Starting phenix.real_space_refine on Thu Jul 2 14:46:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/20zj_67432/07_2026/20zj_67432.cif Found real_map, /net/cci-nas-00/data/ceres_data/20zj_67432/07_2026/20zj_67432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/20zj_67432/07_2026/20zj_67432.cif" } default_model = "/net/cci-nas-00/data/ceres_data/20zj_67432/07_2026/20zj_67432.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/20zj_67432/07_2026/20zj_67432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/20zj_67432/07_2026/20zj_67432.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 5581 2.51 5 N 1491 2.21 5 O 1626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 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: 8758 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1758 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2585 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 410 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 49} 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: 2190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2190 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 266} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 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 Time building chain proxies: 1.93, per 1000 atoms: 0.22 Number of scatterers: 8758 At special positions: 0 Unit cell: (91.3, 119.52, 126.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1626 8.00 N 1491 7.00 C 5581 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.76 Conformation dependent library (CDL) restraints added in 410.6 milliseconds 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 40.4% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.249A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.841A 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 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.126A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.125A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.583A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.639A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 53 through 56 removed outlier: 4.283A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' 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 62 through 91 Processing helix chain 'R' and resid 96 through 100 removed outlier: 3.538A pdb=" N THR R 100 " --> pdb=" O LEU R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 129 Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 140 through 172 Processing helix chain 'R' and resid 172 through 178 removed outlier: 3.704A pdb=" N ALA R 176 " --> pdb=" O HIS R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 201 removed outlier: 3.907A pdb=" N ARG R 184 " --> pdb=" O MET R 180 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE R 189 " --> pdb=" O THR R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 273 Proline residue: R 248 - end of helix Processing helix chain 'R' and resid 293 through 329 removed outlier: 4.262A pdb=" N VAL R 313 " --> pdb=" O VAL R 309 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 335 through 367 removed outlier: 3.627A pdb=" N SER R 356 " --> pdb=" O LEU R 352 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER R 357 " --> pdb=" O PHE R 353 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR R 358 " --> pdb=" O TYR R 354 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 369 through 383 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 9.370A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 4.823A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.714A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.123A 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: 3.609A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.725A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.569A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.246A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.189A 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: 4.453A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.339A 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 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.881A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR D 59 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.106A 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: 6.495A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1362 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: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1440 1.32 - 1.44: 2455 1.44 - 1.57: 4952 1.57 - 1.69: 3 1.69 - 1.82: 88 Bond restraints: 8938 Sorted by residual: bond pdb=" CG PHE R 174 " pdb=" CD1 PHE R 174 " ideal model delta sigma weight residual 1.384 1.255 0.129 2.10e-02 2.27e+03 3.75e+01 bond pdb=" CA SER D 181 " pdb=" CB SER D 181 " ideal model delta sigma weight residual 1.534 1.448 0.086 1.45e-02 4.76e+03 3.50e+01 bond pdb=" CG PHE R 174 " pdb=" CD2 PHE R 174 " ideal model delta sigma weight residual 1.384 1.507 -0.123 2.10e-02 2.27e+03 3.40e+01 bond pdb=" CA SER B 161 " pdb=" CB SER B 161 " ideal model delta sigma weight residual 1.534 1.432 0.102 1.77e-02 3.19e+03 3.34e+01 bond pdb=" CE1 HIS B 142 " pdb=" NE2 HIS B 142 " ideal model delta sigma weight residual 1.321 1.266 0.055 1.00e-02 1.00e+04 2.97e+01 ... (remaining 8933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 10053 2.77 - 5.55: 1772 5.55 - 8.32: 225 8.32 - 11.09: 50 11.09 - 13.87: 9 Bond angle restraints: 12109 Sorted by residual: angle pdb=" CA PHE A 354 " pdb=" CB PHE A 354 " pdb=" CG PHE A 354 " ideal model delta sigma weight residual 113.80 124.35 -10.55 1.00e+00 1.00e+00 1.11e+02 angle pdb=" NE ARG R 184 " pdb=" CZ ARG R 184 " pdb=" NH2 ARG R 184 " ideal model delta sigma weight residual 119.20 110.61 8.59 9.00e-01 1.23e+00 9.11e+01 angle pdb=" N PRO R 173 " pdb=" CA PRO R 173 " pdb=" CB PRO R 173 " ideal model delta sigma weight residual 103.25 93.52 9.73 1.05e+00 9.07e-01 8.58e+01 angle pdb=" C ARG D 179 " pdb=" CA ARG D 179 " pdb=" CB ARG D 179 " ideal model delta sigma weight residual 111.89 124.54 -12.65 1.42e+00 4.96e-01 7.93e+01 angle pdb=" N VAL R 295 " pdb=" CA VAL R 295 " pdb=" CB VAL R 295 " ideal model delta sigma weight residual 110.54 122.46 -11.92 1.36e+00 5.41e-01 7.69e+01 ... (remaining 12104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 4713 17.81 - 35.62: 398 35.62 - 53.44: 147 53.44 - 71.25: 27 71.25 - 89.06: 10 Dihedral angle restraints: 5295 sinusoidal: 2028 harmonic: 3267 Sorted by residual: dihedral pdb=" CD ARG R 182 " pdb=" NE ARG R 182 " pdb=" CZ ARG R 182 " pdb=" NH1 ARG R 182 " ideal model delta sinusoidal sigma weight residual 0.00 89.06 -89.06 1 1.00e+01 1.00e-02 9.44e+01 dihedral pdb=" C TRP R 129 " pdb=" N TRP R 129 " pdb=" CA TRP R 129 " pdb=" CB TRP R 129 " ideal model delta harmonic sigma weight residual -122.60 -142.42 19.82 0 2.50e+00 1.60e-01 6.29e+01 dihedral pdb=" N TRP R 129 " pdb=" C TRP R 129 " pdb=" CA TRP R 129 " pdb=" CB TRP R 129 " ideal model delta harmonic sigma weight residual 122.80 142.38 -19.58 0 2.50e+00 1.60e-01 6.13e+01 ... (remaining 5292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 1120 0.158 - 0.316: 238 0.316 - 0.473: 24 0.473 - 0.631: 5 0.631 - 0.788: 2 Chirality restraints: 1389 Sorted by residual: chirality pdb=" CA TRP R 129 " pdb=" N TRP R 129 " pdb=" C TRP R 129 " pdb=" CB TRP R 129 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.55e+01 chirality pdb=" CA ASN R 360 " pdb=" N ASN R 360 " pdb=" C ASN R 360 " pdb=" CB ASN R 360 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CG LEU D 11 " pdb=" CB LEU D 11 " pdb=" CD1 LEU D 11 " pdb=" CD2 LEU D 11 " both_signs ideal model delta sigma weight residual False -2.59 -1.96 -0.63 2.00e-01 2.50e+01 9.77e+00 ... (remaining 1386 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 184 " -0.747 9.50e-02 1.11e+02 3.44e-01 1.50e+02 pdb=" NE ARG R 184 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG R 184 " 0.165 2.00e-02 2.50e+03 pdb=" NH1 ARG R 184 " -0.053 2.00e-02 2.50e+03 pdb=" NH2 ARG R 184 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 182 " -1.114 9.50e-02 1.11e+02 4.99e-01 1.50e+02 pdb=" NE ARG R 182 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG R 182 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG R 182 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG R 182 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 299 " 0.606 9.50e-02 1.11e+02 2.78e-01 9.24e+01 pdb=" NE ARG R 299 " 0.003 2.00e-02 2.50e+03 pdb=" CZ ARG R 299 " -0.126 2.00e-02 2.50e+03 pdb=" NH1 ARG R 299 " 0.038 2.00e-02 2.50e+03 pdb=" NH2 ARG R 299 " 0.058 2.00e-02 2.50e+03 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1136 2.79 - 3.32: 8786 3.32 - 3.85: 14555 3.85 - 4.37: 17677 4.37 - 4.90: 29313 Nonbonded interactions: 71467 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.268 3.040 nonbonded pdb=" O LEU R 97 " pdb=" OG1 THR R 100 " model vdw 2.320 3.040 nonbonded pdb=" O TYR R 103 " pdb=" N GLY R 106 " model vdw 2.325 3.120 nonbonded pdb=" O GLN R 98 " pdb=" OG SER R 99 " model vdw 2.327 3.040 nonbonded pdb=" O THR D 160 " pdb=" OG1 THR D 160 " model vdw 2.370 3.040 ... (remaining 71462 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: 2.080 Set stop_for_unknowns flag: 0.010 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: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 8.800 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 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 0.129 8938 Z= 0.771 Angle : 2.215 13.867 12109 Z= 1.513 Chirality : 0.132 0.788 1389 Planarity : 0.024 0.499 1520 Dihedral : 16.145 89.062 3185 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 9.68 % Allowed : 8.11 % Favored : 82.21 % Cbeta Deviations : 3.79 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.23), residues: 1099 helix: 1.56 (0.24), residues: 403 sheet: 0.29 (0.31), residues: 237 loop : -1.28 (0.25), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.156 0.011 ARG R 184 TYR 0.050 0.009 TYR D 178 PHE 0.045 0.007 PHE R 174 TRP 0.039 0.009 TRP B 99 HIS 0.023 0.005 HIS R 172 Details of bonding type rmsd/Z covalent geometry : bond 0.01213 / 0.77 ( 8938) covalent geometry : angle 2.21485 / 1.51 (12109) hydrogen bonds : bond 0.19047 / 12.97 ( 479) hydrogen bonds : angle 7.45135 / 5.26 ( 1362) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 395 time to evaluate : 0.394 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 252 SER cc_start: 0.9266 (t) cc_final: 0.8955 (t) REVERT: A 275 GLU cc_start: 0.9059 (tt0) cc_final: 0.8226 (tp30) REVERT: A 308 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8581 (mt-10) REVERT: A 346 ASN cc_start: 0.8717 (m-40) cc_final: 0.8501 (m110) REVERT: B 8 ARG cc_start: 0.8899 (ttm-80) cc_final: 0.8540 (tmm160) REVERT: B 10 GLU cc_start: 0.9353 (tt0) cc_final: 0.8684 (tt0) REVERT: B 16 ASN cc_start: 0.9084 (t0) cc_final: 0.8828 (m-40) REVERT: B 76 ASP cc_start: 0.8072 (p0) cc_final: 0.7777 (p0) REVERT: B 228 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8541 (p0) REVERT: C 22 GLU cc_start: 0.8479 (tt0) cc_final: 0.8246 (mt-10) REVERT: C 36 ASP cc_start: 0.9289 (t0) cc_final: 0.8930 (m-30) REVERT: D 231 THR cc_start: 0.8660 (m) cc_final: 0.8451 (p) REVERT: D 234 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8049 (pp20) REVERT: R 123 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.7223 (pp20) REVERT: R 124 LEU cc_start: 0.7838 (tp) cc_final: 0.7103 (tp) REVERT: R 142 ARG cc_start: -0.1401 (OUTLIER) cc_final: -0.4490 (ttm170) REVERT: R 151 CYS cc_start: 0.8838 (m) cc_final: 0.8311 (p) REVERT: R 152 THR cc_start: 0.8148 (OUTLIER) cc_final: 0.7871 (t) REVERT: R 153 TYR cc_start: 0.5946 (m-80) cc_final: 0.5698 (m-80) REVERT: R 187 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6724 (mmtm) REVERT: R 225 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8195 (t) REVERT: R 263 LEU cc_start: 0.7906 (pp) cc_final: 0.7679 (pp) REVERT: R 334 TRP cc_start: 0.1169 (OUTLIER) cc_final: 0.0631 (m-10) REVERT: R 338 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.6888 (mm) REVERT: R 364 TYR cc_start: 0.6937 (m-10) cc_final: 0.6573 (m-10) REVERT: R 366 LEU cc_start: 0.0289 (OUTLIER) cc_final: -0.0044 (mt) outliers start: 92 outliers final: 12 residues processed: 452 average time/residue: 0.4877 time to fit residues: 235.7634 Evaluate side-chains 265 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 244 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 142 ARG Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 172 HIS Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 187 LYS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 334 TRP Chi-restraints excluded: chain R residue 338 LEU Chi-restraints excluded: chain R residue 342 TYR Chi-restraints excluded: chain R residue 366 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 347 ASN B 75 GLN B 142 HIS ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN C 18 GLN D 174 GLN ** R 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 240 ASN R 320 HIS ** R 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.099871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.072471 restraints weight = 19751.328| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.58 r_work: 0.2950 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8938 Z= 0.207 Angle : 0.781 16.055 12109 Z= 0.411 Chirality : 0.050 0.201 1389 Planarity : 0.006 0.060 1520 Dihedral : 8.230 66.551 1259 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 8.11 % Allowed : 24.11 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.24), residues: 1099 helix: 2.00 (0.24), residues: 410 sheet: 0.50 (0.30), residues: 269 loop : -1.16 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 21 TYR 0.026 0.002 TYR R 339 PHE 0.060 0.003 PHE R 375 TRP 0.022 0.002 TRP R 129 HIS 0.006 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.21 ( 8938) covalent geometry : angle 0.78111 / 0.41 (12109) hydrogen bonds : bond 0.05339 / 3.48 ( 479) hydrogen bonds : angle 5.42204 / 3.91 ( 1362) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 238 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8344 (ttp80) cc_final: 0.7976 (ttm-80) REVERT: A 25 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: A 32 ARG cc_start: 0.8488 (tpp80) cc_final: 0.8259 (tpp80) REVERT: A 53 MET cc_start: 0.7832 (mmp) cc_final: 0.7407 (mpp) REVERT: A 197 LYS cc_start: 0.8551 (mtpt) cc_final: 0.8224 (mtpt) REVERT: A 207 GLU cc_start: 0.8660 (tp30) cc_final: 0.8330 (tp30) REVERT: A 209 LYS cc_start: 0.9194 (mppt) cc_final: 0.8876 (mmtm) REVERT: A 229 ASP cc_start: 0.8701 (m-30) cc_final: 0.8344 (m-30) REVERT: A 245 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8700 (tm-30) REVERT: A 269 ASN cc_start: 0.9148 (m-40) cc_final: 0.8802 (m-40) REVERT: A 273 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8858 (tm) REVERT: B 15 LYS cc_start: 0.8869 (mttp) cc_final: 0.8561 (mttp) REVERT: B 294 CYS cc_start: 0.8743 (m) cc_final: 0.8114 (t) REVERT: C 13 ARG cc_start: 0.8461 (ttm110) cc_final: 0.8055 (ptp-110) REVERT: C 36 ASP cc_start: 0.9056 (t0) cc_final: 0.8633 (m-30) REVERT: C 46 LYS cc_start: 0.9232 (tppt) cc_final: 0.8936 (ttmm) REVERT: D 62 ASP cc_start: 0.8916 (m-30) cc_final: 0.8672 (m-30) REVERT: D 72 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.7992 (ptp-170) REVERT: D 118 THR cc_start: 0.8852 (t) cc_final: 0.8579 (p) REVERT: R 142 ARG cc_start: -0.2366 (OUTLIER) cc_final: -0.3040 (ttt180) REVERT: R 183 SER cc_start: 0.8432 (m) cc_final: 0.7891 (p) REVERT: R 187 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.6762 (mmtm) REVERT: R 340 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7455 (m-30) REVERT: R 343 HIS cc_start: 0.8558 (m-70) cc_final: 0.8277 (m-70) REVERT: R 375 PHE cc_start: 0.7211 (p90) cc_final: 0.6954 (p90) REVERT: L 12 ILE cc_start: 0.2877 (OUTLIER) cc_final: 0.2239 (pp) outliers start: 77 outliers final: 22 residues processed: 290 average time/residue: 0.4632 time to fit residues: 144.0425 Evaluate side-chains 211 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 174 GLN Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 142 ARG Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 187 LYS Chi-restraints excluded: chain R residue 340 ASP Chi-restraints excluded: chain R residue 358 THR Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain L residue 12 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 86 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 306 GLN A 346 ASN A 347 ASN B 176 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN C 11 GLN C 24 ASN D 3 GLN D 174 GLN R 98 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.097343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.069775 restraints weight = 19554.215| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.56 r_work: 0.2889 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.6828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8938 Z= 0.187 Angle : 0.744 12.455 12109 Z= 0.390 Chirality : 0.047 0.207 1389 Planarity : 0.005 0.050 1520 Dihedral : 6.507 56.624 1235 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 7.68 % Allowed : 25.68 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.25), residues: 1099 helix: 1.80 (0.25), residues: 415 sheet: 0.60 (0.31), residues: 263 loop : -1.13 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 205 TYR 0.026 0.002 TYR R 339 PHE 0.031 0.002 PHE R 375 TRP 0.023 0.002 TRP B 82 HIS 0.004 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 ( 8938) covalent geometry : angle 0.74353 / 0.39 (12109) hydrogen bonds : bond 0.04867 / 3.20 ( 479) hydrogen bonds : angle 5.07720 / 3.63 ( 1362) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 193 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8216 (mt-10) REVERT: A 188 HIS cc_start: 0.8880 (m90) cc_final: 0.8200 (m90) REVERT: A 197 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8265 (mtpt) REVERT: A 209 LYS cc_start: 0.9240 (mppt) cc_final: 0.9034 (mmtm) REVERT: A 229 ASP cc_start: 0.8672 (m-30) cc_final: 0.8416 (m-30) REVERT: A 234 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6593 (tm) REVERT: A 269 ASN cc_start: 0.9367 (m-40) cc_final: 0.8772 (m-40) REVERT: B 9 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8528 (mm-40) REVERT: B 15 LYS cc_start: 0.8857 (mttp) cc_final: 0.8500 (mttp) REVERT: B 159 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8453 (p) REVERT: B 294 CYS cc_start: 0.8646 (m) cc_final: 0.8226 (t) REVERT: B 329 THR cc_start: 0.9055 (t) cc_final: 0.8747 (p) REVERT: C 36 ASP cc_start: 0.9078 (t0) cc_final: 0.8656 (m-30) REVERT: C 46 LYS cc_start: 0.9338 (tppt) cc_final: 0.9102 (ttmm) REVERT: D 19 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.9111 (ttmm) REVERT: D 46 GLU cc_start: 0.9241 (tt0) cc_final: 0.9041 (pt0) REVERT: D 72 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.7648 (ptp90) REVERT: D 203 THR cc_start: 0.9210 (m) cc_final: 0.8996 (p) REVERT: R 120 MET cc_start: 0.8622 (tpt) cc_final: 0.8125 (tpt) REVERT: R 123 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7923 (pp20) REVERT: R 124 LEU cc_start: 0.8811 (tp) cc_final: 0.8480 (tp) REVERT: R 142 ARG cc_start: -0.2354 (OUTLIER) cc_final: -0.2783 (ttt180) REVERT: R 183 SER cc_start: 0.8496 (m) cc_final: 0.7997 (p) REVERT: R 187 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.6582 (mmtm) REVERT: R 188 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7054 (t80) REVERT: R 242 PHE cc_start: 0.8944 (t80) cc_final: 0.8356 (m-80) REVERT: R 247 PHE cc_start: 0.8245 (t80) cc_final: 0.7916 (t80) REVERT: R 262 LYS cc_start: 0.8396 (ttmt) cc_final: 0.8024 (ttpt) REVERT: R 339 TYR cc_start: 0.5601 (OUTLIER) cc_final: 0.5386 (p90) REVERT: R 343 HIS cc_start: 0.8677 (m-70) cc_final: 0.8393 (m-70) REVERT: L 12 ILE cc_start: 0.2665 (OUTLIER) cc_final: 0.2200 (pp) REVERT: L 13 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6754 (mm) outliers start: 73 outliers final: 27 residues processed: 244 average time/residue: 0.4761 time to fit residues: 123.8977 Evaluate side-chains 205 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 142 ARG Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 187 LYS Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 339 TYR Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain R residue 358 THR Chi-restraints excluded: chain R residue 360 ASN Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 85 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 346 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS D 3 GLN R 104 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.096667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.069210 restraints weight = 19795.548| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.56 r_work: 0.2878 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.7396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8938 Z= 0.157 Angle : 0.688 11.460 12109 Z= 0.362 Chirality : 0.045 0.209 1389 Planarity : 0.005 0.055 1520 Dihedral : 5.971 55.914 1231 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 6.84 % Allowed : 27.16 % Favored : 66.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.25), residues: 1099 helix: 1.85 (0.26), residues: 414 sheet: 0.54 (0.31), residues: 266 loop : -0.98 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 205 TYR 0.022 0.001 TYR R 339 PHE 0.022 0.002 PHE R 375 TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 8938) covalent geometry : angle 0.68818 / 0.36 (12109) hydrogen bonds : bond 0.04445 / 2.95 ( 479) hydrogen bonds : angle 4.88470 / 3.50 ( 1362) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 188 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8883 (t0) cc_final: 0.8476 (m-30) REVERT: A 25 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8267 (mt-10) REVERT: A 197 LYS cc_start: 0.8735 (mtpt) cc_final: 0.8358 (mtpt) REVERT: A 229 ASP cc_start: 0.8780 (m-30) cc_final: 0.8476 (m-30) REVERT: A 234 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6533 (tm) REVERT: A 276 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8524 (tm-30) REVERT: B 9 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8552 (mm-40) REVERT: B 15 LYS cc_start: 0.8909 (mttp) cc_final: 0.8676 (mttp) REVERT: B 159 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8608 (p) REVERT: B 197 ARG cc_start: 0.8522 (tpt170) cc_final: 0.7926 (ttm-80) REVERT: B 246 ASP cc_start: 0.9203 (t70) cc_final: 0.8735 (m-30) REVERT: B 294 CYS cc_start: 0.8659 (m) cc_final: 0.8314 (t) REVERT: B 329 THR cc_start: 0.9067 (t) cc_final: 0.8857 (p) REVERT: C 9 ILE cc_start: 0.8907 (pp) cc_final: 0.7830 (pp) REVERT: C 13 ARG cc_start: 0.8869 (ttp-110) cc_final: 0.8456 (ptp-170) REVERT: C 36 ASP cc_start: 0.9064 (t0) cc_final: 0.8688 (m-30) REVERT: C 46 LYS cc_start: 0.9319 (tppt) cc_final: 0.9061 (ttmm) REVERT: D 51 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8188 (tt) REVERT: D 72 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8932 (ptm160) REVERT: D 73 ASP cc_start: 0.8541 (t0) cc_final: 0.7959 (t0) REVERT: D 211 ASP cc_start: 0.8506 (t0) cc_final: 0.8195 (t0) REVERT: R 120 MET cc_start: 0.8701 (tpt) cc_final: 0.8323 (tpt) REVERT: R 123 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8087 (pp20) REVERT: R 142 ARG cc_start: -0.2211 (OUTLIER) cc_final: -0.2464 (ttt180) REVERT: R 153 TYR cc_start: 0.7317 (m-80) cc_final: 0.6941 (m-80) REVERT: R 183 SER cc_start: 0.8481 (m) cc_final: 0.7942 (p) REVERT: R 187 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.6372 (mmtt) REVERT: R 188 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.6983 (t80) REVERT: R 242 PHE cc_start: 0.8899 (t80) cc_final: 0.8179 (m-80) REVERT: R 339 TYR cc_start: 0.5801 (OUTLIER) cc_final: 0.5508 (p90) REVERT: R 375 PHE cc_start: 0.7240 (p90) cc_final: 0.6792 (p90) REVERT: L 12 ILE cc_start: 0.2466 (OUTLIER) cc_final: 0.1964 (pp) REVERT: L 13 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6656 (mm) outliers start: 65 outliers final: 27 residues processed: 236 average time/residue: 0.4466 time to fit residues: 112.8069 Evaluate side-chains 219 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 142 ARG Chi-restraints excluded: chain R residue 170 ILE Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 187 LYS Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 334 TRP Chi-restraints excluded: chain R residue 339 TYR Chi-restraints excluded: chain R residue 358 THR Chi-restraints excluded: chain R residue 360 ASN Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 102 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 95 optimal weight: 0.0870 chunk 87 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 0.0470 chunk 74 optimal weight: 0.7980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 346 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN D 3 GLN D 174 GLN R 104 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.097817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.070446 restraints weight = 19637.694| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.55 r_work: 0.2912 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.7733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8938 Z= 0.133 Angle : 0.672 10.593 12109 Z= 0.350 Chirality : 0.043 0.206 1389 Planarity : 0.005 0.056 1520 Dihedral : 5.619 53.920 1231 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.28 % Favored : 96.63 % Rotamer: Outliers : 5.79 % Allowed : 28.63 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.68 (0.25), residues: 1099 helix: 1.82 (0.25), residues: 415 sheet: 0.44 (0.31), residues: 266 loop : -0.92 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 205 TYR 0.022 0.001 TYR A 290 PHE 0.022 0.001 PHE R 146 TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 8938) covalent geometry : angle 0.67241 / 0.35 (12109) hydrogen bonds : bond 0.04098 / 2.73 ( 479) hydrogen bonds : angle 4.77175 / 3.42 ( 1362) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 186 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8883 (t0) cc_final: 0.8500 (m-30) REVERT: A 25 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8301 (mt-10) REVERT: A 53 MET cc_start: 0.8386 (mmm) cc_final: 0.8077 (mpp) REVERT: A 197 LYS cc_start: 0.8774 (mtpt) cc_final: 0.8393 (mtpt) REVERT: A 229 ASP cc_start: 0.8763 (m-30) cc_final: 0.8443 (m-30) REVERT: A 234 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6486 (tm) REVERT: A 269 ASN cc_start: 0.9441 (m-40) cc_final: 0.9006 (m-40) REVERT: A 276 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8453 (tm-30) REVERT: B 9 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8567 (mm-40) REVERT: B 15 LYS cc_start: 0.8912 (mttp) cc_final: 0.8677 (mttp) REVERT: B 197 ARG cc_start: 0.8555 (tpt170) cc_final: 0.7960 (ttm-80) REVERT: B 246 ASP cc_start: 0.9123 (t70) cc_final: 0.8667 (m-30) REVERT: B 294 CYS cc_start: 0.8611 (m) cc_final: 0.8305 (t) REVERT: B 329 THR cc_start: 0.9043 (t) cc_final: 0.8828 (p) REVERT: C 9 ILE cc_start: 0.8930 (pp) cc_final: 0.8587 (pp) REVERT: C 13 ARG cc_start: 0.8892 (ttp-110) cc_final: 0.8477 (ptp-170) REVERT: C 36 ASP cc_start: 0.9014 (t0) cc_final: 0.8640 (m-30) REVERT: C 46 LYS cc_start: 0.9309 (tppt) cc_final: 0.9077 (ttmm) REVERT: D 51 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8185 (tt) REVERT: D 211 ASP cc_start: 0.8582 (t0) cc_final: 0.8255 (t0) REVERT: R 123 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8120 (pp20) REVERT: R 153 TYR cc_start: 0.7335 (m-80) cc_final: 0.7061 (m-80) REVERT: R 183 SER cc_start: 0.8448 (m) cc_final: 0.8106 (p) REVERT: R 185 THR cc_start: 0.7751 (OUTLIER) cc_final: 0.7539 (p) REVERT: R 187 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6273 (mmtm) REVERT: R 188 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.7091 (t80) REVERT: R 339 TYR cc_start: 0.5777 (OUTLIER) cc_final: 0.5499 (p90) REVERT: R 343 HIS cc_start: 0.8768 (m-70) cc_final: 0.8553 (m-70) REVERT: R 360 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8324 (p0) REVERT: R 375 PHE cc_start: 0.7195 (p90) cc_final: 0.6778 (p90) REVERT: L 13 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6464 (mp) outliers start: 55 outliers final: 21 residues processed: 226 average time/residue: 0.4955 time to fit residues: 119.5430 Evaluate side-chains 201 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 187 LYS Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 334 TRP Chi-restraints excluded: chain R residue 339 TYR Chi-restraints excluded: chain R residue 358 THR Chi-restraints excluded: chain R residue 360 ASN Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 53 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 7 optimal weight: 0.0370 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 346 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN C 24 ASN C 59 ASN D 3 GLN D 174 GLN R 104 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.097425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.070020 restraints weight = 19720.833| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.54 r_work: 0.2897 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.7914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8938 Z= 0.138 Angle : 0.679 10.695 12109 Z= 0.350 Chirality : 0.044 0.210 1389 Planarity : 0.005 0.056 1520 Dihedral : 5.283 52.963 1227 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.37 % Favored : 96.45 % Rotamer: Outliers : 6.21 % Allowed : 29.47 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.25), residues: 1099 helix: 1.83 (0.25), residues: 413 sheet: 0.51 (0.31), residues: 266 loop : -0.87 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 205 TYR 0.023 0.001 TYR R 339 PHE 0.026 0.002 PHE R 375 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 8938) covalent geometry : angle 0.67906 / 0.35 (12109) hydrogen bonds : bond 0.03943 / 2.65 ( 479) hydrogen bonds : angle 4.70596 / 3.36 ( 1362) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 177 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8880 (t0) cc_final: 0.8496 (m-30) REVERT: A 25 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8288 (mt-10) REVERT: A 53 MET cc_start: 0.8488 (mmm) cc_final: 0.8175 (mpp) REVERT: A 197 LYS cc_start: 0.8770 (mtpt) cc_final: 0.8374 (mtpt) REVERT: A 234 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6468 (tm) REVERT: A 269 ASN cc_start: 0.9473 (m-40) cc_final: 0.9023 (m-40) REVERT: A 276 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8485 (tm-30) REVERT: B 9 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8604 (mm-40) REVERT: B 15 LYS cc_start: 0.8937 (mttp) cc_final: 0.8698 (mttp) REVERT: B 197 ARG cc_start: 0.8578 (tpt170) cc_final: 0.8002 (ttm-80) REVERT: B 246 ASP cc_start: 0.9109 (t70) cc_final: 0.8611 (m-30) REVERT: B 294 CYS cc_start: 0.8602 (m) cc_final: 0.8313 (t) REVERT: B 329 THR cc_start: 0.9045 (t) cc_final: 0.8811 (p) REVERT: C 9 ILE cc_start: 0.8958 (pp) cc_final: 0.8653 (pp) REVERT: C 13 ARG cc_start: 0.8920 (ttp-110) cc_final: 0.8497 (ptp-110) REVERT: C 36 ASP cc_start: 0.9017 (t0) cc_final: 0.8613 (m-30) REVERT: C 46 LYS cc_start: 0.9293 (tppt) cc_final: 0.9072 (ttmm) REVERT: C 58 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8908 (mt-10) REVERT: D 51 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8257 (tt) REVERT: D 73 ASP cc_start: 0.8670 (t0) cc_final: 0.8219 (t0) REVERT: D 211 ASP cc_start: 0.8657 (t0) cc_final: 0.8283 (OUTLIER) REVERT: R 123 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8142 (pp20) REVERT: R 183 SER cc_start: 0.8498 (m) cc_final: 0.8198 (p) REVERT: R 187 LYS cc_start: 0.7158 (OUTLIER) cc_final: 0.6191 (mmtm) REVERT: R 188 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7151 (t80) REVERT: R 203 MET cc_start: 0.8653 (ttp) cc_final: 0.8370 (ppp) REVERT: R 268 ARG cc_start: 0.8939 (tmm-80) cc_final: 0.8666 (tmm-80) REVERT: R 339 TYR cc_start: 0.5847 (OUTLIER) cc_final: 0.5572 (p90) REVERT: L 13 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6506 (mp) outliers start: 59 outliers final: 27 residues processed: 220 average time/residue: 0.4510 time to fit residues: 106.1222 Evaluate side-chains 203 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 170 ILE Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 187 LYS Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 334 TRP Chi-restraints excluded: chain R residue 339 TYR Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 70 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 4 optimal weight: 0.0980 chunk 54 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 333 GLN A 346 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN D 174 GLN R 104 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.097420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.069840 restraints weight = 19803.808| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.58 r_work: 0.2876 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.8221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8938 Z= 0.141 Angle : 0.685 10.610 12109 Z= 0.353 Chirality : 0.044 0.221 1389 Planarity : 0.004 0.058 1520 Dihedral : 5.078 52.543 1226 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.09 % Favored : 96.82 % Rotamer: Outliers : 5.79 % Allowed : 30.74 % Favored : 63.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1099 helix: 1.76 (0.26), residues: 414 sheet: 0.56 (0.31), residues: 266 loop : -0.88 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 206 TYR 0.027 0.001 TYR A 290 PHE 0.029 0.002 PHE R 375 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 8938) covalent geometry : angle 0.68496 / 0.35 (12109) hydrogen bonds : bond 0.04000 / 2.69 ( 479) hydrogen bonds : angle 4.69519 / 3.35 ( 1362) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 173 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8908 (t0) cc_final: 0.8532 (m-30) REVERT: A 25 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8317 (mt-10) REVERT: A 53 MET cc_start: 0.8540 (mmm) cc_final: 0.8289 (mpp) REVERT: A 197 LYS cc_start: 0.8745 (mtpt) cc_final: 0.8311 (mtpt) REVERT: A 234 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6619 (tm) REVERT: A 269 ASN cc_start: 0.9478 (m-40) cc_final: 0.9048 (m-40) REVERT: A 276 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8391 (tm-30) REVERT: A 280 LYS cc_start: 0.9121 (mmtp) cc_final: 0.8720 (mmtp) REVERT: B 9 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8643 (mm-40) REVERT: B 15 LYS cc_start: 0.8932 (mttp) cc_final: 0.8654 (mttp) REVERT: B 197 ARG cc_start: 0.8553 (tpt170) cc_final: 0.7985 (ttm-80) REVERT: B 246 ASP cc_start: 0.9141 (t70) cc_final: 0.8679 (m-30) REVERT: B 294 CYS cc_start: 0.8537 (m) cc_final: 0.8316 (t) REVERT: C 9 ILE cc_start: 0.8940 (pp) cc_final: 0.8575 (pp) REVERT: C 13 ARG cc_start: 0.8940 (ttp-110) cc_final: 0.8453 (ptp-110) REVERT: C 36 ASP cc_start: 0.9046 (t0) cc_final: 0.8633 (m-30) REVERT: C 46 LYS cc_start: 0.9317 (tppt) cc_final: 0.9104 (ttmm) REVERT: C 58 GLU cc_start: 0.9289 (mt-10) cc_final: 0.8936 (mt-10) REVERT: D 43 LYS cc_start: 0.9134 (mtpt) cc_final: 0.8758 (mtmm) REVERT: D 51 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8313 (tt) REVERT: D 73 ASP cc_start: 0.8714 (t0) cc_final: 0.8238 (t0) REVERT: D 89 GLU cc_start: 0.8705 (mp0) cc_final: 0.8472 (pm20) REVERT: D 211 ASP cc_start: 0.8707 (t0) cc_final: 0.8320 (t0) REVERT: R 123 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8200 (pp20) REVERT: R 183 SER cc_start: 0.8389 (m) cc_final: 0.8014 (p) REVERT: R 187 LYS cc_start: 0.6876 (OUTLIER) cc_final: 0.5901 (mmtm) REVERT: R 188 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.7123 (t80) REVERT: R 203 MET cc_start: 0.8622 (ttp) cc_final: 0.8325 (ppp) REVERT: R 268 ARG cc_start: 0.9022 (tmm-80) cc_final: 0.8777 (tmm-80) REVERT: R 339 TYR cc_start: 0.5966 (OUTLIER) cc_final: 0.5748 (p90) REVERT: R 343 HIS cc_start: 0.8723 (m-70) cc_final: 0.8461 (m-70) REVERT: L 13 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6523 (mp) outliers start: 55 outliers final: 24 residues processed: 216 average time/residue: 0.4383 time to fit residues: 101.4211 Evaluate side-chains 202 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 187 LYS Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 339 TYR Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 95 optimal weight: 0.3980 chunk 105 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 35 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 255 ASN A 304 GLN A 333 GLN A 346 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN D 174 GLN R 104 HIS R 238 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.097786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.070298 restraints weight = 19669.309| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.53 r_work: 0.2898 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.8392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8938 Z= 0.134 Angle : 0.693 11.780 12109 Z= 0.354 Chirality : 0.044 0.226 1389 Planarity : 0.004 0.055 1520 Dihedral : 5.003 50.714 1226 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.82 % Favored : 96.09 % Rotamer: Outliers : 5.05 % Allowed : 31.79 % Favored : 63.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.26), residues: 1099 helix: 1.82 (0.26), residues: 414 sheet: 0.60 (0.32), residues: 266 loop : -0.84 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 205 TYR 0.023 0.001 TYR R 339 PHE 0.030 0.001 PHE R 375 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 8938) covalent geometry : angle 0.69344 / 0.35 (12109) hydrogen bonds : bond 0.03876 / 2.61 ( 479) hydrogen bonds : angle 4.63599 / 3.30 ( 1362) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8908 (t0) cc_final: 0.8535 (m-30) REVERT: A 25 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8342 (mt-10) REVERT: A 53 MET cc_start: 0.8623 (mmm) cc_final: 0.8098 (mmm) REVERT: A 197 LYS cc_start: 0.8770 (mtpt) cc_final: 0.8319 (mtpt) REVERT: A 234 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6559 (tm) REVERT: A 269 ASN cc_start: 0.9450 (m-40) cc_final: 0.9118 (m-40) REVERT: A 276 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8500 (tm-30) REVERT: A 283 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8158 (tt) REVERT: B 9 GLN cc_start: 0.9053 (mm-40) cc_final: 0.8624 (mm-40) REVERT: B 15 LYS cc_start: 0.8930 (mttp) cc_final: 0.8646 (mttp) REVERT: B 197 ARG cc_start: 0.8566 (tpt170) cc_final: 0.7993 (ttm-80) REVERT: B 246 ASP cc_start: 0.9101 (t70) cc_final: 0.8660 (m-30) REVERT: C 9 ILE cc_start: 0.8968 (pp) cc_final: 0.8589 (pp) REVERT: C 13 ARG cc_start: 0.8952 (ttp-110) cc_final: 0.8435 (ptp-110) REVERT: C 36 ASP cc_start: 0.9018 (t0) cc_final: 0.8610 (m-30) REVERT: C 46 LYS cc_start: 0.9290 (tppt) cc_final: 0.9079 (ttmm) REVERT: C 58 GLU cc_start: 0.9297 (mt-10) cc_final: 0.8932 (mt-10) REVERT: D 43 LYS cc_start: 0.9135 (mtpt) cc_final: 0.8694 (mttp) REVERT: D 51 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8354 (tt) REVERT: D 73 ASP cc_start: 0.8719 (t0) cc_final: 0.8241 (t0) REVERT: D 89 GLU cc_start: 0.8741 (mp0) cc_final: 0.8512 (mp0) REVERT: D 211 ASP cc_start: 0.8737 (t0) cc_final: 0.8325 (t0) REVERT: R 123 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8265 (pp20) REVERT: R 183 SER cc_start: 0.8416 (m) cc_final: 0.8014 (p) REVERT: R 187 LYS cc_start: 0.6860 (OUTLIER) cc_final: 0.5875 (mmtm) REVERT: R 188 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.7109 (t80) REVERT: R 203 MET cc_start: 0.8563 (ttp) cc_final: 0.8267 (ppp) REVERT: R 268 ARG cc_start: 0.9022 (tmm-80) cc_final: 0.8775 (tmm-80) REVERT: R 300 HIS cc_start: 0.8498 (m90) cc_final: 0.8282 (t-90) REVERT: R 343 HIS cc_start: 0.8721 (m-70) cc_final: 0.8508 (m-70) REVERT: R 367 VAL cc_start: 0.3420 (OUTLIER) cc_final: 0.1824 (t) REVERT: L 12 ILE cc_start: 0.2460 (OUTLIER) cc_final: 0.1923 (pp) outliers start: 48 outliers final: 23 residues processed: 214 average time/residue: 0.4249 time to fit residues: 97.8011 Evaluate side-chains 198 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain R residue 86 PHE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 187 LYS Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain L residue 12 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 8 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 67 optimal weight: 0.2980 chunk 90 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 294 ASN A 304 GLN A 331 ASN A 333 GLN A 346 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN D 174 GLN R 95 GLN R 98 GLN R 104 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.097077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.069678 restraints weight = 19646.600| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.54 r_work: 0.2885 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.8549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8938 Z= 0.142 Angle : 0.724 15.015 12109 Z= 0.364 Chirality : 0.044 0.262 1389 Planarity : 0.005 0.055 1520 Dihedral : 4.991 50.320 1226 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.46 % Favored : 96.45 % Rotamer: Outliers : 5.05 % Allowed : 31.68 % Favored : 63.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.26), residues: 1099 helix: 1.80 (0.26), residues: 415 sheet: 0.45 (0.31), residues: 279 loop : -0.73 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 206 TYR 0.031 0.001 TYR A 290 PHE 0.030 0.002 PHE R 375 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 8938) covalent geometry : angle 0.72402 / 0.36 (12109) hydrogen bonds : bond 0.03946 / 2.65 ( 479) hydrogen bonds : angle 4.66824 / 3.33 ( 1362) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 183 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8942 (t0) cc_final: 0.8584 (m-30) REVERT: A 25 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8390 (mt-10) REVERT: A 53 MET cc_start: 0.8647 (mmm) cc_final: 0.7915 (mmm) REVERT: A 197 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8320 (mtpt) REVERT: A 234 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6503 (tm) REVERT: A 269 ASN cc_start: 0.9443 (m-40) cc_final: 0.9154 (m-40) REVERT: A 276 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8424 (tm-30) REVERT: A 313 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8396 (ptp-110) REVERT: B 9 GLN cc_start: 0.9077 (mm-40) cc_final: 0.8645 (mm-40) REVERT: B 15 LYS cc_start: 0.8905 (mttp) cc_final: 0.8600 (mttp) REVERT: B 197 ARG cc_start: 0.8521 (tpt170) cc_final: 0.7958 (ttm-80) REVERT: B 246 ASP cc_start: 0.9099 (t70) cc_final: 0.8676 (m-30) REVERT: C 9 ILE cc_start: 0.8965 (pp) cc_final: 0.8546 (pp) REVERT: C 13 ARG cc_start: 0.8952 (ttp-110) cc_final: 0.8424 (ptp-110) REVERT: C 36 ASP cc_start: 0.9026 (t0) cc_final: 0.8619 (m-30) REVERT: C 42 GLU cc_start: 0.9094 (tp30) cc_final: 0.8883 (tp30) REVERT: C 46 LYS cc_start: 0.9320 (tppt) cc_final: 0.9116 (ttmm) REVERT: C 58 GLU cc_start: 0.9304 (mt-10) cc_final: 0.8950 (mt-10) REVERT: D 43 LYS cc_start: 0.9146 (mtpt) cc_final: 0.8727 (mttp) REVERT: D 51 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8395 (tt) REVERT: D 73 ASP cc_start: 0.8735 (t0) cc_final: 0.8235 (t0) REVERT: D 89 GLU cc_start: 0.8773 (mp0) cc_final: 0.8544 (mp0) REVERT: D 211 ASP cc_start: 0.8718 (t0) cc_final: 0.8354 (t0) REVERT: R 118 LEU cc_start: 0.9080 (mt) cc_final: 0.8870 (mm) REVERT: R 123 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8315 (pp20) REVERT: R 183 SER cc_start: 0.8402 (m) cc_final: 0.8054 (p) REVERT: R 187 LYS cc_start: 0.6820 (OUTLIER) cc_final: 0.5836 (mmtt) REVERT: R 188 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.7130 (t80) REVERT: R 203 MET cc_start: 0.8514 (ttp) cc_final: 0.8218 (ppp) REVERT: R 268 ARG cc_start: 0.9054 (tmm-80) cc_final: 0.8772 (tmm-80) REVERT: R 339 TYR cc_start: 0.6190 (OUTLIER) cc_final: 0.5874 (p90) REVERT: R 343 HIS cc_start: 0.8717 (m-70) cc_final: 0.8516 (m-70) REVERT: R 367 VAL cc_start: 0.3332 (OUTLIER) cc_final: 0.1692 (t) outliers start: 48 outliers final: 25 residues processed: 216 average time/residue: 0.4905 time to fit residues: 113.4310 Evaluate side-chains 209 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain R residue 86 PHE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 187 LYS Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 339 TYR Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 50 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 0.0570 chunk 43 optimal weight: 0.7980 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 294 ASN A 304 GLN A 333 GLN B 75 GLN B 183 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS D 3 GLN D 174 GLN R 81 ASN R 104 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.096978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.069128 restraints weight = 19798.741| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.58 r_work: 0.2869 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.8714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8938 Z= 0.156 Angle : 0.755 17.235 12109 Z= 0.377 Chirality : 0.046 0.242 1389 Planarity : 0.005 0.054 1520 Dihedral : 5.034 52.013 1226 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.64 % Favored : 96.27 % Rotamer: Outliers : 4.32 % Allowed : 32.63 % Favored : 63.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.77 (0.26), residues: 1099 helix: 1.77 (0.26), residues: 413 sheet: 0.44 (0.31), residues: 279 loop : -0.72 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 206 TYR 0.023 0.001 TYR R 153 PHE 0.029 0.002 PHE R 375 TRP 0.023 0.002 TRP B 211 HIS 0.005 0.001 HIS R 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 8938) covalent geometry : angle 0.75546 / 0.38 (12109) hydrogen bonds : bond 0.04061 / 2.75 ( 479) hydrogen bonds : angle 4.72823 / 3.37 ( 1362) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8933 (t0) cc_final: 0.8569 (m-30) REVERT: A 25 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8408 (mt-10) REVERT: A 53 MET cc_start: 0.8595 (mmm) cc_final: 0.8305 (mmm) REVERT: A 197 LYS cc_start: 0.8755 (mtpt) cc_final: 0.8288 (mtpt) REVERT: A 234 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6535 (tm) REVERT: A 243 MET cc_start: 0.9152 (tpp) cc_final: 0.8661 (tpp) REVERT: A 269 ASN cc_start: 0.9347 (m-40) cc_final: 0.8655 (m-40) REVERT: A 276 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8525 (tm-30) REVERT: A 313 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8411 (ptp-110) REVERT: B 9 GLN cc_start: 0.9109 (mm-40) cc_final: 0.8670 (mm-40) REVERT: B 15 LYS cc_start: 0.8888 (mttp) cc_final: 0.8576 (mttp) REVERT: B 197 ARG cc_start: 0.8584 (tpt170) cc_final: 0.8016 (ttm-80) REVERT: B 246 ASP cc_start: 0.9138 (t70) cc_final: 0.8681 (m-30) REVERT: C 9 ILE cc_start: 0.8931 (pp) cc_final: 0.8554 (pp) REVERT: C 13 ARG cc_start: 0.8970 (ttp-110) cc_final: 0.8450 (mtm110) REVERT: C 36 ASP cc_start: 0.9047 (t0) cc_final: 0.8596 (m-30) REVERT: C 42 GLU cc_start: 0.9098 (tp30) cc_final: 0.8883 (tp30) REVERT: C 46 LYS cc_start: 0.9332 (tppt) cc_final: 0.9125 (ttmm) REVERT: C 58 GLU cc_start: 0.9309 (mt-10) cc_final: 0.9076 (mt-10) REVERT: D 43 LYS cc_start: 0.9174 (mtpt) cc_final: 0.8782 (mttp) REVERT: D 51 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8423 (tt) REVERT: D 73 ASP cc_start: 0.8725 (t0) cc_final: 0.8191 (t0) REVERT: D 211 ASP cc_start: 0.8722 (t0) cc_final: 0.8381 (t0) REVERT: D 234 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8070 (pp20) REVERT: R 118 LEU cc_start: 0.9078 (mt) cc_final: 0.8856 (mm) REVERT: R 123 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8252 (pp20) REVERT: R 124 LEU cc_start: 0.9172 (tp) cc_final: 0.8786 (tp) REVERT: R 183 SER cc_start: 0.8403 (m) cc_final: 0.8013 (p) REVERT: R 187 LYS cc_start: 0.6759 (OUTLIER) cc_final: 0.5843 (mmtm) REVERT: R 188 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.7144 (t80) REVERT: R 203 MET cc_start: 0.8453 (ttp) cc_final: 0.8230 (ppp) REVERT: R 268 ARG cc_start: 0.9069 (tmm-80) cc_final: 0.8809 (tmm-80) REVERT: R 339 TYR cc_start: 0.6233 (OUTLIER) cc_final: 0.5894 (p90) REVERT: R 343 HIS cc_start: 0.8800 (m-70) cc_final: 0.8583 (m-70) REVERT: R 347 MET cc_start: 0.8317 (pmm) cc_final: 0.8060 (pmm) REVERT: R 350 ASN cc_start: 0.9087 (m-40) cc_final: 0.8570 (m110) outliers start: 41 outliers final: 25 residues processed: 212 average time/residue: 0.4627 time to fit residues: 104.9143 Evaluate side-chains 209 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 170 ILE Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 187 LYS Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 339 TYR Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain R residue 360 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 78 optimal weight: 0.0870 chunk 10 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 294 ASN A 304 GLN A 331 ASN A 333 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS D 3 GLN R 104 HIS ** R 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.096873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.068884 restraints weight = 19694.062| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.58 r_work: 0.2874 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.8866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8938 Z= 0.148 Angle : 0.756 13.527 12109 Z= 0.381 Chirality : 0.045 0.239 1389 Planarity : 0.005 0.054 1520 Dihedral : 5.020 54.035 1226 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.55 % Favored : 96.36 % Rotamer: Outliers : 4.21 % Allowed : 32.84 % Favored : 62.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.26), residues: 1099 helix: 1.77 (0.26), residues: 413 sheet: 0.51 (0.31), residues: 273 loop : -0.71 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 206 TYR 0.039 0.001 TYR A 290 PHE 0.030 0.001 PHE R 375 TRP 0.017 0.001 TRP B 211 HIS 0.005 0.001 HIS R 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 8938) covalent geometry : angle 0.75552 / 0.38 (12109) hydrogen bonds : bond 0.04009 / 2.68 ( 479) hydrogen bonds : angle 4.73315 / 3.36 ( 1362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3624.57 seconds wall clock time: 62 minutes 23.56 seconds (3743.56 seconds total)