cc_final: 0.7732 (mmp) REVERT: A 198 MET cc_start: 0.9050 (ttm) cc_final: 0.8671 (ttp) REVERT: A 241 ASN cc_start: 0.8950 (m-40) cc_final: 0.8080 (m-40) REVERT: A 243 MET cc_start: 0.8242 (tpp) cc_final: 0.7280 (tpp) REVERT: A 244 HIS cc_start: 0.9119 (t70) cc_final: 0.8640 (m170) REVERT: A 247 MET cc_start: 0.9400 (ttm) cc_final: 0.8902 (mtp) REVERT: A 256 ASN cc_start: 0.9266 (t0) cc_final: 0.8733 (t0) REVERT: A 331 ASN cc_start: 0.9074 (p0) cc_final: 0.8801 (p0) REVERT: A 333 GLN cc_start: 0.9554 (tp-100) cc_final: 0.9118 (pt0) REVERT: A 337 ASP cc_start: 0.9243 (t70) cc_final: 0.8885 (m-30) REVERT: A 349 LYS cc_start: 0.9227 (mmmt) cc_final: 0.8814 (tppt) REVERT: B 59 TYR cc_start: 0.8873 (m-10) cc_final: 0.8002 (m-10) REVERT: B 142 HIS cc_start: 0.8856 (OUTLIER) cc_final: 0.8388 (t70) REVERT: B 169 TRP cc_start: 0.8866 (OUTLIER) cc_final: 0.7596 (m-90) REVERT: C 14 LYS cc_start: 0.9517 (mtpp) cc_final: 0.9184 (mmmm) REVERT: C 47 GLU cc_start: 0.7990 (pm20) cc_final: 0.7715 (pm20) REVERT: D 18 ARG cc_start: 0.9108 (tpp80) cc_final: 0.8776 (tpp80) REVERT: D 58 ILE cc_start: 0.9401 (mt) cc_final: 0.9015 (tt) REVERT: D 90 ASP cc_start: 0.9001 (m-30) cc_final: 0.8779 (m-30) REVERT: D 93 MET cc_start: 0.8762 (tpp) cc_final: 0.8314 (tpp) REVERT: D 128 MET cc_start: 0.8338 (mmm) cc_final: 0.8019 (mmm) REVERT: D 148 ARG cc_start: 0.8955 (ttm110) cc_final: 0.8470 (ttp-110) REVERT: D 171 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8311 (mm-40) REVERT: D 189 ASP cc_start: 0.8789 (p0) cc_final: 0.8286 (t0) REVERT: D 218 MET cc_start: 0.8749 (ttp) cc_final: 0.8390 (ttt) REVERT: D 232 LYS cc_start: 0.8902 (ttmm) cc_final: 0.8390 (ttmm) REVERT: R 71 LEU cc_start: 0.9406 (mm) cc_final: 0.9173 (tt) REVERT: R 149 ASP cc_start: 0.8441 (m-30) cc_final: 0.7998 (t0) REVERT: R 180 MET cc_start: 0.9252 (tmm) cc_final: 0.8941 (tmm) REVERT: R 187 LYS cc_start: 0.8947 (tmtt) cc_final: 0.8540 (ptmt) REVERT: R 207 MET cc_start: 0.9383 (mmt) cc_final: 0.8618 (mmm) REVERT: R 249 MET cc_start: 0.8634 (tmm) cc_final: 0.8262 (tmm) REVERT: R 264 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8702 (p) REVERT: R 331 ASP cc_start: 0.8922 (m-30) cc_final: 0.8283 (t0) REVERT: R 357 SER cc_start: 0.8901 (m) cc_final: 0.8628 (p) outliers start: 50 outliers final: 24 residues processed: 227 average time/residue: 0.0859 time to fit residues: 26.3347 Evaluate side-chains 177 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 261 ASN Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain R residue 362 ILE Chi-restraints excluded: chain R residue 368 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 85 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 16 optimal weight: 0.0870 chunk 32 optimal weight: 0.4980 chunk 99 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.1164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN R 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.085834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.064435 restraints weight = 26209.594| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.68 r_work: 0.2871 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9327 Z= 0.140 Angle : 0.666 11.992 12662 Z= 0.337 Chirality : 0.044 0.161 1448 Planarity : 0.003 0.046 1592 Dihedral : 10.255 170.559 1299 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.02 % Allowed : 16.27 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.14 (0.24), residues: 1159 helix: 1.65 (0.25), residues: 416 sheet: -0.49 (0.29), residues: 288 loop : -0.92 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 208 TYR 0.014 0.001 TYR R 339 PHE 0.017 0.002 PHE R 371 TRP 0.017 0.002 TRP R 134 HIS 0.011 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 9324) covalent geometry : angle 0.66565 / 0.34 (12656) SS BOND : bond 0.00630 / 0.30 ( 3) SS BOND : angle 1.24819 / 0.61 ( 6) hydrogen bonds : bond 0.04482 / 3.07 ( 472) hydrogen bonds : angle 5.02673 / 3.60 ( 1350) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 ASN cc_start: 0.9095 (m-40) cc_final: 0.8399 (m-40) REVERT: A 243 MET cc_start: 0.8197 (tpp) cc_final: 0.7372 (tpp) REVERT: A 244 HIS cc_start: 0.9127 (t70) cc_final: 0.8714 (m90) REVERT: A 247 MET cc_start: 0.9393 (ttm) cc_final: 0.8947 (mtp) REVERT: A 256 ASN cc_start: 0.9289 (t0) cc_final: 0.8753 (t0) REVERT: A 331 ASN cc_start: 0.9081 (p0) cc_final: 0.8875 (p0) REVERT: A 333 GLN cc_start: 0.9576 (tp-100) cc_final: 0.8921 (tp-100) REVERT: A 337 ASP cc_start: 0.9226 (t70) cc_final: 0.8729 (p0) REVERT: B 10 GLU cc_start: 0.9494 (tp30) cc_final: 0.9247 (tp30) REVERT: B 59 TYR cc_start: 0.8771 (m-10) cc_final: 0.8009 (m-10) REVERT: B 138 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8656 (mm-30) REVERT: B 142 HIS cc_start: 0.8786 (OUTLIER) cc_final: 0.8060 (t-170) REVERT: B 169 TRP cc_start: 0.8787 (OUTLIER) cc_final: 0.7486 (m-90) REVERT: B 188 MET cc_start: 0.9098 (mmm) cc_final: 0.8883 (mmm) REVERT: C 17 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8629 (mm-30) REVERT: C 20 LYS cc_start: 0.9066 (mtmm) cc_final: 0.8738 (ptpp) REVERT: C 38 MET cc_start: 0.9157 (ttm) cc_final: 0.8871 (mtm) REVERT: C 47 GLU cc_start: 0.7908 (pm20) cc_final: 0.7666 (pm20) REVERT: D 90 ASP cc_start: 0.8961 (m-30) cc_final: 0.8691 (m-30) REVERT: D 93 MET cc_start: 0.8761 (tpp) cc_final: 0.8330 (tpp) REVERT: D 189 ASP cc_start: 0.8741 (p0) cc_final: 0.8278 (t0) REVERT: D 218 MET cc_start: 0.8867 (ttp) cc_final: 0.8512 (ttt) REVERT: D 219 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8581 (pp30) REVERT: R 71 LEU cc_start: 0.9444 (mm) cc_final: 0.9192 (tt) REVERT: R 112 ASP cc_start: 0.9062 (m-30) cc_final: 0.8817 (t70) REVERT: R 149 ASP cc_start: 0.8523 (m-30) cc_final: 0.8086 (t0) REVERT: R 180 MET cc_start: 0.9308 (tmm) cc_final: 0.9032 (tmm) REVERT: R 187 LYS cc_start: 0.8960 (tmtt) cc_final: 0.8559 (ptmt) REVERT: R 207 MET cc_start: 0.9385 (mmt) cc_final: 0.8509 (mmm) REVERT: R 218 HIS cc_start: 0.8275 (t70) cc_final: 0.8015 (t-170) REVERT: R 243 MET cc_start: 0.9042 (tpp) cc_final: 0.8601 (tpp) REVERT: R 249 MET cc_start: 0.8430 (tmm) cc_final: 0.8217 (tmm) REVERT: R 331 ASP cc_start: 0.9011 (m-30) cc_final: 0.8343 (t0) REVERT: R 357 SER cc_start: 0.8932 (m) cc_final: 0.8677 (p) REVERT: R 371 PHE cc_start: 0.9038 (t80) cc_final: 0.8536 (t80) outliers start: 39 outliers final: 23 residues processed: 201 average time/residue: 0.0978 time to fit residues: 26.3434 Evaluate side-chains 173 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 261 ASN Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 328 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 11 optimal weight: 30.0000 chunk 15 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 18 optimal weight: 0.4980 chunk 112 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** D 219 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 = 0.3450 r_free = 0.3450 target = 0.082842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.061348 restraints weight = 26919.620| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.71 r_work: 0.2810 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9327 Z= 0.231 Angle : 0.689 11.159 12662 Z= 0.353 Chirality : 0.045 0.197 1448 Planarity : 0.004 0.050 1592 Dihedral : 9.403 163.269 1296 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.84 % Allowed : 16.79 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.24), residues: 1159 helix: 1.68 (0.25), residues: 415 sheet: -0.29 (0.31), residues: 273 loop : -0.81 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 182 TYR 0.014 0.002 TYR R 354 PHE 0.017 0.002 PHE B 234 TRP 0.014 0.002 TRP R 134 HIS 0.008 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.23 ( 9324) covalent geometry : angle 0.68777 / 0.35 (12656) SS BOND : bond 0.00888 / 0.43 ( 3) SS BOND : angle 1.83469 / 0.90 ( 6) hydrogen bonds : bond 0.04638 / 3.15 ( 472) hydrogen bonds : angle 5.04086 / 3.62 ( 1350) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7989 (mmp) cc_final: 0.7750 (mmp) REVERT: A 243 MET cc_start: 0.8335 (tpp) cc_final: 0.7351 (tpp) REVERT: A 247 MET cc_start: 0.9381 (ttm) cc_final: 0.8999 (mtp) REVERT: A 256 ASN cc_start: 0.9397 (t0) cc_final: 0.8901 (t0) REVERT: B 10 GLU cc_start: 0.9535 (tp30) cc_final: 0.9250 (tp30) REVERT: B 59 TYR cc_start: 0.8903 (m-10) cc_final: 0.8493 (m-80) REVERT: B 142 HIS cc_start: 0.8720 (OUTLIER) cc_final: 0.8408 (t70) REVERT: B 169 TRP cc_start: 0.8929 (OUTLIER) cc_final: 0.7512 (m-90) REVERT: C 17 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8601 (mm-30) REVERT: C 47 GLU cc_start: 0.7812 (pm20) cc_final: 0.7603 (pm20) REVERT: D 18 ARG cc_start: 0.9022 (tpp80) cc_final: 0.8802 (tpp80) REVERT: D 58 ILE cc_start: 0.9372 (mt) cc_final: 0.9054 (tt) REVERT: D 90 ASP cc_start: 0.9214 (m-30) cc_final: 0.8982 (m-30) REVERT: D 93 MET cc_start: 0.8759 (tpp) cc_final: 0.8357 (tpp) REVERT: D 98 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8417 (ppt-90) REVERT: D 189 ASP cc_start: 0.8851 (p0) cc_final: 0.8489 (t0) REVERT: D 211 ASP cc_start: 0.8332 (t0) cc_final: 0.8049 (t0) REVERT: R 71 LEU cc_start: 0.9482 (mm) cc_final: 0.9250 (tt) REVERT: R 112 ASP cc_start: 0.9083 (m-30) cc_final: 0.8810 (t70) REVERT: R 149 ASP cc_start: 0.8555 (m-30) cc_final: 0.8047 (t0) REVERT: R 187 LYS cc_start: 0.8787 (tmtt) cc_final: 0.8410 (mtmm) REVERT: R 207 MET cc_start: 0.9360 (mmt) cc_final: 0.8608 (mmm) REVERT: R 331 ASP cc_start: 0.9009 (m-30) cc_final: 0.8338 (t0) REVERT: R 357 SER cc_start: 0.8917 (m) cc_final: 0.8605 (p) REVERT: R 371 PHE cc_start: 0.9038 (t80) cc_final: 0.8526 (t80) REVERT: L 13 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8763 (tm) outliers start: 47 outliers final: 33 residues processed: 187 average time/residue: 0.0881 time to fit residues: 22.3739 Evaluate side-chains 171 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 261 ASN Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 57 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 10 optimal weight: 0.0970 chunk 86 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 15 optimal weight: 0.0470 chunk 82 optimal weight: 10.0000 overall best weight: 2.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.084949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.063151 restraints weight = 26547.966| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.69 r_work: 0.2851 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9327 Z= 0.137 Angle : 0.634 10.030 12662 Z= 0.320 Chirality : 0.042 0.153 1448 Planarity : 0.003 0.048 1592 Dihedral : 8.648 161.920 1295 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.71 % Allowed : 19.88 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.55 (0.25), residues: 1159 helix: 1.88 (0.25), residues: 415 sheet: -0.12 (0.31), residues: 263 loop : -0.66 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 208 TYR 0.011 0.001 TYR R 339 PHE 0.013 0.001 PHE R 371 TRP 0.014 0.001 TRP R 134 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 9324) covalent geometry : angle 0.63371 / 0.32 (12656) SS BOND : bond 0.00581 / 0.28 ( 3) SS BOND : angle 0.99765 / 0.49 ( 6) hydrogen bonds : bond 0.04112 / 2.79 ( 472) hydrogen bonds : angle 4.86523 / 3.48 ( 1350) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8362 (tpp) cc_final: 0.7459 (tpp) REVERT: A 247 MET cc_start: 0.9278 (ttm) cc_final: 0.8958 (mtp) REVERT: A 256 ASN cc_start: 0.9362 (t0) cc_final: 0.8925 (t0) REVERT: A 333 GLN cc_start: 0.9542 (tp-100) cc_final: 0.9248 (pt0) REVERT: A 337 ASP cc_start: 0.9179 (t70) cc_final: 0.8954 (p0) REVERT: B 3 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8045 (tm-30) REVERT: B 7 LEU cc_start: 0.9408 (mt) cc_final: 0.9174 (mm) REVERT: B 10 GLU cc_start: 0.9565 (tp30) cc_final: 0.9301 (tp30) REVERT: B 23 LYS cc_start: 0.8981 (mttt) cc_final: 0.8695 (mttt) REVERT: B 59 TYR cc_start: 0.8967 (m-10) cc_final: 0.8656 (m-80) REVERT: B 138 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8767 (mm-30) REVERT: B 142 HIS cc_start: 0.8682 (OUTLIER) cc_final: 0.8324 (t70) REVERT: B 169 TRP cc_start: 0.8807 (OUTLIER) cc_final: 0.7706 (m-90) REVERT: B 270 ILE cc_start: 0.9430 (pt) cc_final: 0.9080 (mp) REVERT: C 17 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8751 (mm-30) REVERT: C 20 LYS cc_start: 0.9098 (mtmm) cc_final: 0.8741 (ptpp) REVERT: D 58 ILE cc_start: 0.9354 (mt) cc_final: 0.9086 (tt) REVERT: D 90 ASP cc_start: 0.9083 (m-30) cc_final: 0.8799 (m-30) REVERT: D 93 MET cc_start: 0.8791 (tpp) cc_final: 0.8474 (tpp) REVERT: D 189 ASP cc_start: 0.8821 (p0) cc_final: 0.8519 (t0) REVERT: D 211 ASP cc_start: 0.8346 (t0) cc_final: 0.7973 (t0) REVERT: D 219 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8710 (pp30) REVERT: R 71 LEU cc_start: 0.9470 (mm) cc_final: 0.9247 (tt) REVERT: R 112 ASP cc_start: 0.9114 (m-30) cc_final: 0.8853 (t70) REVERT: R 149 ASP cc_start: 0.8444 (m-30) cc_final: 0.8038 (t70) REVERT: R 180 MET cc_start: 0.9338 (tmm) cc_final: 0.8996 (ppp) REVERT: R 186 LYS cc_start: 0.9219 (mmtp) cc_final: 0.8942 (mmtp) REVERT: R 187 LYS cc_start: 0.8760 (tmtt) cc_final: 0.8360 (mtmp) REVERT: R 207 MET cc_start: 0.9353 (mmt) cc_final: 0.8618 (mmm) REVERT: R 331 ASP cc_start: 0.8969 (m-30) cc_final: 0.8394 (t0) REVERT: R 357 SER cc_start: 0.8972 (m) cc_final: 0.8663 (p) REVERT: R 371 PHE cc_start: 0.9027 (t80) cc_final: 0.8425 (t80) REVERT: L 13 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8699 (tm) outliers start: 36 outliers final: 27 residues processed: 188 average time/residue: 0.0829 time to fit residues: 21.3127 Evaluate side-chains 172 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 261 ASN Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.0570 chunk 3 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN R 218 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.085516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.063843 restraints weight = 26408.615| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.69 r_work: 0.2870 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9327 Z= 0.127 Angle : 0.638 11.839 12662 Z= 0.318 Chirality : 0.042 0.157 1448 Planarity : 0.003 0.051 1592 Dihedral : 7.921 160.236 1295 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.63 % Allowed : 18.95 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.73 (0.25), residues: 1159 helix: 2.00 (0.25), residues: 415 sheet: 0.17 (0.32), residues: 269 loop : -0.67 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 208 TYR 0.013 0.001 TYR R 103 PHE 0.012 0.001 PHE R 371 TRP 0.030 0.002 TRP B 82 HIS 0.006 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 9324) covalent geometry : angle 0.63779 / 0.32 (12656) SS BOND : bond 0.00568 / 0.28 ( 3) SS BOND : angle 0.94141 / 0.45 ( 6) hydrogen bonds : bond 0.03915 / 2.66 ( 472) hydrogen bonds : angle 4.77566 / 3.41 ( 1350) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8356 (tpp) cc_final: 0.7438 (tpp) REVERT: A 247 MET cc_start: 0.9310 (ttm) cc_final: 0.8946 (mtp) REVERT: A 256 ASN cc_start: 0.9359 (t0) cc_final: 0.8943 (t0) REVERT: B 3 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7890 (tm-30) REVERT: B 7 LEU cc_start: 0.9398 (mt) cc_final: 0.9124 (mm) REVERT: B 10 GLU cc_start: 0.9524 (tp30) cc_final: 0.9248 (tp30) REVERT: B 23 LYS cc_start: 0.8928 (mttt) cc_final: 0.8616 (mttt) REVERT: B 59 TYR cc_start: 0.8980 (m-10) cc_final: 0.8603 (m-80) REVERT: B 138 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8776 (mm-30) REVERT: B 270 ILE cc_start: 0.9412 (pt) cc_final: 0.9062 (mp) REVERT: B 292 PHE cc_start: 0.9181 (m-10) cc_final: 0.8790 (m-10) REVERT: C 17 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8771 (mm-30) REVERT: C 20 LYS cc_start: 0.9149 (mtmm) cc_final: 0.8787 (ptpp) REVERT: D 90 ASP cc_start: 0.8938 (m-30) cc_final: 0.8593 (m-30) REVERT: D 93 MET cc_start: 0.8775 (tpp) cc_final: 0.8454 (tpp) REVERT: D 189 ASP cc_start: 0.8819 (p0) cc_final: 0.8519 (t0) REVERT: D 211 ASP cc_start: 0.8283 (t0) cc_final: 0.7917 (t0) REVERT: D 219 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8676 (pp30) REVERT: R 85 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8973 (mm) REVERT: R 112 ASP cc_start: 0.8931 (m-30) cc_final: 0.8722 (t70) REVERT: R 149 ASP cc_start: 0.8389 (m-30) cc_final: 0.8048 (t70) REVERT: R 180 MET cc_start: 0.9374 (tmm) cc_final: 0.9090 (ppp) REVERT: R 187 LYS cc_start: 0.8711 (tmtt) cc_final: 0.8288 (mtmm) REVERT: R 207 MET cc_start: 0.9333 (mmt) cc_final: 0.8622 (mmm) REVERT: R 241 THR cc_start: 0.7932 (t) cc_final: 0.7702 (t) REVERT: R 249 MET cc_start: 0.8862 (tpp) cc_final: 0.8000 (tpp) REVERT: R 263 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8022 (tt) REVERT: R 264 THR cc_start: 0.9081 (m) cc_final: 0.8745 (p) REVERT: R 331 ASP cc_start: 0.9050 (m-30) cc_final: 0.8393 (t0) REVERT: R 357 SER cc_start: 0.8933 (m) cc_final: 0.8684 (p) REVERT: R 371 PHE cc_start: 0.8987 (t80) cc_final: 0.8452 (t80) REVERT: R 373 HIS cc_start: 0.8812 (p90) cc_final: 0.8565 (p90) REVERT: L 13 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8566 (tm) outliers start: 45 outliers final: 30 residues processed: 189 average time/residue: 0.0928 time to fit residues: 23.9246 Evaluate side-chains 178 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 261 ASN Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 78 optimal weight: 0.0980 chunk 45 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 105 optimal weight: 40.0000 chunk 28 optimal weight: 1.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.084837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.063294 restraints weight = 26416.158| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.71 r_work: 0.2861 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9327 Z= 0.143 Angle : 0.651 11.068 12662 Z= 0.324 Chirality : 0.043 0.196 1448 Planarity : 0.003 0.056 1592 Dihedral : 7.010 159.345 1293 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.81 % Allowed : 19.67 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.81 (0.25), residues: 1159 helix: 2.03 (0.25), residues: 415 sheet: 0.25 (0.32), residues: 271 loop : -0.61 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 208 TYR 0.011 0.001 TYR R 103 PHE 0.015 0.001 PHE R 205 TRP 0.016 0.001 TRP B 82 HIS 0.013 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 9324) covalent geometry : angle 0.65046 / 0.32 (12656) SS BOND : bond 0.00593 / 0.29 ( 3) SS BOND : angle 1.08374 / 0.54 ( 6) hydrogen bonds : bond 0.03965 / 2.67 ( 472) hydrogen bonds : angle 4.76574 / 3.40 ( 1350) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8378 (tpp) cc_final: 0.7531 (tpp) REVERT: A 247 MET cc_start: 0.9293 (ttm) cc_final: 0.8935 (mtp) REVERT: A 256 ASN cc_start: 0.9379 (t0) cc_final: 0.8964 (t0) REVERT: B 10 GLU cc_start: 0.9526 (tp30) cc_final: 0.9259 (tp30) REVERT: B 23 LYS cc_start: 0.9037 (mttt) cc_final: 0.8734 (mttt) REVERT: B 59 TYR cc_start: 0.8909 (m-10) cc_final: 0.8523 (m-80) REVERT: B 138 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8780 (mm-30) REVERT: B 261 LEU cc_start: 0.9261 (tp) cc_final: 0.8941 (tp) REVERT: B 270 ILE cc_start: 0.9425 (pt) cc_final: 0.9078 (mp) REVERT: B 292 PHE cc_start: 0.9205 (m-10) cc_final: 0.8803 (m-10) REVERT: C 58 GLU cc_start: 0.9605 (pm20) cc_final: 0.9334 (pm20) REVERT: D 77 ASN cc_start: 0.8886 (m-40) cc_final: 0.8567 (m-40) REVERT: D 90 ASP cc_start: 0.8958 (m-30) cc_final: 0.8585 (m-30) REVERT: D 93 MET cc_start: 0.8755 (tpp) cc_final: 0.8382 (tpp) REVERT: D 189 ASP cc_start: 0.8825 (p0) cc_final: 0.8523 (t0) REVERT: D 211 ASP cc_start: 0.8247 (t0) cc_final: 0.7942 (t0) REVERT: D 219 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8509 (pp30) REVERT: R 85 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8962 (mm) REVERT: R 112 ASP cc_start: 0.9011 (m-30) cc_final: 0.8790 (t70) REVERT: R 149 ASP cc_start: 0.8612 (m-30) cc_final: 0.8062 (t0) REVERT: R 180 MET cc_start: 0.9388 (tmm) cc_final: 0.9156 (ppp) REVERT: R 187 LYS cc_start: 0.8724 (tmtt) cc_final: 0.8302 (mttp) REVERT: R 207 MET cc_start: 0.9258 (mmt) cc_final: 0.8828 (mmm) REVERT: R 243 MET cc_start: 0.8811 (tpp) cc_final: 0.8484 (tpp) REVERT: R 249 MET cc_start: 0.8895 (tpp) cc_final: 0.8188 (tpt) REVERT: R 263 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8026 (tt) REVERT: R 331 ASP cc_start: 0.9035 (m-30) cc_final: 0.8436 (t0) REVERT: R 345 PHE cc_start: 0.8435 (t80) cc_final: 0.7977 (t80) REVERT: R 357 SER cc_start: 0.8940 (m) cc_final: 0.8693 (p) REVERT: R 371 PHE cc_start: 0.8995 (t80) cc_final: 0.8443 (t80) REVERT: R 373 HIS cc_start: 0.8864 (p90) cc_final: 0.8570 (p90) outliers start: 37 outliers final: 31 residues processed: 181 average time/residue: 0.0825 time to fit residues: 20.5553 Evaluate side-chains 176 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 261 ASN Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain R residue 358 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 84 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 101 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.082316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.061989 restraints weight = 27146.921| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.56 r_work: 0.2862 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9327 Z= 0.221 Angle : 0.721 11.770 12662 Z= 0.359 Chirality : 0.044 0.221 1448 Planarity : 0.004 0.064 1592 Dihedral : 7.131 161.681 1293 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.02 % Allowed : 19.46 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.72 (0.25), residues: 1159 helix: 1.93 (0.25), residues: 415 sheet: 0.12 (0.32), residues: 274 loop : -0.57 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 208 TYR 0.017 0.002 TYR R 103 PHE 0.016 0.002 PHE B 234 TRP 0.013 0.002 TRP B 82 HIS 0.012 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 ( 9324) covalent geometry : angle 0.72015 / 0.36 (12656) SS BOND : bond 0.00786 / 0.38 ( 3) SS BOND : angle 1.61565 / 0.79 ( 6) hydrogen bonds : bond 0.04304 / 2.91 ( 472) hydrogen bonds : angle 4.90845 / 3.51 ( 1350) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8415 (tpp) cc_final: 0.7496 (tpp) REVERT: A 247 MET cc_start: 0.9292 (ttm) cc_final: 0.9023 (mtp) REVERT: A 256 ASN cc_start: 0.9490 (t0) cc_final: 0.9052 (t0) REVERT: A 297 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8870 (pp20) REVERT: A 333 GLN cc_start: 0.9449 (tp-100) cc_final: 0.9249 (pm20) REVERT: A 337 ASP cc_start: 0.9150 (t70) cc_final: 0.8927 (p0) REVERT: B 10 GLU cc_start: 0.9476 (tp30) cc_final: 0.9220 (tp30) REVERT: B 23 LYS cc_start: 0.9074 (mttt) cc_final: 0.8794 (mttt) REVERT: B 59 TYR cc_start: 0.8966 (m-10) cc_final: 0.8662 (m-80) REVERT: B 270 ILE cc_start: 0.9458 (pt) cc_final: 0.9158 (mp) REVERT: D 77 ASN cc_start: 0.8817 (m-40) cc_final: 0.8506 (m-40) REVERT: D 90 ASP cc_start: 0.9185 (m-30) cc_final: 0.8961 (m-30) REVERT: D 93 MET cc_start: 0.8692 (tpp) cc_final: 0.8296 (tpp) REVERT: D 189 ASP cc_start: 0.8870 (p0) cc_final: 0.8564 (t0) REVERT: D 211 ASP cc_start: 0.8047 (t0) cc_final: 0.7811 (t0) REVERT: D 219 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8647 (pp30) REVERT: R 85 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8983 (mm) REVERT: R 112 ASP cc_start: 0.8981 (m-30) cc_final: 0.8685 (t70) REVERT: R 149 ASP cc_start: 0.8599 (m-30) cc_final: 0.8091 (t70) REVERT: R 180 MET cc_start: 0.9371 (tmm) cc_final: 0.9169 (ppp) REVERT: R 187 LYS cc_start: 0.8805 (tmtt) cc_final: 0.8384 (mttp) REVERT: R 207 MET cc_start: 0.9390 (mmt) cc_final: 0.8889 (mmm) REVERT: R 243 MET cc_start: 0.8875 (tpp) cc_final: 0.8540 (tpp) REVERT: R 249 MET cc_start: 0.8989 (tpp) cc_final: 0.8221 (tpt) REVERT: R 331 ASP cc_start: 0.8962 (m-30) cc_final: 0.8389 (t0) REVERT: R 357 SER cc_start: 0.8944 (m) cc_final: 0.8624 (p) REVERT: R 371 PHE cc_start: 0.8931 (t80) cc_final: 0.8379 (t80) outliers start: 39 outliers final: 35 residues processed: 171 average time/residue: 0.0866 time to fit residues: 20.1386 Evaluate side-chains 171 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 261 ASN Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 328 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 101 optimal weight: 9.9990 chunk 25 optimal weight: 0.0870 chunk 29 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.083901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.063625 restraints weight = 26811.184| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.59 r_work: 0.2901 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9327 Z= 0.139 Angle : 0.700 11.976 12662 Z= 0.343 Chirality : 0.043 0.251 1448 Planarity : 0.003 0.069 1592 Dihedral : 7.052 164.823 1293 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.12 % Allowed : 20.29 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.84 (0.25), residues: 1159 helix: 2.04 (0.25), residues: 415 sheet: 0.28 (0.32), residues: 270 loop : -0.57 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 208 TYR 0.013 0.001 TYR R 103 PHE 0.016 0.001 PHE A 354 TRP 0.013 0.001 TRP R 134 HIS 0.009 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 9324) covalent geometry : angle 0.69987 / 0.34 (12656) SS BOND : bond 0.00542 / 0.26 ( 3) SS BOND : angle 1.07749 / 0.53 ( 6) hydrogen bonds : bond 0.03972 / 2.70 ( 472) hydrogen bonds : angle 4.81614 / 3.44 ( 1350) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8344 (tpp) cc_final: 0.7482 (tpp) REVERT: A 247 MET cc_start: 0.9255 (ttm) cc_final: 0.8990 (mtp) REVERT: A 256 ASN cc_start: 0.9418 (t0) cc_final: 0.9054 (t0) REVERT: A 297 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8850 (pp20) REVERT: A 333 GLN cc_start: 0.9441 (tp-100) cc_final: 0.9220 (pm20) REVERT: A 337 ASP cc_start: 0.9090 (t70) cc_final: 0.8877 (p0) REVERT: B 3 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7938 (tm-30) REVERT: B 4 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8753 (tp) REVERT: B 7 LEU cc_start: 0.9384 (mt) cc_final: 0.9144 (mm) REVERT: B 8 ARG cc_start: 0.9409 (ttm110) cc_final: 0.8460 (mtt-85) REVERT: B 10 GLU cc_start: 0.9484 (tp30) cc_final: 0.9223 (tp30) REVERT: B 23 LYS cc_start: 0.9030 (mttt) cc_final: 0.8701 (mttt) REVERT: B 59 TYR cc_start: 0.8928 (m-10) cc_final: 0.8583 (m-80) REVERT: B 261 LEU cc_start: 0.9265 (tp) cc_final: 0.8947 (tp) REVERT: B 270 ILE cc_start: 0.9413 (pt) cc_final: 0.9101 (mp) REVERT: B 292 PHE cc_start: 0.9188 (m-10) cc_final: 0.8836 (m-10) REVERT: C 58 GLU cc_start: 0.9575 (pm20) cc_final: 0.9337 (pm20) REVERT: D 77 ASN cc_start: 0.8906 (m-40) cc_final: 0.8605 (m-40) REVERT: D 90 ASP cc_start: 0.9000 (m-30) cc_final: 0.8613 (m-30) REVERT: D 93 MET cc_start: 0.8664 (tpp) cc_final: 0.8273 (tpp) REVERT: D 189 ASP cc_start: 0.8858 (p0) cc_final: 0.8563 (t0) REVERT: D 211 ASP cc_start: 0.7972 (t0) cc_final: 0.7705 (t0) REVERT: D 219 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8685 (pp30) REVERT: D 222 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8636 (pt0) REVERT: R 85 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9000 (mm) REVERT: R 112 ASP cc_start: 0.9010 (m-30) cc_final: 0.8739 (t70) REVERT: R 149 ASP cc_start: 0.8427 (m-30) cc_final: 0.8027 (t70) REVERT: R 187 LYS cc_start: 0.8657 (tmtt) cc_final: 0.8342 (mttp) REVERT: R 207 MET cc_start: 0.9400 (mmt) cc_final: 0.8865 (mmm) REVERT: R 243 MET cc_start: 0.8920 (tpp) cc_final: 0.8594 (tpp) REVERT: R 249 MET cc_start: 0.8934 (tpp) cc_final: 0.8249 (tpt) REVERT: R 263 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8139 (tt) REVERT: R 331 ASP cc_start: 0.9079 (m-30) cc_final: 0.8549 (t0) REVERT: R 345 PHE cc_start: 0.8474 (t80) cc_final: 0.8078 (t80) REVERT: R 357 SER cc_start: 0.8927 (m) cc_final: 0.8599 (p) REVERT: R 371 PHE cc_start: 0.8940 (t80) cc_final: 0.8417 (t80) REVERT: R 373 HIS cc_start: 0.8897 (p90) cc_final: 0.8657 (p90) outliers start: 40 outliers final: 34 residues processed: 185 average time/residue: 0.0792 time to fit residues: 19.6535 Evaluate side-chains 181 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 261 ASN Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 328 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 6 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.083501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.063272 restraints weight = 26928.054| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.58 r_work: 0.2894 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9327 Z= 0.159 Angle : 0.718 12.593 12662 Z= 0.352 Chirality : 0.043 0.255 1448 Planarity : 0.004 0.072 1592 Dihedral : 7.025 165.719 1292 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.36 % Favored : 96.55 % Rotamer: Outliers : 4.02 % Allowed : 20.49 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.81 (0.25), residues: 1159 helix: 2.01 (0.25), residues: 415 sheet: 0.22 (0.32), residues: 272 loop : -0.55 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 208 TYR 0.012 0.001 TYR R 103 PHE 0.015 0.001 PHE A 354 TRP 0.012 0.001 TRP R 134 HIS 0.009 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 9324) covalent geometry : angle 0.71745 / 0.35 (12656) SS BOND : bond 0.00668 / 0.32 ( 3) SS BOND : angle 1.28293 / 0.61 ( 6) hydrogen bonds : bond 0.04000 / 2.71 ( 472) hydrogen bonds : angle 4.78757 / 3.42 ( 1350) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 144 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8379 (tpp) cc_final: 0.7522 (tpp) REVERT: A 247 MET cc_start: 0.9249 (ttm) cc_final: 0.8989 (mtp) REVERT: A 256 ASN cc_start: 0.9417 (t0) cc_final: 0.9078 (t0) REVERT: A 297 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8862 (pp20) REVERT: A 333 GLN cc_start: 0.9434 (tp-100) cc_final: 0.9024 (pt0) REVERT: A 337 ASP cc_start: 0.9093 (t70) cc_final: 0.8737 (m-30) REVERT: B 4 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8746 (tp) REVERT: B 8 ARG cc_start: 0.9413 (ttm110) cc_final: 0.8471 (mtt-85) REVERT: B 10 GLU cc_start: 0.9488 (tp30) cc_final: 0.9234 (tp30) REVERT: B 23 LYS cc_start: 0.9042 (mttt) cc_final: 0.8710 (mttt) REVERT: B 59 TYR cc_start: 0.8940 (m-10) cc_final: 0.8584 (m-80) REVERT: B 261 LEU cc_start: 0.9287 (tp) cc_final: 0.8977 (tp) REVERT: B 270 ILE cc_start: 0.9420 (pt) cc_final: 0.9112 (mp) REVERT: C 58 GLU cc_start: 0.9557 (pm20) cc_final: 0.9322 (pm20) REVERT: D 77 ASN cc_start: 0.8899 (m-40) cc_final: 0.8600 (m-40) REVERT: D 90 ASP cc_start: 0.8970 (m-30) cc_final: 0.8609 (m-30) REVERT: D 93 MET cc_start: 0.8669 (tpp) cc_final: 0.8332 (tpp) REVERT: D 189 ASP cc_start: 0.8860 (p0) cc_final: 0.8571 (t0) REVERT: D 211 ASP cc_start: 0.7980 (t0) cc_final: 0.7703 (t0) REVERT: D 219 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8693 (pp30) REVERT: R 85 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8993 (mm) REVERT: R 112 ASP cc_start: 0.9014 (m-30) cc_final: 0.8743 (t70) REVERT: R 149 ASP cc_start: 0.8361 (m-30) cc_final: 0.7986 (t70) REVERT: R 180 MET cc_start: 0.9136 (ppp) cc_final: 0.8931 (ppp) REVERT: R 187 LYS cc_start: 0.8674 (tmtt) cc_final: 0.8351 (mttp) REVERT: R 207 MET cc_start: 0.9390 (mmt) cc_final: 0.8856 (mmm) REVERT: R 243 MET cc_start: 0.8936 (tpp) cc_final: 0.8600 (tpp) REVERT: R 249 MET cc_start: 0.8894 (tpp) cc_final: 0.8229 (tpt) REVERT: R 331 ASP cc_start: 0.9063 (m-30) cc_final: 0.8530 (t0) REVERT: R 345 PHE cc_start: 0.8481 (t80) cc_final: 0.8080 (t80) REVERT: R 357 SER cc_start: 0.8926 (m) cc_final: 0.8597 (p) REVERT: R 371 PHE cc_start: 0.8901 (t80) cc_final: 0.8373 (t80) outliers start: 39 outliers final: 35 residues processed: 175 average time/residue: 0.1035 time to fit residues: 24.6763 Evaluate side-chains 180 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 261 ASN Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 328 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 96 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 27 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.084754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.064598 restraints weight = 26560.396| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.58 r_work: 0.2926 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9327 Z= 0.131 Angle : 0.709 12.682 12662 Z= 0.346 Chirality : 0.043 0.258 1448 Planarity : 0.004 0.071 1592 Dihedral : 6.898 166.466 1288 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.11 % Favored : 96.81 % Rotamer: Outliers : 3.60 % Allowed : 21.11 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1159 helix: 2.02 (0.25), residues: 416 sheet: 0.31 (0.32), residues: 274 loop : -0.56 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 208 TYR 0.012 0.001 TYR A 320 PHE 0.015 0.001 PHE A 354 TRP 0.015 0.001 TRP R 134 HIS 0.008 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 9324) covalent geometry : angle 0.70887 / 0.35 (12656) SS BOND : bond 0.00508 / 0.25 ( 3) SS BOND : angle 1.03084 / 0.53 ( 6) hydrogen bonds : bond 0.03809 / 2.58 ( 472) hydrogen bonds : angle 4.73483 / 3.38 ( 1350) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1789.47 seconds wall clock time: 31 minutes 32.23 seconds (1892.23 seconds total)