Starting phenix.real_space_refine on Thu Jul 2 14:56:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vaz_64910/07_2026/9vaz_64910.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vaz_64910/07_2026/9vaz_64910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vaz_64910/07_2026/9vaz_64910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vaz_64910/07_2026/9vaz_64910.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vaz_64910/07_2026/9vaz_64910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vaz_64910/07_2026/9vaz_64910.map" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.008 sd= 0.071 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 62 5.16 5 C 5680 2.51 5 N 1522 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 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: 8934 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1754 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1758 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2374 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 294} Chain breaks: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'TRP:plan': 2, 'PHE:plan': 3, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 45 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: 2.24, per 1000 atoms: 0.25 Number of scatterers: 8934 At special positions: 0 Unit cell: (92.6833, 121.733, 128.65, 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 62 16.00 O 1670 8.00 N 1522 7.00 C 5680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.82 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: 0.77 Conformation dependent library (CDL) restraints added in 546.7 milliseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 15 sheets defined 40.5% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 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 212 removed outlier: 4.191A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.619A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.771A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.109A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.686A 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 352 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.711A 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 removed outlier: 3.549A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) 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: 3.607A 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 59 through 91 Processing helix chain 'R' and resid 98 through 128 Proline residue: R 121 - end of helix removed outlier: 3.614A pdb=" N LEU R 124 " --> pdb=" O MET R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 171 removed outlier: 3.635A pdb=" N TYR R 145 " --> pdb=" O CYS R 141 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE R 146 " --> pdb=" O ARG R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 180 removed outlier: 3.615A pdb=" N LYS R 177 " --> pdb=" O PRO R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 206 Proline residue: R 202 - end of helix 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 Proline residue: R 318 - end of helix removed outlier: 4.201A pdb=" N MET R 325 " --> pdb=" O VAL R 321 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE R 326 " --> pdb=" O ARG R 322 " (cutoff:3.500A) Processing helix chain 'R' and resid 330 through 334 Processing helix chain 'R' and resid 335 through 368 Proline residue: R 361 - end of helix removed outlier: 4.231A pdb=" N VAL R 367 " --> pdb=" O LEU R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 368 through 383 removed outlier: 3.728A 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 190 removed outlier: 6.286A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N THR A 324 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU A 268 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 5.749A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.775A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.111A 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: 6.184A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.809A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.517A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.180A 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: 6.691A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.394A 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: 3.712A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 317 through 320 Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.659A pdb=" N GLY D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.659A pdb=" N GLY D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 128 through 130 Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.474A pdb=" N VAL D 135 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 207 through 208 477 hydrogen bonds defined for protein. 1353 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: 1.75 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.21: 23 1.21 - 1.38: 3029 1.38 - 1.55: 5783 1.55 - 1.72: 190 1.72 - 1.89: 91 Bond restraints: 9116 Sorted by residual: bond pdb=" CB LYS R 177 " pdb=" CG LYS R 177 " ideal model delta sigma weight residual 1.520 1.065 0.455 3.00e-02 1.11e+03 2.30e+02 bond pdb=" CB ILE R 60 " pdb=" CG2 ILE R 60 " ideal model delta sigma weight residual 1.521 1.035 0.486 3.30e-02 9.18e+02 2.17e+02 bond pdb=" CB SER R 52 " pdb=" OG SER R 52 " ideal model delta sigma weight residual 1.417 1.145 0.272 2.00e-02 2.50e+03 1.85e+02 bond pdb=" CA SER R 330 " pdb=" CB SER R 330 " ideal model delta sigma weight residual 1.528 1.319 0.209 1.66e-02 3.63e+03 1.59e+02 bond pdb=" CA GLU R 332 " pdb=" CB GLU R 332 " ideal model delta sigma weight residual 1.530 1.347 0.182 1.56e-02 4.11e+03 1.37e+02 ... (remaining 9111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.89: 11428 3.89 - 7.79: 854 7.79 - 11.68: 51 11.68 - 15.58: 21 15.58 - 19.47: 7 Bond angle restraints: 12361 Sorted by residual: angle pdb=" NE ARG R 306 " pdb=" CZ ARG R 306 " pdb=" NH2 ARG R 306 " ideal model delta sigma weight residual 119.20 106.40 12.80 9.00e-01 1.23e+00 2.02e+02 angle pdb=" CD ARG R 90 " pdb=" NE ARG R 90 " pdb=" CZ ARG R 90 " ideal model delta sigma weight residual 124.40 139.38 -14.98 1.40e+00 5.10e-01 1.14e+02 angle pdb=" CD ARG R 322 " pdb=" NE ARG R 322 " pdb=" CZ ARG R 322 " ideal model delta sigma weight residual 124.40 139.21 -14.81 1.40e+00 5.10e-01 1.12e+02 angle pdb=" CA VAL R 64 " pdb=" CB VAL R 64 " pdb=" CG1 VAL R 64 " ideal model delta sigma weight residual 110.40 93.57 16.83 1.70e+00 3.46e-01 9.80e+01 angle pdb=" CA LYS R 177 " pdb=" CB LYS R 177 " pdb=" CG LYS R 177 " ideal model delta sigma weight residual 114.10 133.57 -19.47 2.00e+00 2.50e-01 9.48e+01 ... (remaining 12356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4823 17.73 - 35.46: 437 35.46 - 53.18: 108 53.18 - 70.91: 27 70.91 - 88.64: 10 Dihedral angle restraints: 5405 sinusoidal: 2054 harmonic: 3351 Sorted by residual: dihedral pdb=" N PHE R 326 " pdb=" C PHE R 326 " pdb=" CA PHE R 326 " pdb=" CB PHE R 326 " ideal model delta harmonic sigma weight residual 122.80 141.13 -18.33 0 2.50e+00 1.60e-01 5.38e+01 dihedral pdb=" C GLU R 332 " pdb=" N GLU R 332 " pdb=" CA GLU R 332 " pdb=" CB GLU R 332 " ideal model delta harmonic sigma weight residual -122.60 -140.44 17.84 0 2.50e+00 1.60e-01 5.09e+01 dihedral pdb=" N GLU R 332 " pdb=" C GLU R 332 " pdb=" CA GLU R 332 " pdb=" CB GLU R 332 " ideal model delta harmonic sigma weight residual 122.80 140.31 -17.51 0 2.50e+00 1.60e-01 4.91e+01 ... (remaining 5402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.353: 1401 0.353 - 0.707: 20 0.707 - 1.060: 2 1.060 - 1.414: 0 1.414 - 1.767: 1 Chirality restraints: 1424 Sorted by residual: chirality pdb=" CB ILE R 60 " pdb=" CA ILE R 60 " pdb=" CG1 ILE R 60 " pdb=" CG2 ILE R 60 " both_signs ideal model delta sigma weight residual False 2.64 0.88 1.77 2.00e-01 2.50e+01 7.81e+01 chirality pdb=" CG LEU R 71 " pdb=" CB LEU R 71 " pdb=" CD1 LEU R 71 " pdb=" CD2 LEU R 71 " both_signs ideal model delta sigma weight residual False -2.59 -3.53 0.94 2.00e-01 2.50e+01 2.20e+01 chirality pdb=" CA GLU R 332 " pdb=" N GLU R 332 " pdb=" C GLU R 332 " pdb=" CB GLU R 332 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.11e+01 ... (remaining 1421 not shown) Planarity restraints: 1559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 322 " 0.943 9.50e-02 1.11e+02 4.31e-01 1.96e+02 pdb=" NE ARG R 322 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG R 322 " -0.172 2.00e-02 2.50e+03 pdb=" NH1 ARG R 322 " 0.062 2.00e-02 2.50e+03 pdb=" NH2 ARG R 322 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 182 " 0.956 9.50e-02 1.11e+02 4.29e-01 1.11e+02 pdb=" NE ARG R 182 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG R 182 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG R 182 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG R 182 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 268 " -0.600 9.50e-02 1.11e+02 2.77e-01 1.00e+02 pdb=" NE ARG R 268 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG R 268 " 0.136 2.00e-02 2.50e+03 pdb=" NH1 ARG R 268 " -0.041 2.00e-02 2.50e+03 pdb=" NH2 ARG R 268 " -0.061 2.00e-02 2.50e+03 ... (remaining 1556 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 1343 2.82 - 3.34: 9481 3.34 - 3.86: 14576 3.86 - 4.38: 17442 4.38 - 4.90: 28873 Nonbonded interactions: 71715 Sorted by model distance: nonbonded pdb=" O GLN R 98 " pdb=" N VAL R 101 " model vdw 2.306 3.120 nonbonded pdb=" O SER B 227 " pdb=" OG SER B 245 " model vdw 2.331 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.379 3.040 nonbonded pdb=" O SER R 99 " pdb=" N HIS R 102 " model vdw 2.416 3.120 nonbonded pdb=" N ASP B 228 " pdb=" OD1 ASP B 228 " model vdw 2.417 3.120 ... (remaining 71710 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.510 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 : 0.018 0.790 9117 Z= 0.984 Angle : 2.312 19.474 12363 Z= 1.571 Chirality : 0.146 1.767 1424 Planarity : 0.026 0.431 1559 Dihedral : 15.651 88.641 3238 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 7.24 % Allowed : 11.38 % Favored : 81.39 % Cbeta Deviations : 3.14 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.22), residues: 1130 helix: -1.42 (0.22), residues: 419 sheet: -1.20 (0.33), residues: 220 loop : -1.96 (0.24), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.161 0.011 ARG R 322 TYR 0.049 0.008 TYR A 296 PHE 0.113 0.007 PHE R 174 TRP 0.044 0.009 TRP R 334 HIS 0.027 0.006 HIS R 132 Details of bonding type rmsd/Z covalent geometry : bond 0.01604 / 0.89 ( 9116) covalent geometry : angle 2.31053 / 1.57 (12361) SS BOND : bond 0.79019 / 41.59 ( 1) SS BOND : angle 6.02403 / 3.48 ( 2) hydrogen bonds : bond 0.22052 / 14.91 ( 471) hydrogen bonds : angle 8.85895 / 6.26 ( 1353) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 346 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8649 (mtm-85) cc_final: 0.8290 (mmt180) REVERT: A 193 ASP cc_start: 0.9270 (m-30) cc_final: 0.8959 (p0) REVERT: A 197 LYS cc_start: 0.9034 (mtpt) cc_final: 0.8784 (mtmm) REVERT: A 205 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7904 (ppt-90) REVERT: A 242 ARG cc_start: 0.8516 (ttm170) cc_final: 0.7401 (mtm-85) REVERT: A 302 TYR cc_start: 0.8614 (t80) cc_final: 0.8409 (t80) REVERT: A 304 GLN cc_start: 0.8857 (tt0) cc_final: 0.8408 (tm-30) REVERT: A 313 ARG cc_start: 0.8940 (ptp90) cc_final: 0.8676 (ptp-170) REVERT: A 315 ASP cc_start: 0.8361 (p0) cc_final: 0.7819 (p0) REVERT: A 333 GLN cc_start: 0.9149 (tp40) cc_final: 0.8803 (tp40) REVERT: A 345 LYS cc_start: 0.9552 (mttp) cc_final: 0.9331 (tppt) REVERT: B 4 LEU cc_start: 0.9519 (pp) cc_final: 0.9293 (pp) REVERT: B 16 ASN cc_start: 0.8884 (t0) cc_final: 0.8421 (t0) REVERT: B 17 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8807 (pt0) REVERT: B 173 THR cc_start: 0.8967 (p) cc_final: 0.8447 (t) REVERT: B 267 ASP cc_start: 0.9378 (m-30) cc_final: 0.9167 (p0) REVERT: B 297 TRP cc_start: 0.8783 (m100) cc_final: 0.8478 (m100) REVERT: C 9 ILE cc_start: 0.8660 (tt) cc_final: 0.8389 (pt) REVERT: C 13 ARG cc_start: 0.9755 (mtt180) cc_final: 0.9514 (ptp-110) REVERT: C 14 LYS cc_start: 0.9661 (ttmp) cc_final: 0.9370 (mttm) REVERT: C 15 LEU cc_start: 0.9660 (mt) cc_final: 0.9453 (pp) REVERT: D 87 ARG cc_start: 0.8729 (mtm180) cc_final: 0.8489 (mtm180) REVERT: D 164 TRP cc_start: 0.8589 (m100) cc_final: 0.8233 (m100) REVERT: D 171 GLN cc_start: 0.9341 (mt0) cc_final: 0.9096 (mm-40) REVERT: D 206 ARG cc_start: 0.9088 (ttp80) cc_final: 0.8787 (ttp80) REVERT: R 175 LYS cc_start: 0.4739 (OUTLIER) cc_final: 0.4368 (mmtt) REVERT: R 178 THR cc_start: 0.8850 (m) cc_final: 0.8478 (p) REVERT: R 316 TRP cc_start: 0.8714 (m-10) cc_final: 0.8414 (m-10) REVERT: R 372 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8057 (ppt-90) REVERT: R 375 PHE cc_start: 0.9611 (t80) cc_final: 0.9365 (t80) outliers start: 70 outliers final: 23 residues processed: 393 average time/residue: 0.1165 time to fit residues: 60.4607 Evaluate side-chains 266 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 240 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 178 TYR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 175 LYS Chi-restraints excluded: chain R residue 224 CYS Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 240 ASN Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 273 GLN Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 309 VAL Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain R residue 322 ARG Chi-restraints excluded: chain R residue 335 THR Chi-restraints excluded: chain R residue 353 PHE Chi-restraints excluded: chain R residue 364 TYR Chi-restraints excluded: chain R residue 372 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN B 230 ASN B 239 ASN B 259 GLN B 340 ASN C 18 GLN D 182 ASN R 126 ASN ** R 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 261 ASN R 333 GLN R 360 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.106958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.079654 restraints weight = 25041.820| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 4.19 r_work: 0.3220 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 9117 Z= 0.210 Angle : 0.814 11.778 12363 Z= 0.427 Chirality : 0.049 0.183 1424 Planarity : 0.005 0.062 1559 Dihedral : 8.520 74.050 1301 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.86 % Allowed : 18.82 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.24), residues: 1130 helix: 0.72 (0.24), residues: 410 sheet: -0.52 (0.29), residues: 274 loop : -1.55 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG R 322 TYR 0.017 0.002 TYR R 364 PHE 0.028 0.002 PHE R 353 TRP 0.020 0.002 TRP R 334 HIS 0.008 0.002 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.21 ( 9116) covalent geometry : angle 0.81427 / 0.43 (12361) SS BOND : bond 0.00215 / 0.11 ( 1) SS BOND : angle 1.41357 / 0.73 ( 2) hydrogen bonds : bond 0.06270 / 4.28 ( 471) hydrogen bonds : angle 5.89191 / 4.12 ( 1353) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 243 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8055 (ppt-90) REVERT: A 242 ARG cc_start: 0.7812 (ttm170) cc_final: 0.7555 (mtm-85) REVERT: A 243 MET cc_start: 0.7856 (tpp) cc_final: 0.7395 (tpp) REVERT: A 247 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8265 (mtm) REVERT: A 304 GLN cc_start: 0.8772 (tt0) cc_final: 0.8434 (pp30) REVERT: A 313 ARG cc_start: 0.9177 (ptp90) cc_final: 0.8949 (ptp-170) REVERT: B 217 MET cc_start: 0.8999 (pmm) cc_final: 0.8784 (pmm) REVERT: B 323 ASP cc_start: 0.8775 (t0) cc_final: 0.8315 (t0) REVERT: B 325 MET cc_start: 0.8866 (tpt) cc_final: 0.8638 (mmm) REVERT: C 11 GLN cc_start: 0.9397 (pp30) cc_final: 0.9060 (pp30) REVERT: C 14 LYS cc_start: 0.9563 (ttmp) cc_final: 0.9359 (mttm) REVERT: C 15 LEU cc_start: 0.9652 (mt) cc_final: 0.9422 (pp) REVERT: C 22 GLU cc_start: 0.8943 (tp30) cc_final: 0.8733 (mm-30) REVERT: C 29 LYS cc_start: 0.8552 (mtpp) cc_final: 0.8176 (tppt) REVERT: C 32 LYS cc_start: 0.9034 (tptp) cc_final: 0.8735 (tmtt) REVERT: D 164 TRP cc_start: 0.8575 (m100) cc_final: 0.8227 (m100) REVERT: D 206 ARG cc_start: 0.8448 (ttp80) cc_final: 0.7991 (ttp80) REVERT: D 218 MET cc_start: 0.7736 (ttp) cc_final: 0.7505 (ttp) REVERT: R 81 ASN cc_start: 0.8472 (m-40) cc_final: 0.8195 (m-40) REVERT: R 102 HIS cc_start: 0.8652 (m-70) cc_final: 0.8431 (m90) REVERT: R 375 PHE cc_start: 0.9221 (t80) cc_final: 0.8850 (t80) outliers start: 47 outliers final: 23 residues processed: 271 average time/residue: 0.1118 time to fit residues: 40.3067 Evaluate side-chains 226 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 240 ASN Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 322 ARG Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 335 THR Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 353 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 90 optimal weight: 0.3980 chunk 109 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 119 ASN D 219 GLN R 350 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.105612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.078537 restraints weight = 25111.589| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 4.11 r_work: 0.3202 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9117 Z= 0.186 Angle : 0.760 9.634 12363 Z= 0.391 Chirality : 0.047 0.185 1424 Planarity : 0.005 0.045 1559 Dihedral : 6.652 65.152 1266 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.24 % Allowed : 19.75 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.25 (0.24), residues: 1130 helix: 1.14 (0.24), residues: 417 sheet: -0.29 (0.29), residues: 272 loop : -1.30 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 68 TYR 0.022 0.002 TYR B 85 PHE 0.022 0.002 PHE R 174 TRP 0.018 0.002 TRP B 82 HIS 0.006 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 ( 9116) covalent geometry : angle 0.75969 / 0.39 (12361) SS BOND : bond 0.00350 / 0.18 ( 1) SS BOND : angle 1.16988 / 0.56 ( 2) hydrogen bonds : bond 0.05267 / 3.61 ( 471) hydrogen bonds : angle 5.37227 / 3.75 ( 1353) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 214 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.9113 (m-30) cc_final: 0.8876 (m-30) REVERT: A 26 ASP cc_start: 0.8607 (m-30) cc_final: 0.8332 (m-30) REVERT: A 205 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8098 (ppt-90) REVERT: A 229 ASP cc_start: 0.8392 (m-30) cc_final: 0.7765 (t70) REVERT: A 242 ARG cc_start: 0.8159 (ttm170) cc_final: 0.7945 (mtt-85) REVERT: A 247 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8213 (mtm) REVERT: A 304 GLN cc_start: 0.8760 (tt0) cc_final: 0.8462 (pp30) REVERT: A 313 ARG cc_start: 0.9230 (ptp90) cc_final: 0.8720 (ptp-170) REVERT: A 333 GLN cc_start: 0.9280 (tp40) cc_final: 0.9032 (tp40) REVERT: B 13 GLN cc_start: 0.9391 (mm110) cc_final: 0.9176 (mm110) REVERT: B 32 GLN cc_start: 0.9367 (mt0) cc_final: 0.9076 (pt0) REVERT: B 226 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8213 (mp0) REVERT: B 228 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7269 (p0) REVERT: B 264 TYR cc_start: 0.9026 (m-80) cc_final: 0.8282 (m-80) REVERT: B 323 ASP cc_start: 0.8807 (t0) cc_final: 0.8278 (t0) REVERT: B 325 MET cc_start: 0.9100 (tpt) cc_final: 0.8731 (mmm) REVERT: C 15 LEU cc_start: 0.9651 (mt) cc_final: 0.9384 (pp) REVERT: C 29 LYS cc_start: 0.8328 (mtpp) cc_final: 0.8015 (tppp) REVERT: C 32 LYS cc_start: 0.8910 (tptp) cc_final: 0.8529 (tmtt) REVERT: D 128 MET cc_start: 0.7340 (mmm) cc_final: 0.7040 (mmp) REVERT: D 206 ARG cc_start: 0.8541 (ttp80) cc_final: 0.8064 (ttp80) REVERT: D 218 MET cc_start: 0.7749 (ttp) cc_final: 0.7353 (ttp) REVERT: R 120 MET cc_start: 0.9233 (mmm) cc_final: 0.9024 (mmm) REVERT: R 243 MET cc_start: 0.9333 (tpp) cc_final: 0.8967 (mmt) REVERT: R 375 PHE cc_start: 0.9204 (t80) cc_final: 0.8897 (t80) outliers start: 41 outliers final: 20 residues processed: 242 average time/residue: 0.1084 time to fit residues: 35.4470 Evaluate side-chains 217 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 240 ASN Chi-restraints excluded: chain R residue 335 THR Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 353 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 90 optimal weight: 0.0170 chunk 15 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 overall best weight: 4.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 159 ASN ** R 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.103043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.076182 restraints weight = 26120.066| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 4.02 r_work: 0.3157 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 9117 Z= 0.222 Angle : 0.745 8.667 12363 Z= 0.384 Chirality : 0.046 0.174 1424 Planarity : 0.005 0.045 1559 Dihedral : 6.224 62.150 1260 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.86 % Allowed : 20.99 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.12 (0.24), residues: 1130 helix: 1.26 (0.24), residues: 414 sheet: -0.19 (0.30), residues: 273 loop : -1.26 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 68 TYR 0.024 0.002 TYR D 178 PHE 0.016 0.002 PHE B 234 TRP 0.015 0.002 TRP D 36 HIS 0.008 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.22 ( 9116) covalent geometry : angle 0.74499 / 0.38 (12361) SS BOND : bond 0.00021 / 0.01 ( 1) SS BOND : angle 0.83363 / 0.41 ( 2) hydrogen bonds : bond 0.04934 / 3.33 ( 471) hydrogen bonds : angle 5.27750 / 3.68 ( 1353) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 198 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8107 (ppt-90) REVERT: A 229 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.7648 (t0) REVERT: A 242 ARG cc_start: 0.8339 (ttm170) cc_final: 0.7957 (mtm-85) REVERT: A 247 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8139 (mtm) REVERT: A 304 GLN cc_start: 0.8844 (tt0) cc_final: 0.8438 (pp30) REVERT: A 313 ARG cc_start: 0.9208 (ptp90) cc_final: 0.8607 (ptp-170) REVERT: A 333 GLN cc_start: 0.9260 (tp40) cc_final: 0.8995 (tp40) REVERT: B 13 GLN cc_start: 0.9413 (mm110) cc_final: 0.9186 (mm110) REVERT: B 32 GLN cc_start: 0.9481 (mt0) cc_final: 0.9054 (pt0) REVERT: B 75 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8701 (mm-40) REVERT: B 85 TYR cc_start: 0.8844 (m-80) cc_final: 0.8046 (m-80) REVERT: B 142 HIS cc_start: 0.8632 (OUTLIER) cc_final: 0.7725 (t70) REVERT: B 226 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8235 (mp0) REVERT: B 228 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7466 (p0) REVERT: B 264 TYR cc_start: 0.9169 (m-80) cc_final: 0.8725 (m-80) REVERT: B 323 ASP cc_start: 0.8899 (t0) cc_final: 0.8422 (t0) REVERT: B 325 MET cc_start: 0.9319 (tpt) cc_final: 0.8970 (mmm) REVERT: C 29 LYS cc_start: 0.8280 (mtpp) cc_final: 0.8026 (tppt) REVERT: C 32 LYS cc_start: 0.8961 (tptp) cc_final: 0.8661 (tmtt) REVERT: D 18 ARG cc_start: 0.8840 (tpp80) cc_final: 0.8568 (tpp80) REVERT: D 128 MET cc_start: 0.7334 (mmm) cc_final: 0.6996 (mmp) REVERT: D 148 ARG cc_start: 0.8769 (mtm110) cc_final: 0.8563 (ttp80) REVERT: D 206 ARG cc_start: 0.8529 (ttp80) cc_final: 0.7960 (ttp80) REVERT: D 218 MET cc_start: 0.7840 (ttp) cc_final: 0.7555 (ttp) REVERT: R 108 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8566 (mp) REVERT: R 375 PHE cc_start: 0.9216 (t80) cc_final: 0.8934 (t80) outliers start: 47 outliers final: 28 residues processed: 229 average time/residue: 0.1162 time to fit residues: 35.3438 Evaluate side-chains 222 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 240 ASN Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 353 PHE Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain R residue 370 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.104299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.077397 restraints weight = 25447.809| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 4.05 r_work: 0.3169 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9117 Z= 0.170 Angle : 0.729 12.747 12363 Z= 0.370 Chirality : 0.045 0.212 1424 Planarity : 0.004 0.045 1559 Dihedral : 5.960 59.430 1259 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.34 % Allowed : 21.82 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.03 (0.25), residues: 1130 helix: 1.35 (0.25), residues: 417 sheet: -0.17 (0.30), residues: 271 loop : -1.23 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 68 TYR 0.031 0.002 TYR A 302 PHE 0.017 0.001 PHE R 337 TRP 0.015 0.002 TRP R 334 HIS 0.009 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 ( 9116) covalent geometry : angle 0.72882 / 0.37 (12361) SS BOND : bond 0.00076 / 0.04 ( 1) SS BOND : angle 0.66199 / 0.32 ( 2) hydrogen bonds : bond 0.04575 / 3.08 ( 471) hydrogen bonds : angle 5.15750 / 3.58 ( 1353) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8027 (ppt-90) REVERT: A 229 ASP cc_start: 0.8370 (m-30) cc_final: 0.7467 (t0) REVERT: A 242 ARG cc_start: 0.8345 (ttm170) cc_final: 0.7950 (mtm-85) REVERT: A 247 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.7920 (mpp) REVERT: A 296 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.7821 (t80) REVERT: A 304 GLN cc_start: 0.8802 (tt0) cc_final: 0.8393 (pp30) REVERT: A 333 GLN cc_start: 0.9233 (tp40) cc_final: 0.8964 (tp40) REVERT: B 13 GLN cc_start: 0.9429 (mm110) cc_final: 0.8764 (mm110) REVERT: B 32 GLN cc_start: 0.9451 (mt0) cc_final: 0.9029 (pt0) REVERT: B 85 TYR cc_start: 0.8745 (m-80) cc_final: 0.8370 (m-80) REVERT: B 142 HIS cc_start: 0.8678 (OUTLIER) cc_final: 0.7989 (t70) REVERT: B 228 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7407 (p0) REVERT: B 264 TYR cc_start: 0.9127 (m-80) cc_final: 0.8433 (m-80) REVERT: B 323 ASP cc_start: 0.8769 (t0) cc_final: 0.8562 (t0) REVERT: B 325 MET cc_start: 0.9242 (tpt) cc_final: 0.9042 (mmm) REVERT: C 9 ILE cc_start: 0.8911 (pt) cc_final: 0.8658 (pt) REVERT: C 13 ARG cc_start: 0.9611 (OUTLIER) cc_final: 0.9378 (ptp90) REVERT: C 32 LYS cc_start: 0.8990 (tptp) cc_final: 0.8689 (tmtt) REVERT: D 18 ARG cc_start: 0.8877 (tpp80) cc_final: 0.8542 (tpp80) REVERT: D 19 LYS cc_start: 0.9398 (tttm) cc_final: 0.9141 (tttm) REVERT: D 128 MET cc_start: 0.7594 (mmm) cc_final: 0.7255 (mmp) REVERT: D 148 ARG cc_start: 0.8665 (mtm110) cc_final: 0.8460 (ttp80) REVERT: D 218 MET cc_start: 0.7737 (ttp) cc_final: 0.7499 (ttp) REVERT: D 232 LYS cc_start: 0.7902 (ttpp) cc_final: 0.6953 (ttpp) REVERT: D 234 GLU cc_start: 0.7014 (pm20) cc_final: 0.6513 (pm20) REVERT: R 120 MET cc_start: 0.9185 (mmm) cc_final: 0.8947 (mmm) REVERT: R 207 MET cc_start: 0.7733 (tpp) cc_final: 0.7081 (tpp) REVERT: R 375 PHE cc_start: 0.9158 (t80) cc_final: 0.8903 (t80) outliers start: 42 outliers final: 26 residues processed: 226 average time/residue: 0.1144 time to fit residues: 34.6315 Evaluate side-chains 215 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 240 ASN Chi-restraints excluded: chain R residue 322 ARG Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 353 PHE Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 0.0870 chunk 2 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 108 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 2.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN A 306 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** R 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 131 HIS ** R 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 373 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.104679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.077811 restraints weight = 25427.387| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 4.07 r_work: 0.3174 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9117 Z= 0.163 Angle : 0.738 11.845 12363 Z= 0.374 Chirality : 0.044 0.219 1424 Planarity : 0.004 0.043 1559 Dihedral : 5.835 56.523 1259 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.93 % Allowed : 23.16 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.13 (0.25), residues: 1130 helix: 1.50 (0.25), residues: 419 sheet: -0.06 (0.31), residues: 266 loop : -1.17 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG R 322 TYR 0.021 0.002 TYR D 178 PHE 0.014 0.001 PHE R 353 TRP 0.012 0.001 TRP R 334 HIS 0.010 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 9116) covalent geometry : angle 0.73824 / 0.37 (12361) SS BOND : bond 0.00062 / 0.03 ( 1) SS BOND : angle 0.50337 / 0.24 ( 2) hydrogen bonds : bond 0.04408 / 2.91 ( 471) hydrogen bonds : angle 5.09289 / 3.54 ( 1353) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 193 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8124 (ppt-90) REVERT: A 229 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7410 (t0) REVERT: A 242 ARG cc_start: 0.8300 (ttm170) cc_final: 0.7897 (mtt-85) REVERT: A 247 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8139 (mtm) REVERT: A 304 GLN cc_start: 0.8829 (tt0) cc_final: 0.8413 (pp30) REVERT: A 333 GLN cc_start: 0.9239 (tp40) cc_final: 0.8987 (tp40) REVERT: B 32 GLN cc_start: 0.9469 (mt0) cc_final: 0.9125 (pt0) REVERT: B 85 TYR cc_start: 0.8873 (m-80) cc_final: 0.8586 (m-80) REVERT: B 142 HIS cc_start: 0.8582 (OUTLIER) cc_final: 0.7843 (t70) REVERT: B 228 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7009 (p0) REVERT: B 264 TYR cc_start: 0.9162 (m-80) cc_final: 0.8426 (m-80) REVERT: B 323 ASP cc_start: 0.8866 (t0) cc_final: 0.8646 (t0) REVERT: B 325 MET cc_start: 0.9260 (tpt) cc_final: 0.9040 (mmm) REVERT: C 32 LYS cc_start: 0.8901 (tptp) cc_final: 0.8570 (tmtt) REVERT: D 18 ARG cc_start: 0.8823 (tpp80) cc_final: 0.8450 (tpp80) REVERT: D 128 MET cc_start: 0.7538 (mmm) cc_final: 0.7133 (mmp) REVERT: D 189 ASP cc_start: 0.9231 (t70) cc_final: 0.8954 (t0) REVERT: D 206 ARG cc_start: 0.8474 (ttp80) cc_final: 0.7972 (ttp80) REVERT: D 218 MET cc_start: 0.7722 (ttp) cc_final: 0.7468 (ttp) REVERT: D 232 LYS cc_start: 0.7876 (ttpp) cc_final: 0.7142 (ttpp) REVERT: R 120 MET cc_start: 0.9239 (mmm) cc_final: 0.8969 (mmm) REVERT: R 375 PHE cc_start: 0.9134 (t80) cc_final: 0.8885 (t80) outliers start: 38 outliers final: 26 residues processed: 219 average time/residue: 0.1150 time to fit residues: 33.4411 Evaluate side-chains 218 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 240 ASN Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 353 PHE Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 72 optimal weight: 40.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN B 75 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 GLN D 219 GLN ** R 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 373 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.103894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.076136 restraints weight = 26092.836| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 4.15 r_work: 0.3144 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9117 Z= 0.185 Angle : 0.744 11.290 12363 Z= 0.378 Chirality : 0.045 0.195 1424 Planarity : 0.005 0.044 1559 Dihedral : 5.776 53.153 1259 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.55 % Allowed : 23.89 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.10 (0.25), residues: 1130 helix: 1.43 (0.25), residues: 418 sheet: 0.08 (0.31), residues: 258 loop : -1.22 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 148 TYR 0.024 0.002 TYR D 178 PHE 0.013 0.001 PHE B 234 TRP 0.013 0.002 TRP R 334 HIS 0.009 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 9116) covalent geometry : angle 0.74450 / 0.38 (12361) SS BOND : bond 0.00033 / 0.02 ( 1) SS BOND : angle 0.57468 / 0.28 ( 2) hydrogen bonds : bond 0.04465 / 2.95 ( 471) hydrogen bonds : angle 5.08971 / 3.55 ( 1353) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8104 (ppt-90) REVERT: A 229 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.7458 (t0) REVERT: A 242 ARG cc_start: 0.8341 (ttm170) cc_final: 0.7981 (mtm-85) REVERT: A 247 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8178 (mtm) REVERT: A 304 GLN cc_start: 0.8710 (tt0) cc_final: 0.8238 (pp30) REVERT: A 333 GLN cc_start: 0.9216 (tp40) cc_final: 0.8954 (tp40) REVERT: A 345 LYS cc_start: 0.9413 (mttp) cc_final: 0.9022 (tptt) REVERT: B 32 GLN cc_start: 0.9333 (mt0) cc_final: 0.8956 (pt0) REVERT: B 142 HIS cc_start: 0.8612 (OUTLIER) cc_final: 0.7944 (t70) REVERT: B 228 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7159 (p0) REVERT: B 264 TYR cc_start: 0.9188 (m-80) cc_final: 0.8441 (m-80) REVERT: B 280 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8227 (mtpt) REVERT: C 32 LYS cc_start: 0.8990 (tptp) cc_final: 0.8686 (tmtt) REVERT: D 18 ARG cc_start: 0.8862 (tpp80) cc_final: 0.8599 (tpp80) REVERT: D 128 MET cc_start: 0.7575 (mmm) cc_final: 0.7204 (mmp) REVERT: D 148 ARG cc_start: 0.8720 (mtm110) cc_final: 0.8484 (mtm110) REVERT: D 189 ASP cc_start: 0.9258 (t70) cc_final: 0.8977 (t0) REVERT: D 206 ARG cc_start: 0.8508 (ttp80) cc_final: 0.8009 (ttp80) REVERT: D 218 MET cc_start: 0.7872 (ttp) cc_final: 0.7610 (ttp) REVERT: D 232 LYS cc_start: 0.8342 (ttpp) cc_final: 0.7772 (ttpp) REVERT: R 81 ASN cc_start: 0.8633 (m-40) cc_final: 0.8219 (p0) REVERT: R 207 MET cc_start: 0.8061 (tpp) cc_final: 0.7681 (tpp) REVERT: R 316 TRP cc_start: 0.8874 (m-10) cc_final: 0.8585 (m-10) REVERT: R 375 PHE cc_start: 0.9179 (t80) cc_final: 0.8918 (t80) outliers start: 44 outliers final: 31 residues processed: 217 average time/residue: 0.1130 time to fit residues: 32.4615 Evaluate side-chains 216 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 240 ASN Chi-restraints excluded: chain R residue 322 ARG Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 353 PHE Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN ** R 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.101234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.074429 restraints weight = 25944.066| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.97 r_work: 0.3108 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.6000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9117 Z= 0.268 Angle : 0.806 10.336 12363 Z= 0.413 Chirality : 0.047 0.240 1424 Planarity : 0.005 0.053 1559 Dihedral : 5.962 51.443 1259 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.65 % Allowed : 24.72 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.00 (0.25), residues: 1130 helix: 1.18 (0.25), residues: 426 sheet: 0.07 (0.32), residues: 257 loop : -1.17 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG R 322 TYR 0.057 0.002 TYR R 346 PHE 0.018 0.002 PHE B 234 TRP 0.017 0.002 TRP D 36 HIS 0.010 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.27 ( 9116) covalent geometry : angle 0.80584 / 0.41 (12361) SS BOND : bond 0.00255 / 0.13 ( 1) SS BOND : angle 0.55771 / 0.26 ( 2) hydrogen bonds : bond 0.04717 / 3.11 ( 471) hydrogen bonds : angle 5.27586 / 3.67 ( 1353) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 0.332 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 205 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8160 (ppt-90) REVERT: A 229 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7608 (t0) REVERT: A 242 ARG cc_start: 0.8393 (ttm170) cc_final: 0.8020 (mtm-85) REVERT: A 247 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8273 (mtm) REVERT: A 304 GLN cc_start: 0.8815 (tt0) cc_final: 0.8348 (pp30) REVERT: A 333 GLN cc_start: 0.9235 (tp40) cc_final: 0.8984 (tp40) REVERT: A 345 LYS cc_start: 0.9433 (mttp) cc_final: 0.9001 (tptt) REVERT: B 12 GLU cc_start: 0.9371 (tp30) cc_final: 0.9081 (tp30) REVERT: B 13 GLN cc_start: 0.9383 (mm110) cc_final: 0.9123 (mm110) REVERT: B 32 GLN cc_start: 0.9304 (mt0) cc_final: 0.9023 (pt0) REVERT: B 142 HIS cc_start: 0.8618 (OUTLIER) cc_final: 0.7791 (t70) REVERT: B 228 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7243 (p0) REVERT: B 264 TYR cc_start: 0.9195 (m-80) cc_final: 0.8728 (m-80) REVERT: B 270 ILE cc_start: 0.9385 (pt) cc_final: 0.9111 (mm) REVERT: B 280 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8212 (mtpt) REVERT: C 32 LYS cc_start: 0.8974 (tptp) cc_final: 0.8725 (tmtt) REVERT: D 18 ARG cc_start: 0.8920 (tpp80) cc_final: 0.8654 (tpp80) REVERT: D 128 MET cc_start: 0.7608 (mmm) cc_final: 0.7298 (mmp) REVERT: D 148 ARG cc_start: 0.8584 (mtm110) cc_final: 0.8333 (mtm-85) REVERT: D 206 ARG cc_start: 0.8513 (ttp80) cc_final: 0.7992 (ttp80) REVERT: D 218 MET cc_start: 0.7991 (ttp) cc_final: 0.7645 (ttp) REVERT: D 232 LYS cc_start: 0.8394 (ttpp) cc_final: 0.7828 (ttpp) REVERT: R 81 ASN cc_start: 0.8744 (m-40) cc_final: 0.8320 (p0) REVERT: R 207 MET cc_start: 0.8078 (tpp) cc_final: 0.7711 (tpp) REVERT: R 316 TRP cc_start: 0.8925 (m-10) cc_final: 0.8513 (m-10) REVERT: R 375 PHE cc_start: 0.9182 (t80) cc_final: 0.8868 (t80) outliers start: 45 outliers final: 33 residues processed: 217 average time/residue: 0.1126 time to fit residues: 32.6912 Evaluate side-chains 214 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 240 ASN Chi-restraints excluded: chain R residue 322 ARG Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 353 PHE Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 58 optimal weight: 0.1980 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN D 219 GLN ** R 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 320 HIS ** R 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.105267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.078141 restraints weight = 25519.998| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 4.07 r_work: 0.3187 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.6150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9117 Z= 0.146 Angle : 0.802 11.326 12363 Z= 0.403 Chirality : 0.047 0.286 1424 Planarity : 0.005 0.072 1559 Dihedral : 5.726 50.077 1259 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.83 % Allowed : 26.99 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.01 (0.25), residues: 1130 helix: 1.10 (0.25), residues: 425 sheet: 0.14 (0.31), residues: 263 loop : -1.15 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG R 322 TYR 0.043 0.002 TYR R 346 PHE 0.030 0.001 PHE R 245 TRP 0.011 0.001 TRP R 334 HIS 0.010 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 9116) covalent geometry : angle 0.80159 / 0.40 (12361) SS BOND : bond 0.00211 / 0.11 ( 1) SS BOND : angle 0.58526 / 0.28 ( 2) hydrogen bonds : bond 0.04370 / 2.88 ( 471) hydrogen bonds : angle 5.11802 / 3.59 ( 1353) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8155 (tmm-80) cc_final: 0.7292 (tmm-80) REVERT: A 205 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8213 (ppt-90) REVERT: A 229 ASP cc_start: 0.8357 (m-30) cc_final: 0.7310 (t0) REVERT: A 242 ARG cc_start: 0.8346 (ttm170) cc_final: 0.7885 (mtt-85) REVERT: A 247 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8139 (mtm) REVERT: A 304 GLN cc_start: 0.8728 (tt0) cc_final: 0.8248 (pp30) REVERT: A 333 GLN cc_start: 0.9303 (tp40) cc_final: 0.9052 (tp40) REVERT: A 345 LYS cc_start: 0.9352 (mttp) cc_final: 0.8979 (tptt) REVERT: B 13 GLN cc_start: 0.9479 (mm110) cc_final: 0.9274 (mm110) REVERT: B 142 HIS cc_start: 0.8426 (OUTLIER) cc_final: 0.7761 (t70) REVERT: B 228 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7097 (p0) REVERT: B 264 TYR cc_start: 0.9201 (m-80) cc_final: 0.8364 (m-80) REVERT: B 280 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.7981 (mtpt) REVERT: C 20 LYS cc_start: 0.9323 (pttm) cc_final: 0.8987 (pttt) REVERT: C 32 LYS cc_start: 0.8942 (tptp) cc_final: 0.8642 (tmtt) REVERT: D 18 ARG cc_start: 0.8964 (tpp80) cc_final: 0.8528 (tpp80) REVERT: D 128 MET cc_start: 0.7503 (mmm) cc_final: 0.7145 (mmp) REVERT: D 148 ARG cc_start: 0.8586 (mtm110) cc_final: 0.8302 (mtm110) REVERT: D 189 ASP cc_start: 0.9242 (t70) cc_final: 0.8961 (t0) REVERT: D 206 ARG cc_start: 0.8482 (ttp80) cc_final: 0.7944 (ttp80) REVERT: D 218 MET cc_start: 0.7654 (ttp) cc_final: 0.7351 (ttp) REVERT: D 232 LYS cc_start: 0.8496 (ttpp) cc_final: 0.7896 (ttpp) REVERT: R 81 ASN cc_start: 0.8871 (m-40) cc_final: 0.8454 (p0) REVERT: R 193 TRP cc_start: 0.8615 (m100) cc_final: 0.7366 (m-10) REVERT: R 207 MET cc_start: 0.8262 (tpp) cc_final: 0.7930 (tpp) REVERT: R 316 TRP cc_start: 0.8889 (m-10) cc_final: 0.8603 (m-10) REVERT: R 325 MET cc_start: 0.8391 (mmp) cc_final: 0.8132 (tpp) REVERT: R 375 PHE cc_start: 0.9177 (t80) cc_final: 0.8894 (t80) outliers start: 37 outliers final: 28 residues processed: 219 average time/residue: 0.1096 time to fit residues: 32.3064 Evaluate side-chains 209 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 322 ARG Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 353 PHE 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 11 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 48 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 89 optimal weight: 0.4980 chunk 15 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 GLN ** R 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.104779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.077366 restraints weight = 26056.675| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 4.15 r_work: 0.3188 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.6228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.194 9117 Z= 0.302 Angle : 1.096 59.190 12363 Z= 0.600 Chirality : 0.049 0.313 1424 Planarity : 0.005 0.066 1559 Dihedral : 5.691 49.987 1257 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.62 % Allowed : 27.82 % Favored : 68.56 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.23 % 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: -0.01 (0.25), residues: 1130 helix: 1.08 (0.25), residues: 425 sheet: 0.16 (0.32), residues: 263 loop : -1.15 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 322 TYR 0.036 0.002 TYR R 346 PHE 0.022 0.002 PHE R 245 TRP 0.095 0.004 TRP B 82 HIS 0.020 0.001 HIS R 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.30 ( 9116) covalent geometry : angle 1.09636 / 0.60 (12361) SS BOND : bond 0.00157 / 0.08 ( 1) SS BOND : angle 0.61979 / 0.30 ( 2) hydrogen bonds : bond 0.04363 / 2.88 ( 471) hydrogen bonds : angle 5.15248 / 3.62 ( 1353) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8228 (tmm-80) cc_final: 0.7365 (tmm-80) REVERT: A 205 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8187 (ppt-90) REVERT: A 229 ASP cc_start: 0.8344 (m-30) cc_final: 0.7346 (t0) REVERT: A 242 ARG cc_start: 0.8357 (ttm170) cc_final: 0.7911 (mtt-85) REVERT: A 247 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8198 (mtm) REVERT: A 304 GLN cc_start: 0.8748 (tt0) cc_final: 0.8274 (pp30) REVERT: A 333 GLN cc_start: 0.9297 (tp40) cc_final: 0.9052 (tp40) REVERT: A 345 LYS cc_start: 0.9359 (mttp) cc_final: 0.8998 (tptt) REVERT: B 142 HIS cc_start: 0.8515 (OUTLIER) cc_final: 0.7894 (t70) REVERT: B 228 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7275 (p0) REVERT: B 264 TYR cc_start: 0.9157 (m-80) cc_final: 0.8332 (m-80) REVERT: B 280 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8027 (mtpt) REVERT: C 32 LYS cc_start: 0.8995 (tptp) cc_final: 0.8690 (tmtt) REVERT: D 18 ARG cc_start: 0.8952 (tpp80) cc_final: 0.8516 (tpp80) REVERT: D 19 LYS cc_start: 0.9162 (tptt) cc_final: 0.8808 (tptm) REVERT: D 128 MET cc_start: 0.7595 (mmm) cc_final: 0.7233 (mmp) REVERT: D 148 ARG cc_start: 0.8573 (mtm110) cc_final: 0.8306 (mtm110) REVERT: D 189 ASP cc_start: 0.9273 (t70) cc_final: 0.8989 (t0) REVERT: D 206 ARG cc_start: 0.8504 (ttp80) cc_final: 0.7966 (ttp80) REVERT: D 219 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.6966 (pp30) REVERT: D 232 LYS cc_start: 0.8586 (ttpp) cc_final: 0.7949 (ttpp) REVERT: R 81 ASN cc_start: 0.8860 (m-40) cc_final: 0.8449 (p0) REVERT: R 193 TRP cc_start: 0.8637 (m100) cc_final: 0.7345 (m-10) REVERT: R 207 MET cc_start: 0.8224 (tpp) cc_final: 0.7907 (tpp) REVERT: R 316 TRP cc_start: 0.8909 (m-10) cc_final: 0.8607 (m-10) REVERT: R 375 PHE cc_start: 0.9148 (t80) cc_final: 0.8873 (t80) outliers start: 35 outliers final: 27 residues processed: 201 average time/residue: 0.1133 time to fit residues: 30.5048 Evaluate side-chains 211 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 322 ARG Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 353 PHE 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 95 optimal weight: 3.9990 chunk 57 optimal weight: 0.0970 chunk 89 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.104810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.077732 restraints weight = 25615.792| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 4.10 r_work: 0.3198 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.6228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.194 9117 Z= 0.299 Angle : 1.094 58.998 12363 Z= 0.599 Chirality : 0.049 0.315 1424 Planarity : 0.005 0.066 1559 Dihedral : 5.691 49.984 1257 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.52 % Allowed : 27.92 % Favored : 68.56 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.23 % 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: -0.01 (0.25), residues: 1130 helix: 1.08 (0.25), residues: 425 sheet: 0.16 (0.32), residues: 263 loop : -1.15 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 322 TYR 0.036 0.002 TYR R 346 PHE 0.021 0.002 PHE R 245 TRP 0.095 0.004 TRP B 82 HIS 0.020 0.001 HIS R 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00658 / 0.30 ( 9116) covalent geometry : angle 1.09454 / 0.60 (12361) SS BOND : bond 0.00160 / 0.08 ( 1) SS BOND : angle 0.61853 / 0.30 ( 2) hydrogen bonds : bond 0.04363 / 2.88 ( 471) hydrogen bonds : angle 5.15235 / 3.62 ( 1353) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2755.45 seconds wall clock time: 48 minutes 11.73 seconds (2891.73 seconds total)