Starting phenix.real_space_refine on Thu Jul 2 16:03:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/20zg_67429/07_2026/20zg_67429.cif Found real_map, /net/cci-nas-00/data/ceres_data/20zg_67429/07_2026/20zg_67429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/20zg_67429/07_2026/20zg_67429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/20zg_67429/07_2026/20zg_67429.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/20zg_67429/07_2026/20zg_67429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/20zg_67429/07_2026/20zg_67429.map" } resolution = 2.4 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= 0.014 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 61 5.16 5 C 5684 2.51 5 N 1521 2.21 5 O 1666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 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: 8932 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1747 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2584 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 404 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1762 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "R" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2382 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 296} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 1.70, per 1000 atoms: 0.19 Number of scatterers: 8932 At special positions: 0 Unit cell: (90.47, 121.18, 129.48, 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 61 16.00 O 1666 8.00 N 1521 7.00 C 5684 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.53 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.33 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.41 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 341.9 milliseconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 39.5% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.611A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.500A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.901A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.352A 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 270 through 281 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 352 removed outlier: 3.668A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.630A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 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: 4.324A 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 'D' and resid 87 through 91 Processing helix chain 'R' and resid 51 through 55 removed outlier: 3.506A pdb=" N LEU R 54 " --> pdb=" O SER R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 91 Processing helix chain 'R' and resid 98 through 128 removed outlier: 3.867A pdb=" N LEU R 108 " --> pdb=" O HIS R 104 " (cutoff:3.500A) Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 136 through 172 Processing helix chain 'R' and resid 172 through 180 Processing helix chain 'R' and resid 181 through 199 Processing helix chain 'R' and resid 201 through 206 removed outlier: 3.901A pdb=" N PHE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR R 206 " --> pdb=" O PRO R 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 201 through 206' Processing helix chain 'R' and resid 229 through 245 removed outlier: 3.784A pdb=" N VAL R 235 " --> pdb=" O ALA R 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 273 removed outlier: 3.551A pdb=" N ALA R 271 " --> pdb=" O VAL R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 329 Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 335 through 365 Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 369 through 375 removed outlier: 3.854A pdb=" N HIS R 373 " --> pdb=" O ALA R 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 8.982A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.819A 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: 3.641A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.502A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.399A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.601A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.706A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.114A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.492A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.307A 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: 6.724A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.739A 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: 4.095A 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: 6.614A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN D 182 " --> pdb=" O TYR D 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 207 through 211 removed outlier: 3.546A pdb=" N THR R 225 " --> pdb=" O GLY R 208 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.50 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1451 1.30 - 1.44: 2533 1.44 - 1.57: 5044 1.57 - 1.70: 2 1.70 - 1.83: 90 Bond restraints: 9120 Sorted by residual: bond pdb=" CA SER B 161 " pdb=" CB SER B 161 " ideal model delta sigma weight residual 1.530 1.431 0.099 1.52e-02 4.33e+03 4.26e+01 bond pdb=" CA SER B 72 " pdb=" CB SER B 72 " ideal model delta sigma weight residual 1.533 1.433 0.100 1.69e-02 3.50e+03 3.48e+01 bond pdb=" CA SER D 181 " pdb=" CB SER D 181 " ideal model delta sigma weight residual 1.528 1.451 0.077 1.33e-02 5.65e+03 3.34e+01 bond pdb=" CA SER D 185 " pdb=" CB SER D 185 " ideal model delta sigma weight residual 1.529 1.432 0.097 1.70e-02 3.46e+03 3.25e+01 bond pdb=" CG HIS B 142 " pdb=" CD2 HIS B 142 " ideal model delta sigma weight residual 1.354 1.293 0.061 1.10e-02 8.26e+03 3.12e+01 ... (remaining 9115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 10356 2.48 - 4.96: 1773 4.96 - 7.44: 190 7.44 - 9.91: 38 9.91 - 12.39: 12 Bond angle restraints: 12369 Sorted by residual: angle pdb=" CA TYR D 178 " pdb=" C TYR D 178 " pdb=" O TYR D 178 " ideal model delta sigma weight residual 121.11 109.56 11.55 1.17e+00 7.31e-01 9.74e+01 angle pdb=" N GLY A 352 " pdb=" CA GLY A 352 " pdb=" C GLY A 352 " ideal model delta sigma weight residual 115.43 104.55 10.88 1.41e+00 5.03e-01 5.95e+01 angle pdb=" CA THR R 100 " pdb=" CB THR R 100 " pdb=" OG1 THR R 100 " ideal model delta sigma weight residual 109.60 98.22 11.38 1.50e+00 4.44e-01 5.75e+01 angle pdb=" N THR R 100 " pdb=" CA THR R 100 " pdb=" C THR R 100 " ideal model delta sigma weight residual 111.28 103.26 8.02 1.09e+00 8.42e-01 5.42e+01 angle pdb=" C TYR R 167 " pdb=" CA TYR R 167 " pdb=" CB TYR R 167 " ideal model delta sigma weight residual 110.88 99.58 11.30 1.57e+00 4.06e-01 5.18e+01 ... (remaining 12364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 4989 17.33 - 34.65: 292 34.65 - 51.98: 88 51.98 - 69.31: 17 69.31 - 86.63: 9 Dihedral angle restraints: 5395 sinusoidal: 2047 harmonic: 3348 Sorted by residual: dihedral pdb=" CD ARG R 90 " pdb=" NE ARG R 90 " pdb=" CZ ARG R 90 " pdb=" NH1 ARG R 90 " ideal model delta sinusoidal sigma weight residual 0.00 86.63 -86.63 1 1.00e+01 1.00e-02 9.04e+01 dihedral pdb=" CB CYS R 141 " pdb=" SG CYS R 141 " pdb=" SG CYS R 224 " pdb=" CB CYS R 224 " ideal model delta sinusoidal sigma weight residual -86.00 -165.89 79.89 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 168.34 -75.34 1 1.00e+01 1.00e-02 7.17e+01 ... (remaining 5392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 882 0.093 - 0.186: 388 0.186 - 0.278: 110 0.278 - 0.371: 27 0.371 - 0.464: 10 Chirality restraints: 1417 Sorted by residual: chirality pdb=" CA ARG D 179 " pdb=" N ARG D 179 " pdb=" C ARG D 179 " pdb=" CB ARG D 179 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CA ASP R 149 " pdb=" N ASP R 149 " pdb=" C ASP R 149 " pdb=" CB ASP R 149 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.19e+00 chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.15e+00 ... (remaining 1414 not shown) Planarity restraints: 1560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 90 " -1.116 9.50e-02 1.11e+02 5.00e-01 1.51e+02 pdb=" NE ARG R 90 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG R 90 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG R 90 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG R 90 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 179 " -0.450 9.50e-02 1.11e+02 2.05e-01 4.03e+01 pdb=" NE ARG D 179 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG D 179 " 0.073 2.00e-02 2.50e+03 pdb=" NH1 ARG D 179 " -0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG D 179 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 115 " -0.030 2.00e-02 2.50e+03 6.22e-02 3.87e+01 pdb=" C GLY B 115 " 0.108 2.00e-02 2.50e+03 pdb=" O GLY B 115 " -0.041 2.00e-02 2.50e+03 pdb=" N GLY B 116 " -0.037 2.00e-02 2.50e+03 ... (remaining 1557 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 777 2.75 - 3.29: 8823 3.29 - 3.83: 14385 3.83 - 4.36: 18314 4.36 - 4.90: 30816 Nonbonded interactions: 73115 Sorted by model distance: nonbonded pdb=" O ASP R 112 " pdb=" OG1 THR R 115 " model vdw 2.215 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.241 3.040 nonbonded pdb=" O ASN R 158 " pdb=" OG SER R 161 " model vdw 2.267 3.040 nonbonded pdb=" OG1 THR B 29 " pdb=" OE1 GLN B 32 " model vdw 2.324 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.336 3.040 ... (remaining 73110 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: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 8.240 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 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 : 0.014 0.500 9123 Z= 0.889 Angle : 1.918 12.393 12375 Z= 1.290 Chirality : 0.115 0.464 1417 Planarity : 0.020 0.500 1560 Dihedral : 13.123 86.633 3226 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.16 % Allowed : 6.14 % Favored : 89.70 % Cbeta Deviations : 1.67 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.23), residues: 1132 helix: 1.72 (0.23), residues: 400 sheet: 0.33 (0.30), residues: 262 loop : -0.82 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.068 0.006 ARG D 179 TYR 0.043 0.007 TYR D 161 PHE 0.074 0.008 PHE R 174 TRP 0.041 0.008 TRP B 297 HIS 0.021 0.005 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.01242 / 0.81 ( 9120) covalent geometry : angle 1.91651 / 1.29 (12369) SS BOND : bond 0.39958 / 19.01 ( 3) SS BOND : angle 3.62692 / 1.93 ( 6) hydrogen bonds : bond 0.19749 / 13.01 ( 473) hydrogen bonds : angle 7.60114 / 5.31 ( 1344) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 309 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 192 LYS cc_start: 0.8589 (tppp) cc_final: 0.8353 (mtmt) REVERT: A 243 MET cc_start: 0.9128 (tpp) cc_final: 0.8861 (tpp) REVERT: A 287 TYR cc_start: 0.7944 (m-10) cc_final: 0.6674 (m-80) REVERT: A 293 SER cc_start: 0.7282 (p) cc_final: 0.6548 (p) REVERT: A 328 ASP cc_start: 0.6880 (OUTLIER) cc_final: 0.6321 (t70) REVERT: A 332 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8532 (t) REVERT: A 333 GLN cc_start: 0.9111 (tp40) cc_final: 0.8733 (tp40) REVERT: B 5 ASP cc_start: 0.8623 (m-30) cc_final: 0.8399 (m-30) REVERT: B 9 GLN cc_start: 0.9318 (mm110) cc_final: 0.9018 (mm-40) REVERT: B 42 ARG cc_start: 0.8996 (ttt-90) cc_final: 0.8677 (ttt-90) REVERT: B 247 ASP cc_start: 0.8699 (m-30) cc_final: 0.8360 (OUTLIER) REVERT: B 291 ASP cc_start: 0.8820 (t0) cc_final: 0.8572 (t0) REVERT: D 90 ASP cc_start: 0.8871 (m-30) cc_final: 0.8624 (m-30) REVERT: R 81 ASN cc_start: 0.9138 (m-40) cc_final: 0.8893 (m110) REVERT: R 96 SER cc_start: 0.7588 (OUTLIER) cc_final: 0.6973 (p) REVERT: R 98 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8128 (mt0) REVERT: R 102 HIS cc_start: 0.9063 (m-70) cc_final: 0.8703 (m-70) REVERT: R 184 ARG cc_start: 0.8769 (mtt90) cc_final: 0.8271 (ttp80) REVERT: R 207 MET cc_start: 0.8863 (mmt) cc_final: 0.8512 (mmt) REVERT: R 252 ILE cc_start: 0.8735 (mm) cc_final: 0.8491 (mp) REVERT: R 300 HIS cc_start: 0.8336 (t70) cc_final: 0.7940 (t70) REVERT: R 350 ASN cc_start: 0.9116 (m-40) cc_final: 0.8898 (m-40) outliers start: 40 outliers final: 9 residues processed: 336 average time/residue: 0.5629 time to fit residues: 200.8141 Evaluate side-chains 188 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 98 GLN Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 356 SER Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.3980 chunk 106 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS A 269 ASN A 347 ASN B 6 GLN B 17 GLN B 88 ASN B 91 HIS B 175 GLN B 259 GLN B 311 HIS D 130 GLN D 182 ASN R 81 ASN ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 269 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.082418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.064095 restraints weight = 18186.578| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.13 r_work: 0.2941 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9123 Z= 0.145 Angle : 0.649 10.961 12375 Z= 0.337 Chirality : 0.043 0.153 1417 Planarity : 0.004 0.054 1560 Dihedral : 5.951 53.935 1263 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 4.06 % Allowed : 17.17 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.24), residues: 1132 helix: 2.15 (0.24), residues: 403 sheet: 0.47 (0.30), residues: 282 loop : -0.66 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 134 TYR 0.017 0.002 TYR R 70 PHE 0.026 0.002 PHE A 336 TRP 0.019 0.002 TRP B 339 HIS 0.003 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 9120) covalent geometry : angle 0.64755 / 0.34 (12369) SS BOND : bond 0.00929 / 0.47 ( 3) SS BOND : angle 2.28990 / 1.07 ( 6) hydrogen bonds : bond 0.04793 / 3.21 ( 473) hydrogen bonds : angle 5.13704 / 3.62 ( 1344) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 190 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 273 LEU cc_start: 0.9144 (mp) cc_final: 0.8869 (tm) REVERT: A 287 TYR cc_start: 0.7716 (m-10) cc_final: 0.7364 (m-80) REVERT: A 302 TYR cc_start: 0.9183 (t80) cc_final: 0.8877 (t80) REVERT: A 306 GLN cc_start: 0.9338 (mm-40) cc_final: 0.8908 (mp10) REVERT: A 311 ASN cc_start: 0.8097 (p0) cc_final: 0.7776 (p0) REVERT: A 313 ARG cc_start: 0.8703 (ptp-170) cc_final: 0.8461 (ptp-170) REVERT: A 328 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.5890 (p0) REVERT: A 331 ASN cc_start: 0.8898 (m-40) cc_final: 0.8180 (m110) REVERT: B 291 ASP cc_start: 0.8144 (t0) cc_final: 0.7823 (t0) REVERT: D 211 ASP cc_start: 0.8647 (t0) cc_final: 0.8423 (t0) REVERT: R 98 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7814 (tp-100) REVERT: R 117 LEU cc_start: 0.9159 (mt) cc_final: 0.8895 (mp) REVERT: R 300 HIS cc_start: 0.7949 (t70) cc_final: 0.7387 (t70) REVERT: R 303 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8149 (ttm-80) outliers start: 39 outliers final: 10 residues processed: 212 average time/residue: 0.5847 time to fit residues: 131.5731 Evaluate side-chains 178 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain R residue 98 GLN Chi-restraints excluded: chain R residue 175 LYS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 303 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 108 optimal weight: 0.0870 chunk 69 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN D 159 ASN D 182 ASN R 98 GLN R 104 HIS R 269 GLN R 360 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.079479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.060518 restraints weight = 18109.674| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.10 r_work: 0.2851 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9141 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9123 Z= 0.171 Angle : 0.622 11.801 12375 Z= 0.323 Chirality : 0.043 0.137 1417 Planarity : 0.004 0.055 1560 Dihedral : 5.094 54.551 1254 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.64 % Allowed : 18.73 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.25), residues: 1132 helix: 2.31 (0.24), residues: 410 sheet: 0.62 (0.31), residues: 282 loop : -0.56 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 182 TYR 0.020 0.002 TYR R 145 PHE 0.028 0.002 PHE A 336 TRP 0.013 0.001 TRP B 297 HIS 0.006 0.001 HIS R 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 9120) covalent geometry : angle 0.61906 / 0.32 (12369) SS BOND : bond 0.01568 / 0.82 ( 3) SS BOND : angle 2.71341 / 1.29 ( 6) hydrogen bonds : bond 0.04624 / 3.07 ( 473) hydrogen bonds : angle 4.86895 / 3.42 ( 1344) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 0.322 Fit side-chains REVERT: A 273 LEU cc_start: 0.9210 (mp) cc_final: 0.8945 (tm) REVERT: A 311 ASN cc_start: 0.8291 (p0) cc_final: 0.8066 (p0) REVERT: A 328 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6276 (p0) REVERT: A 331 ASN cc_start: 0.8609 (m-40) cc_final: 0.8012 (m110) REVERT: B 37 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8620 (pt) REVERT: B 254 ASP cc_start: 0.8517 (t70) cc_final: 0.8301 (t70) REVERT: B 291 ASP cc_start: 0.8304 (t0) cc_final: 0.8055 (t0) REVERT: D 13 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8781 (mp10) REVERT: D 211 ASP cc_start: 0.8760 (t0) cc_final: 0.8469 (t0) REVERT: R 104 HIS cc_start: 0.8638 (OUTLIER) cc_final: 0.8376 (m170) REVERT: R 110 LEU cc_start: 0.9256 (tp) cc_final: 0.8945 (tm) REVERT: R 117 LEU cc_start: 0.9152 (mt) cc_final: 0.8896 (mt) REVERT: R 165 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8321 (mt-10) REVERT: R 207 MET cc_start: 0.9150 (mmm) cc_final: 0.8828 (mmm) REVERT: R 210 GLN cc_start: 0.8475 (tt0) cc_final: 0.7967 (mt0) REVERT: R 300 HIS cc_start: 0.8021 (t70) cc_final: 0.7435 (t70) REVERT: R 303 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8177 (ttm-80) outliers start: 35 outliers final: 11 residues processed: 199 average time/residue: 0.5580 time to fit residues: 117.8625 Evaluate side-chains 180 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain R residue 104 HIS Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 303 ARG Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain R residue 366 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS D 174 GLN R 104 HIS ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 158 ASN R 238 GLN R 360 ASN R 365 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.078109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.058620 restraints weight = 18402.071| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.12 r_work: 0.2805 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9178 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9123 Z= 0.191 Angle : 0.626 12.915 12375 Z= 0.321 Chirality : 0.044 0.158 1417 Planarity : 0.004 0.048 1560 Dihedral : 4.770 53.940 1250 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.64 % Allowed : 19.25 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.25), residues: 1132 helix: 2.40 (0.25), residues: 410 sheet: 0.66 (0.30), residues: 284 loop : -0.61 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 182 TYR 0.018 0.002 TYR R 145 PHE 0.024 0.002 PHE A 336 TRP 0.011 0.001 TRP B 297 HIS 0.012 0.002 HIS R 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 ( 9120) covalent geometry : angle 0.62270 / 0.32 (12369) SS BOND : bond 0.01623 / 0.85 ( 3) SS BOND : angle 2.86011 / 1.37 ( 6) hydrogen bonds : bond 0.04591 / 3.05 ( 473) hydrogen bonds : angle 4.84748 / 3.41 ( 1344) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.378 Fit side-chains REVERT: A 24 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8138 (mtp-110) REVERT: A 193 ASP cc_start: 0.8515 (t0) cc_final: 0.8305 (t0) REVERT: A 273 LEU cc_start: 0.9269 (mp) cc_final: 0.8968 (tm) REVERT: A 306 GLN cc_start: 0.9309 (mm-40) cc_final: 0.8811 (mp10) REVERT: A 311 ASN cc_start: 0.8349 (p0) cc_final: 0.8119 (p0) REVERT: B 254 ASP cc_start: 0.8485 (t70) cc_final: 0.8248 (t70) REVERT: B 291 ASP cc_start: 0.8346 (t0) cc_final: 0.8090 (t0) REVERT: D 76 LYS cc_start: 0.8963 (mtmm) cc_final: 0.8653 (mttp) REVERT: D 211 ASP cc_start: 0.8827 (t0) cc_final: 0.8589 (t0) REVERT: R 104 HIS cc_start: 0.8774 (OUTLIER) cc_final: 0.8561 (m170) REVERT: R 175 LYS cc_start: 0.8851 (ttmt) cc_final: 0.8547 (mtpp) REVERT: R 207 MET cc_start: 0.9057 (mmm) cc_final: 0.8608 (mmm) REVERT: R 210 GLN cc_start: 0.8523 (tt0) cc_final: 0.8001 (mt0) REVERT: R 300 HIS cc_start: 0.8111 (t70) cc_final: 0.7534 (t70) REVERT: R 303 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8203 (ttm-80) outliers start: 35 outliers final: 15 residues processed: 184 average time/residue: 0.5927 time to fit residues: 115.7280 Evaluate side-chains 180 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain R residue 104 HIS Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 303 ARG Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain R residue 366 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 69 optimal weight: 0.0010 chunk 108 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN D 174 GLN R 104 HIS ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 238 GLN R 360 ASN R 365 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.079326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.060106 restraints weight = 18293.379| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.12 r_work: 0.2842 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9150 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9123 Z= 0.126 Angle : 0.582 11.329 12375 Z= 0.297 Chirality : 0.042 0.188 1417 Planarity : 0.004 0.046 1560 Dihedral : 4.474 52.813 1248 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.23 % Allowed : 20.29 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.25), residues: 1132 helix: 2.42 (0.25), residues: 410 sheet: 0.53 (0.30), residues: 280 loop : -0.59 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 32 TYR 0.016 0.001 TYR R 145 PHE 0.014 0.001 PHE A 336 TRP 0.013 0.001 TRP B 297 HIS 0.013 0.001 HIS R 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 9120) covalent geometry : angle 0.58091 / 0.30 (12369) SS BOND : bond 0.01016 / 0.53 ( 3) SS BOND : angle 1.80754 / 0.86 ( 6) hydrogen bonds : bond 0.04133 / 2.75 ( 473) hydrogen bonds : angle 4.71353 / 3.32 ( 1344) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 193 ASP cc_start: 0.8594 (t0) cc_final: 0.8333 (t0) REVERT: A 273 LEU cc_start: 0.9269 (mp) cc_final: 0.8971 (tm) REVERT: A 306 GLN cc_start: 0.9289 (mm-40) cc_final: 0.8784 (mp10) REVERT: A 311 ASN cc_start: 0.8285 (p0) cc_final: 0.8045 (p0) REVERT: B 46 ARG cc_start: 0.8849 (mmm-85) cc_final: 0.8594 (mtp-110) REVERT: B 215 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8683 (mp0) REVERT: B 254 ASP cc_start: 0.8481 (t70) cc_final: 0.8266 (t70) REVERT: B 291 ASP cc_start: 0.8308 (t0) cc_final: 0.8009 (t0) REVERT: D 211 ASP cc_start: 0.8789 (t0) cc_final: 0.8536 (t0) REVERT: R 110 LEU cc_start: 0.9235 (tp) cc_final: 0.8926 (tm) REVERT: R 113 LEU cc_start: 0.9400 (tp) cc_final: 0.9152 (tm) REVERT: R 175 LYS cc_start: 0.8860 (ttmt) cc_final: 0.8555 (mtpp) REVERT: R 207 MET cc_start: 0.8983 (mmm) cc_final: 0.8595 (mmm) REVERT: R 210 GLN cc_start: 0.8442 (tt0) cc_final: 0.7987 (mt0) REVERT: R 300 HIS cc_start: 0.8043 (t70) cc_final: 0.7462 (t70) REVERT: R 303 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8149 (ttm-80) outliers start: 31 outliers final: 16 residues processed: 186 average time/residue: 0.6298 time to fit residues: 123.9872 Evaluate side-chains 176 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 303 ARG Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain R residue 366 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 86 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 67 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 99 optimal weight: 0.0370 chunk 16 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 GLN ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 238 GLN R 360 ASN R 365 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.079406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.060448 restraints weight = 18423.232| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.10 r_work: 0.2849 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9145 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9123 Z= 0.125 Angle : 0.588 10.230 12375 Z= 0.295 Chirality : 0.042 0.193 1417 Planarity : 0.004 0.046 1560 Dihedral : 4.373 52.264 1248 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.50 % Allowed : 22.06 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.25), residues: 1132 helix: 2.43 (0.25), residues: 416 sheet: 0.43 (0.30), residues: 281 loop : -0.52 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 32 TYR 0.015 0.001 TYR R 145 PHE 0.015 0.001 PHE A 336 TRP 0.012 0.001 TRP B 297 HIS 0.005 0.001 HIS R 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 9120) covalent geometry : angle 0.58689 / 0.29 (12369) SS BOND : bond 0.01027 / 0.53 ( 3) SS BOND : angle 1.76084 / 0.84 ( 6) hydrogen bonds : bond 0.04008 / 2.66 ( 473) hydrogen bonds : angle 4.64616 / 3.28 ( 1344) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.359 Fit side-chains REVERT: A 53 MET cc_start: 0.9002 (tpp) cc_final: 0.8098 (mpp) REVERT: A 193 ASP cc_start: 0.8605 (t0) cc_final: 0.8342 (t0) REVERT: A 273 LEU cc_start: 0.9283 (mp) cc_final: 0.8983 (tm) REVERT: A 306 GLN cc_start: 0.9279 (mm-40) cc_final: 0.8788 (mp10) REVERT: A 311 ASN cc_start: 0.8276 (p0) cc_final: 0.8026 (p0) REVERT: B 37 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8533 (pt) REVERT: B 46 ARG cc_start: 0.8861 (mmm-85) cc_final: 0.8602 (mtp-110) REVERT: B 215 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8708 (mp0) REVERT: B 291 ASP cc_start: 0.8299 (t0) cc_final: 0.8005 (t0) REVERT: D 211 ASP cc_start: 0.8729 (t0) cc_final: 0.8496 (t0) REVERT: R 110 LEU cc_start: 0.9253 (tp) cc_final: 0.8985 (tm) REVERT: R 113 LEU cc_start: 0.9405 (tp) cc_final: 0.9136 (tm) REVERT: R 175 LYS cc_start: 0.8838 (ttmt) cc_final: 0.8543 (mtmt) REVERT: R 207 MET cc_start: 0.8910 (mmm) cc_final: 0.8539 (mmm) REVERT: R 210 GLN cc_start: 0.8411 (tt0) cc_final: 0.7990 (mt0) REVERT: R 238 GLN cc_start: 0.8900 (mt0) cc_final: 0.8675 (mt0) REVERT: R 300 HIS cc_start: 0.8067 (t70) cc_final: 0.7514 (t70) outliers start: 24 outliers final: 15 residues processed: 182 average time/residue: 0.5617 time to fit residues: 108.6098 Evaluate side-chains 177 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain R residue 366 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 76 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN B 36 ASN D 174 GLN ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 269 GLN R 360 ASN R 365 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.077546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.058308 restraints weight = 18388.263| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.12 r_work: 0.2805 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9177 moved from start: 0.5431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9123 Z= 0.177 Angle : 0.624 10.449 12375 Z= 0.318 Chirality : 0.043 0.185 1417 Planarity : 0.004 0.046 1560 Dihedral : 4.497 53.053 1248 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.12 % Allowed : 21.75 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.25), residues: 1132 helix: 2.42 (0.25), residues: 416 sheet: 0.39 (0.30), residues: 282 loop : -0.50 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 32 TYR 0.017 0.002 TYR R 145 PHE 0.015 0.002 PHE A 336 TRP 0.011 0.001 TRP R 316 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 ( 9120) covalent geometry : angle 0.62253 / 0.32 (12369) SS BOND : bond 0.01427 / 0.75 ( 3) SS BOND : angle 2.29120 / 1.09 ( 6) hydrogen bonds : bond 0.04349 / 2.90 ( 473) hydrogen bonds : angle 4.72492 / 3.31 ( 1344) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.437 Fit side-chains REVERT: A 53 MET cc_start: 0.9060 (tpp) cc_final: 0.8173 (mpp) REVERT: A 193 ASP cc_start: 0.8657 (t0) cc_final: 0.8435 (t0) REVERT: A 273 LEU cc_start: 0.9285 (mp) cc_final: 0.8987 (tm) REVERT: A 306 GLN cc_start: 0.9295 (mm-40) cc_final: 0.8740 (mp10) REVERT: A 311 ASN cc_start: 0.8408 (p0) cc_final: 0.8143 (p0) REVERT: B 46 ARG cc_start: 0.8855 (mmm-85) cc_final: 0.8581 (mtp-110) REVERT: B 215 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8780 (mp0) REVERT: B 291 ASP cc_start: 0.8381 (t0) cc_final: 0.8088 (t0) REVERT: D 211 ASP cc_start: 0.8801 (t0) cc_final: 0.8536 (t0) REVERT: R 102 HIS cc_start: 0.8380 (m90) cc_final: 0.8091 (m90) REVERT: R 113 LEU cc_start: 0.9400 (tp) cc_final: 0.9139 (tm) REVERT: R 175 LYS cc_start: 0.8855 (ttmt) cc_final: 0.8602 (mtpm) REVERT: R 207 MET cc_start: 0.8885 (mmm) cc_final: 0.8550 (mmm) REVERT: R 210 GLN cc_start: 0.8421 (tt0) cc_final: 0.8000 (mt0) REVERT: R 218 HIS cc_start: 0.7517 (t-90) cc_final: 0.7190 (t-90) REVERT: R 238 GLN cc_start: 0.8892 (mt0) cc_final: 0.8641 (mt0) REVERT: R 300 HIS cc_start: 0.8156 (t70) cc_final: 0.7588 (t70) REVERT: R 366 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7883 (tp) outliers start: 30 outliers final: 13 residues processed: 180 average time/residue: 0.5564 time to fit residues: 106.7863 Evaluate side-chains 174 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 149 ASP Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain R residue 366 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 GLN R 269 GLN R 360 ASN R 365 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.078681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.059643 restraints weight = 18473.632| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.12 r_work: 0.2832 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9156 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9123 Z= 0.138 Angle : 0.611 9.388 12375 Z= 0.310 Chirality : 0.043 0.194 1417 Planarity : 0.004 0.046 1560 Dihedral : 4.449 52.844 1248 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.60 % Allowed : 22.89 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.25), residues: 1132 helix: 2.31 (0.25), residues: 415 sheet: 0.40 (0.30), residues: 282 loop : -0.43 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 32 TYR 0.016 0.001 TYR R 145 PHE 0.053 0.002 PHE A 336 TRP 0.010 0.001 TRP B 297 HIS 0.011 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 9120) covalent geometry : angle 0.61009 / 0.31 (12369) SS BOND : bond 0.01058 / 0.55 ( 3) SS BOND : angle 1.82926 / 0.87 ( 6) hydrogen bonds : bond 0.04068 / 2.70 ( 473) hydrogen bonds : angle 4.69541 / 3.30 ( 1344) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.406 Fit side-chains REVERT: A 273 LEU cc_start: 0.9283 (mp) cc_final: 0.8988 (tm) REVERT: A 311 ASN cc_start: 0.8323 (p0) cc_final: 0.8079 (p0) REVERT: B 42 ARG cc_start: 0.8089 (ttt-90) cc_final: 0.7803 (ttt-90) REVERT: B 46 ARG cc_start: 0.8880 (mmm-85) cc_final: 0.8605 (mtp-110) REVERT: B 215 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8797 (mp0) REVERT: B 291 ASP cc_start: 0.8353 (t0) cc_final: 0.8056 (t0) REVERT: D 87 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7454 (mtt-85) REVERT: D 211 ASP cc_start: 0.8753 (t0) cc_final: 0.8501 (t0) REVERT: R 102 HIS cc_start: 0.8367 (m90) cc_final: 0.7915 (m90) REVERT: R 110 LEU cc_start: 0.9282 (tp) cc_final: 0.9022 (tm) REVERT: R 113 LEU cc_start: 0.9375 (tp) cc_final: 0.9153 (tm) REVERT: R 175 LYS cc_start: 0.8825 (ttmt) cc_final: 0.8570 (mtpm) REVERT: R 207 MET cc_start: 0.8856 (mmm) cc_final: 0.8517 (mmm) REVERT: R 210 GLN cc_start: 0.8397 (tt0) cc_final: 0.8004 (mt0) REVERT: R 218 HIS cc_start: 0.7534 (t-90) cc_final: 0.7202 (t-90) REVERT: R 238 GLN cc_start: 0.8885 (mt0) cc_final: 0.8638 (mt0) REVERT: R 303 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8308 (mtm-85) REVERT: R 366 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7889 (tp) outliers start: 25 outliers final: 11 residues processed: 178 average time/residue: 0.5860 time to fit residues: 110.6738 Evaluate side-chains 175 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 303 ARG Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain R residue 366 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN B 36 ASN D 174 GLN R 365 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.078671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.059696 restraints weight = 18256.066| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.09 r_work: 0.2835 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9146 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9123 Z= 0.142 Angle : 0.633 9.522 12375 Z= 0.324 Chirality : 0.043 0.202 1417 Planarity : 0.004 0.053 1560 Dihedral : 4.428 52.464 1248 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.50 % Allowed : 23.62 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.25), residues: 1132 helix: 2.26 (0.25), residues: 418 sheet: 0.45 (0.30), residues: 281 loop : -0.47 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 32 TYR 0.015 0.001 TYR R 145 PHE 0.011 0.001 PHE A 336 TRP 0.009 0.001 TRP B 297 HIS 0.010 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 9120) covalent geometry : angle 0.63225 / 0.32 (12369) SS BOND : bond 0.01068 / 0.56 ( 3) SS BOND : angle 1.85041 / 0.88 ( 6) hydrogen bonds : bond 0.04030 / 2.66 ( 473) hydrogen bonds : angle 4.71529 / 3.33 ( 1344) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.279 Fit side-chains REVERT: A 53 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.7972 (mpp) REVERT: A 273 LEU cc_start: 0.9290 (mp) cc_final: 0.9012 (tm) REVERT: A 311 ASN cc_start: 0.8305 (p0) cc_final: 0.8057 (p0) REVERT: B 46 ARG cc_start: 0.8863 (mmm-85) cc_final: 0.8594 (mtp-110) REVERT: B 215 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8913 (mp0) REVERT: B 291 ASP cc_start: 0.8365 (t0) cc_final: 0.8062 (t0) REVERT: D 87 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7498 (mtt-85) REVERT: D 211 ASP cc_start: 0.8757 (t0) cc_final: 0.8516 (t0) REVERT: R 102 HIS cc_start: 0.8436 (m90) cc_final: 0.8018 (m90) REVERT: R 110 LEU cc_start: 0.9271 (tp) cc_final: 0.9039 (tm) REVERT: R 113 LEU cc_start: 0.9338 (tp) cc_final: 0.9088 (tm) REVERT: R 175 LYS cc_start: 0.8772 (ttmt) cc_final: 0.8518 (mtpm) REVERT: R 207 MET cc_start: 0.8828 (mmm) cc_final: 0.8501 (mmm) REVERT: R 210 GLN cc_start: 0.8351 (tt0) cc_final: 0.7970 (mt0) REVERT: R 218 HIS cc_start: 0.7521 (t-90) cc_final: 0.7186 (t-90) REVERT: R 238 GLN cc_start: 0.8850 (mt0) cc_final: 0.8606 (mt0) REVERT: R 303 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8301 (mtm-85) REVERT: R 366 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7932 (tp) outliers start: 24 outliers final: 14 residues processed: 172 average time/residue: 0.5624 time to fit residues: 102.4691 Evaluate side-chains 175 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 148 ARG Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 303 ARG Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain R residue 366 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 0.0970 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 89 optimal weight: 0.0270 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN B 36 ASN ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 GLN R 126 ASN R 360 ASN R 365 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.079618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.060731 restraints weight = 18202.292| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.10 r_work: 0.2861 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9132 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9123 Z= 0.123 Angle : 0.624 9.776 12375 Z= 0.316 Chirality : 0.044 0.385 1417 Planarity : 0.004 0.061 1560 Dihedral : 4.325 51.192 1248 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.08 % Allowed : 24.66 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.25), residues: 1132 helix: 2.23 (0.25), residues: 418 sheet: 0.51 (0.30), residues: 281 loop : -0.46 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 32 TYR 0.014 0.001 TYR R 145 PHE 0.028 0.001 PHE A 336 TRP 0.011 0.001 TRP B 297 HIS 0.008 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 9120) covalent geometry : angle 0.62330 / 0.32 (12369) SS BOND : bond 0.00832 / 0.43 ( 3) SS BOND : angle 1.54531 / 0.74 ( 6) hydrogen bonds : bond 0.03820 / 2.51 ( 473) hydrogen bonds : angle 4.65067 / 3.28 ( 1344) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.271 Fit side-chains REVERT: A 53 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8121 (mpp) REVERT: A 242 ARG cc_start: 0.8905 (mtm-85) cc_final: 0.8308 (mtm-85) REVERT: A 273 LEU cc_start: 0.9290 (mp) cc_final: 0.9013 (tm) REVERT: A 311 ASN cc_start: 0.8211 (p0) cc_final: 0.7973 (p0) REVERT: B 42 ARG cc_start: 0.7838 (ttt-90) cc_final: 0.7353 (ttt-90) REVERT: B 46 ARG cc_start: 0.8870 (mmm-85) cc_final: 0.8613 (mtp-110) REVERT: B 215 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8908 (mp0) REVERT: B 291 ASP cc_start: 0.8292 (t0) cc_final: 0.7988 (t0) REVERT: C 58 GLU cc_start: 0.9160 (mp0) cc_final: 0.8945 (pm20) REVERT: D 211 ASP cc_start: 0.8704 (t0) cc_final: 0.8503 (t0) REVERT: R 110 LEU cc_start: 0.9245 (tp) cc_final: 0.9019 (tm) REVERT: R 113 LEU cc_start: 0.9335 (tp) cc_final: 0.9063 (tm) REVERT: R 175 LYS cc_start: 0.8732 (ttmt) cc_final: 0.8471 (mtmt) REVERT: R 207 MET cc_start: 0.8787 (mmm) cc_final: 0.8492 (mmm) REVERT: R 210 GLN cc_start: 0.8341 (tt0) cc_final: 0.7998 (mt0) REVERT: R 218 HIS cc_start: 0.7550 (t-90) cc_final: 0.7218 (t-90) REVERT: R 238 GLN cc_start: 0.8865 (mt0) cc_final: 0.8624 (mt0) outliers start: 20 outliers final: 11 residues processed: 172 average time/residue: 0.5777 time to fit residues: 105.4669 Evaluate side-chains 169 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN D 174 GLN ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.078986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.059987 restraints weight = 18131.150| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.09 r_work: 0.2844 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9148 moved from start: 0.5785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9123 Z= 0.140 Angle : 0.630 10.290 12375 Z= 0.321 Chirality : 0.044 0.325 1417 Planarity : 0.004 0.059 1560 Dihedral : 4.357 51.575 1248 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.87 % Allowed : 25.29 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.25), residues: 1132 helix: 2.39 (0.25), residues: 412 sheet: 0.46 (0.30), residues: 283 loop : -0.52 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 32 TYR 0.015 0.001 TYR R 70 PHE 0.046 0.001 PHE A 336 TRP 0.009 0.001 TRP B 297 HIS 0.006 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 9120) covalent geometry : angle 0.62920 / 0.32 (12369) SS BOND : bond 0.01098 / 0.57 ( 3) SS BOND : angle 1.93091 / 0.93 ( 6) hydrogen bonds : bond 0.03913 / 2.59 ( 473) hydrogen bonds : angle 4.66850 / 3.30 ( 1344) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4217.45 seconds wall clock time: 72 minutes 24.41 seconds (4344.41 seconds total)