Starting phenix.real_space_refine on Thu Jun 4 01:32:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t17_55425/06_2026/9t17_55425_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t17_55425/06_2026/9t17_55425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9t17_55425/06_2026/9t17_55425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t17_55425/06_2026/9t17_55425.map" model { file = "/net/cci-nas-00/data/ceres_data/9t17_55425/06_2026/9t17_55425_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t17_55425/06_2026/9t17_55425_trim.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 2 5.21 5 S 62 5.16 5 C 5841 2.51 5 N 1592 2.21 5 O 1807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9313 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3379 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 410} Chain breaks: 1 Chain: "B" Number of atoms: 3364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3364 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Chain: "C" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2473 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 11, 'TRANS': 303} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ACP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.31, per 1000 atoms: 0.25 Number of scatterers: 9313 At special positions: 0 Unit cell: (72.96, 105.6, 108.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 62 16.00 P 9 15.00 Mg 2 11.99 O 1807 8.00 N 1592 7.00 C 5841 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 336.6 milliseconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 10 sheets defined 51.9% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.671A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 removed outlier: 4.468A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 128 removed outlier: 3.730A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 3.994A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 4.236A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 217 Processing helix chain 'A' and resid 223 through 240 removed outlier: 3.600A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.221A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.842A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 384 through 400 removed outlier: 3.800A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.927A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 437 removed outlier: 4.006A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 41 through 46 removed outlier: 4.531A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.380A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.727A pdb=" N PHE B 85 " --> pdb=" O GLY B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 107 through 126 removed outlier: 3.556A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 180 through 196 removed outlier: 4.036A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.568A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N CYS B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.709A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.068A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.790A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 27 Processing helix chain 'C' and resid 58 through 66 Processing helix chain 'C' and resid 66 through 76 removed outlier: 3.816A pdb=" N ILE C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.818A pdb=" N MET C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 122 Processing helix chain 'C' and resid 176 through 191 removed outlier: 3.917A pdb=" N ASN C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 246 through 272 removed outlier: 3.653A pdb=" N GLY C 272 " --> pdb=" O ALA C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 281 Processing helix chain 'C' and resid 282 through 288 Processing helix chain 'C' and resid 310 through 325 Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.105A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N HIS A 139 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL A 9 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.505A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.161A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 9.657A pdb=" N ILE B 163 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP B 203 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 11.674A pdb=" N PHE B 270 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N LYS B 350 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ALA B 352 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA B 315 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N CYS B 354 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N PHE B 317 " --> pdb=" O CYS B 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.697A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 51 through 53 removed outlier: 7.014A pdb=" N VAL C 12 " --> pdb=" O ARG C 51 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N PHE C 53 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N CYS C 14 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU C 13 " --> pdb=" O ILE C 302 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N CYS C 304 " --> pdb=" O LEU C 13 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ARG C 15 " --> pdb=" O CYS C 304 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR C 81 " --> pdb=" O THR C 299 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE C 301 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE C 83 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N CYS C 303 " --> pdb=" O PHE C 83 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N TYR C 85 " --> pdb=" O CYS C 303 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 51 through 53 removed outlier: 7.014A pdb=" N VAL C 12 " --> pdb=" O ARG C 51 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N PHE C 53 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N CYS C 14 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU C 13 " --> pdb=" O ILE C 302 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N CYS C 304 " --> pdb=" O LEU C 13 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ARG C 15 " --> pdb=" O CYS C 304 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR C 81 " --> pdb=" O THR C 299 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE C 301 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE C 83 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N CYS C 303 " --> pdb=" O PHE C 83 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N TYR C 85 " --> pdb=" O CYS C 303 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AA9, first strand: chain 'C' and resid 156 through 158 Processing sheet with id=AB1, first strand: chain 'C' and resid 193 through 194 489 hydrogen bonds defined for protein. 1386 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: 1.71 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3091 1.35 - 1.48: 2342 1.48 - 1.61: 3972 1.61 - 1.74: 5 1.74 - 1.87: 102 Bond restraints: 9512 Sorted by residual: bond pdb=" N ARG A 2 " pdb=" CA ARG A 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.10e+00 bond pdb=" CB GLN C 104 " pdb=" CG GLN C 104 " ideal model delta sigma weight residual 1.520 1.571 -0.051 3.00e-02 1.11e+03 2.93e+00 bond pdb=" CB ARG C 297 " pdb=" CG ARG C 297 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.76e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.74e+00 bond pdb=" N SER C 9 " pdb=" CA SER C 9 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+00 ... (remaining 9507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 12446 1.55 - 3.10: 366 3.10 - 4.65: 69 4.65 - 6.19: 17 6.19 - 7.74: 3 Bond angle restraints: 12901 Sorted by residual: angle pdb=" CA GLN C 104 " pdb=" CB GLN C 104 " pdb=" CG GLN C 104 " ideal model delta sigma weight residual 114.10 121.84 -7.74 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CB GLU C 178 " pdb=" CG GLU C 178 " pdb=" CD GLU C 178 " ideal model delta sigma weight residual 112.60 118.72 -6.12 1.70e+00 3.46e-01 1.29e+01 angle pdb=" CB GLN C 104 " pdb=" CG GLN C 104 " pdb=" CD GLN C 104 " ideal model delta sigma weight residual 112.60 118.34 -5.74 1.70e+00 3.46e-01 1.14e+01 angle pdb=" N ARG C 297 " pdb=" CA ARG C 297 " pdb=" C ARG C 297 " ideal model delta sigma weight residual 110.80 117.84 -7.04 2.13e+00 2.20e-01 1.09e+01 angle pdb=" C ASP C 232 " pdb=" CA ASP C 232 " pdb=" CB ASP C 232 " ideal model delta sigma weight residual 111.31 116.74 -5.43 1.68e+00 3.54e-01 1.04e+01 ... (remaining 12896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.88: 5469 33.88 - 67.77: 237 67.77 - 101.65: 20 101.65 - 135.53: 1 135.53 - 169.41: 2 Dihedral angle restraints: 5729 sinusoidal: 2338 harmonic: 3391 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.32 -169.41 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -34.10 138.69 1 2.00e+01 2.50e-03 4.20e+01 dihedral pdb=" O5' GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PA GTP A 501 " pdb=" PB GTP A 501 " ideal model delta sinusoidal sigma weight residual 274.12 142.26 131.86 1 2.00e+01 2.50e-03 4.00e+01 ... (remaining 5726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 855 0.034 - 0.067: 375 0.067 - 0.101: 108 0.101 - 0.135: 71 0.135 - 0.168: 10 Chirality restraints: 1419 Sorted by residual: chirality pdb=" CA ASN B 347 " pdb=" N ASN B 347 " pdb=" C ASN B 347 " pdb=" CB ASN B 347 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" CA VAL B 349 " pdb=" N VAL B 349 " pdb=" C VAL B 349 " pdb=" CB VAL B 349 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CB VAL B 66 " pdb=" CA VAL B 66 " pdb=" CG1 VAL B 66 " pdb=" CG2 VAL B 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 1416 not shown) Planarity restraints: 1670 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 144 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C GLY B 144 " -0.060 2.00e-02 2.50e+03 pdb=" O GLY B 144 " 0.022 2.00e-02 2.50e+03 pdb=" N SER B 145 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 347 " -0.015 2.00e-02 2.50e+03 3.12e-02 9.71e+00 pdb=" CG ASN B 347 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN B 347 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN B 347 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 250 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.61e+00 pdb=" C LEU B 250 " 0.041 2.00e-02 2.50e+03 pdb=" O LEU B 250 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG B 251 " -0.014 2.00e-02 2.50e+03 ... (remaining 1667 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 6 2.43 - 3.05: 6108 3.05 - 3.66: 13550 3.66 - 4.28: 21413 4.28 - 4.90: 36232 Nonbonded interactions: 77309 Sorted by model distance: nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.810 2.170 nonbonded pdb=" O ASP C 232 " pdb=" OD1 ASP C 232 " model vdw 2.091 3.040 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 2.180 2.170 nonbonded pdb=" O2G G2P B 501 " pdb="MG MG B 502 " model vdw 2.398 2.170 nonbonded pdb=" O MET B 1 " pdb=" OE1 GLU B 3 " model vdw 2.402 3.040 ... (remaining 77304 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: 9.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.410 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 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 : 0.005 0.052 9512 Z= 0.213 Angle : 0.665 7.743 12901 Z= 0.365 Chirality : 0.046 0.168 1419 Planarity : 0.006 0.079 1670 Dihedral : 17.811 169.414 3551 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.69 % Allowed : 2.67 % Favored : 96.65 % Rotamer: Outliers : 2.47 % Allowed : 25.37 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.38 (0.23), residues: 1163 helix: 0.72 (0.21), residues: 505 sheet: 0.86 (0.34), residues: 189 loop : -0.41 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 213 TYR 0.017 0.001 TYR B 281 PHE 0.021 0.002 PHE C 117 TRP 0.012 0.002 TRP A 21 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 ( 9512) covalent geometry : angle 0.66459 / 0.37 (12901) hydrogen bonds : bond 0.15382 / 10.14 ( 462) hydrogen bonds : angle 6.22344 / 4.50 ( 1386) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 71 GLU cc_start: 0.7680 (tt0) cc_final: 0.7011 (tt0) REVERT: A 155 GLU cc_start: 0.8008 (tt0) cc_final: 0.7504 (mt-10) REVERT: A 170 SER cc_start: 0.8743 (m) cc_final: 0.8439 (p) REVERT: A 191 THR cc_start: 0.8312 (t) cc_final: 0.7871 (p) REVERT: A 196 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8377 (mm-30) REVERT: A 239 THR cc_start: 0.8621 (m) cc_final: 0.8209 (p) REVERT: A 251 ASP cc_start: 0.7081 (p0) cc_final: 0.5984 (p0) REVERT: A 254 GLU cc_start: 0.7524 (tt0) cc_final: 0.7158 (mt-10) REVERT: A 282 TYR cc_start: 0.8633 (m-80) cc_final: 0.8144 (m-10) REVERT: A 337 THR cc_start: 0.7964 (t) cc_final: 0.7444 (p) REVERT: A 339 ARG cc_start: 0.8651 (tpp-160) cc_final: 0.8351 (mmt180) REVERT: A 340 SER cc_start: 0.8873 (OUTLIER) cc_final: 0.8490 (t) REVERT: A 361 THR cc_start: 0.8736 (t) cc_final: 0.8362 (p) REVERT: B 88 ASP cc_start: 0.9128 (m-30) cc_final: 0.8783 (m-30) REVERT: B 194 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8124 (mm-30) REVERT: B 282 ARG cc_start: 0.8738 (ttm170) cc_final: 0.8368 (ttm170) REVERT: B 320 ARG cc_start: 0.8497 (mmp80) cc_final: 0.7876 (mmt-90) REVERT: B 328 GLU cc_start: 0.8479 (tt0) cc_final: 0.7963 (tt0) REVERT: B 332 ASN cc_start: 0.8164 (t0) cc_final: 0.7734 (m-40) REVERT: B 339 SER cc_start: 0.8365 (OUTLIER) cc_final: 0.8162 (p) REVERT: B 362 LYS cc_start: 0.8562 (ptmt) cc_final: 0.8342 (ptmt) REVERT: B 376 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7862 (mt-10) REVERT: B 424 GLN cc_start: 0.8388 (tm-30) cc_final: 0.8130 (tm-30) REVERT: C 29 LYS cc_start: 0.8073 (mtpp) cc_final: 0.7690 (mptp) REVERT: C 35 GLN cc_start: 0.8285 (tt0) cc_final: 0.8006 (pp30) REVERT: C 60 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8076 (tp30) REVERT: C 63 TYR cc_start: 0.7578 (t80) cc_final: 0.6332 (t80) REVERT: C 160 LYS cc_start: 0.8996 (tptp) cc_final: 0.8575 (ptpp) REVERT: C 162 ARG cc_start: 0.7985 (mtm-85) cc_final: 0.7332 (mtp85) REVERT: C 172 ARG cc_start: 0.8089 (mtt-85) cc_final: 0.7790 (mtp85) REVERT: C 186 GLU cc_start: 0.8722 (tt0) cc_final: 0.8348 (tt0) REVERT: C 202 SER cc_start: 0.8930 (t) cc_final: 0.8550 (p) REVERT: C 222 GLN cc_start: 0.8524 (mm110) cc_final: 0.8132 (mm-40) REVERT: C 238 LYS cc_start: 0.8558 (ttmt) cc_final: 0.8061 (ttpp) REVERT: C 267 SER cc_start: 0.8757 (OUTLIER) cc_final: 0.8467 (p) REVERT: C 301 PHE cc_start: 0.8395 (m-80) cc_final: 0.8143 (t80) REVERT: C 322 GLN cc_start: 0.8509 (tt0) cc_final: 0.8161 (tp-100) outliers start: 25 outliers final: 11 residues processed: 209 average time/residue: 0.5957 time to fit residues: 132.8479 Evaluate side-chains 181 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 297 ARG Chi-restraints excluded: chain C residue 304 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS A 11 GLN A 18 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN C 59 GLN C 215 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.105235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.082219 restraints weight = 12996.705| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.24 r_work: 0.2903 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9512 Z= 0.200 Angle : 0.600 6.430 12901 Z= 0.318 Chirality : 0.046 0.160 1419 Planarity : 0.005 0.039 1670 Dihedral : 11.216 170.316 1371 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.32 % Favored : 97.59 % Rotamer: Outliers : 4.94 % Allowed : 20.53 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.24), residues: 1163 helix: 1.45 (0.23), residues: 518 sheet: 0.79 (0.34), residues: 197 loop : -0.11 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 213 TYR 0.016 0.001 TYR A 185 PHE 0.027 0.002 PHE C 117 TRP 0.013 0.001 TRP A 21 HIS 0.005 0.001 HIS A 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 ( 9512) covalent geometry : angle 0.59998 / 0.32 (12901) hydrogen bonds : bond 0.05241 / 3.54 ( 462) hydrogen bonds : angle 4.57159 / 3.33 ( 1386) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 167 time to evaluate : 0.484 Fit side-chains REVERT: A 71 GLU cc_start: 0.8102 (tt0) cc_final: 0.7890 (tt0) REVERT: A 155 GLU cc_start: 0.8360 (tt0) cc_final: 0.7924 (mt-10) REVERT: A 191 THR cc_start: 0.8700 (t) cc_final: 0.8481 (p) REVERT: A 254 GLU cc_start: 0.8184 (tt0) cc_final: 0.7879 (mt-10) REVERT: A 282 TYR cc_start: 0.8702 (m-80) cc_final: 0.8314 (m-10) REVERT: A 337 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.7964 (p) REVERT: A 339 ARG cc_start: 0.8540 (tpp-160) cc_final: 0.8322 (mmt180) REVERT: B 53 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7516 (tm-30) REVERT: B 88 ASP cc_start: 0.9222 (m-30) cc_final: 0.8940 (m-30) REVERT: B 111 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8240 (mp0) REVERT: B 143 THR cc_start: 0.8077 (m) cc_final: 0.7658 (m) REVERT: B 280 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8567 (pm20) REVERT: B 320 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8075 (mmt-90) REVERT: B 328 GLU cc_start: 0.8787 (tt0) cc_final: 0.8410 (tt0) REVERT: B 332 ASN cc_start: 0.8347 (t0) cc_final: 0.8043 (m-40) REVERT: B 391 ARG cc_start: 0.9358 (OUTLIER) cc_final: 0.6941 (mtm180) REVERT: B 424 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8460 (tm-30) REVERT: C 21 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8734 (mp10) REVERT: C 29 LYS cc_start: 0.8077 (mtpp) cc_final: 0.7728 (ttpp) REVERT: C 60 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8229 (tp30) REVERT: C 123 MET cc_start: 0.6811 (mmm) cc_final: 0.6453 (mmm) REVERT: C 160 LYS cc_start: 0.8976 (tptp) cc_final: 0.8559 (ptpp) REVERT: C 162 ARG cc_start: 0.8001 (mtm-85) cc_final: 0.7350 (mtp85) REVERT: C 186 GLU cc_start: 0.8236 (tt0) cc_final: 0.7934 (tt0) REVERT: C 222 GLN cc_start: 0.8530 (mm110) cc_final: 0.8078 (mm-40) REVERT: C 238 LYS cc_start: 0.8368 (ttmt) cc_final: 0.7908 (tttm) REVERT: C 322 GLN cc_start: 0.8400 (tt0) cc_final: 0.8008 (tp-100) outliers start: 50 outliers final: 13 residues processed: 194 average time/residue: 0.6626 time to fit residues: 136.4880 Evaluate side-chains 164 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 391 ARG Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 297 ARG Chi-restraints excluded: chain C residue 299 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 0.3980 chunk 75 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.105873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.082942 restraints weight = 13046.009| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.29 r_work: 0.2922 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9512 Z= 0.143 Angle : 0.538 6.264 12901 Z= 0.283 Chirality : 0.043 0.148 1419 Planarity : 0.004 0.040 1670 Dihedral : 10.512 171.359 1354 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.32 % Favored : 97.59 % Rotamer: Outliers : 4.05 % Allowed : 22.31 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.25), residues: 1163 helix: 1.76 (0.23), residues: 520 sheet: 1.10 (0.35), residues: 197 loop : -0.07 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 213 TYR 0.009 0.001 TYR B 425 PHE 0.023 0.001 PHE C 117 TRP 0.014 0.001 TRP A 21 HIS 0.004 0.001 HIS A 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 9512) covalent geometry : angle 0.53837 / 0.28 (12901) hydrogen bonds : bond 0.04565 / 3.08 ( 462) hydrogen bonds : angle 4.24063 / 3.10 ( 1386) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 71 GLU cc_start: 0.7935 (tt0) cc_final: 0.7389 (tt0) REVERT: A 90 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8895 (mm-30) REVERT: A 155 GLU cc_start: 0.8277 (tt0) cc_final: 0.7850 (mt-10) REVERT: A 191 THR cc_start: 0.8648 (t) cc_final: 0.8413 (p) REVERT: A 254 GLU cc_start: 0.8215 (tt0) cc_final: 0.7885 (mt-10) REVERT: A 282 TYR cc_start: 0.8735 (m-80) cc_final: 0.8359 (m-10) REVERT: A 337 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.7887 (p) REVERT: A 339 ARG cc_start: 0.8541 (tpp-160) cc_final: 0.8290 (mmt180) REVERT: B 88 ASP cc_start: 0.9229 (m-30) cc_final: 0.8942 (m-30) REVERT: B 111 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8478 (mp0) REVERT: B 156 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.7351 (tpm170) REVERT: B 205 GLU cc_start: 0.8166 (tt0) cc_final: 0.7956 (mt-10) REVERT: B 280 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8513 (pm20) REVERT: B 320 ARG cc_start: 0.8451 (mtp85) cc_final: 0.8011 (mmt-90) REVERT: B 328 GLU cc_start: 0.8755 (tt0) cc_final: 0.8377 (tt0) REVERT: B 332 ASN cc_start: 0.8307 (t0) cc_final: 0.7981 (m-40) REVERT: B 391 ARG cc_start: 0.9315 (OUTLIER) cc_final: 0.6846 (mtm180) REVERT: B 424 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8405 (tm-30) REVERT: C 29 LYS cc_start: 0.8010 (mtpp) cc_final: 0.7677 (ttpp) REVERT: C 60 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8271 (tp30) REVERT: C 69 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8269 (mm110) REVERT: C 123 MET cc_start: 0.6927 (mmm) cc_final: 0.6552 (mmm) REVERT: C 160 LYS cc_start: 0.8961 (tptp) cc_final: 0.8527 (ptpp) REVERT: C 162 ARG cc_start: 0.8061 (mtm-85) cc_final: 0.7421 (mtp85) REVERT: C 238 LYS cc_start: 0.8275 (ttmt) cc_final: 0.7833 (ttpp) outliers start: 41 outliers final: 14 residues processed: 179 average time/residue: 0.5945 time to fit residues: 113.5537 Evaluate side-chains 177 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 391 ARG Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 297 ARG Chi-restraints excluded: chain C residue 299 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 3 optimal weight: 0.0370 chunk 43 optimal weight: 1.9990 overall best weight: 0.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.106944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.084012 restraints weight = 13091.812| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.30 r_work: 0.2936 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9512 Z= 0.124 Angle : 0.511 6.246 12901 Z= 0.267 Chirality : 0.043 0.151 1419 Planarity : 0.004 0.040 1670 Dihedral : 10.394 171.653 1354 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.15 % Favored : 97.76 % Rotamer: Outliers : 4.54 % Allowed : 21.32 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.25), residues: 1163 helix: 1.98 (0.23), residues: 518 sheet: 0.90 (0.36), residues: 204 loop : -0.01 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 213 TYR 0.009 0.001 TYR C 279 PHE 0.022 0.001 PHE C 117 TRP 0.013 0.001 TRP A 21 HIS 0.003 0.001 HIS A 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 9512) covalent geometry : angle 0.51088 / 0.27 (12901) hydrogen bonds : bond 0.04113 / 2.75 ( 462) hydrogen bonds : angle 4.05061 / 2.96 ( 1386) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.7800 (tt0) cc_final: 0.7223 (tt0) REVERT: A 90 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8902 (mm-30) REVERT: A 91 GLN cc_start: 0.8680 (mt0) cc_final: 0.8453 (mt0) REVERT: A 155 GLU cc_start: 0.8257 (tt0) cc_final: 0.7816 (mt-10) REVERT: A 191 THR cc_start: 0.8627 (t) cc_final: 0.8258 (p) REVERT: A 254 GLU cc_start: 0.8187 (tt0) cc_final: 0.7863 (mt-10) REVERT: A 282 TYR cc_start: 0.8760 (m-80) cc_final: 0.8373 (m-10) REVERT: A 337 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.7975 (p) REVERT: A 339 ARG cc_start: 0.8514 (tpp-160) cc_final: 0.8261 (mmt180) REVERT: B 53 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7766 (tm-30) REVERT: B 88 ASP cc_start: 0.9237 (m-30) cc_final: 0.8946 (m-30) REVERT: B 156 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.7414 (tpm170) REVERT: B 205 GLU cc_start: 0.8198 (tt0) cc_final: 0.7959 (mt-10) REVERT: B 257 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8699 (mmm) REVERT: B 280 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8526 (pm20) REVERT: B 320 ARG cc_start: 0.8451 (mtp85) cc_final: 0.7990 (mmt-90) REVERT: B 328 GLU cc_start: 0.8743 (tt0) cc_final: 0.8388 (tt0) REVERT: B 332 ASN cc_start: 0.8256 (t0) cc_final: 0.7970 (m-40) REVERT: B 391 ARG cc_start: 0.9303 (OUTLIER) cc_final: 0.6835 (mtm180) REVERT: B 424 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8376 (tm-30) REVERT: C 29 LYS cc_start: 0.8014 (mtpp) cc_final: 0.7692 (ttpp) REVERT: C 60 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8276 (tp30) REVERT: C 69 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8271 (mm110) REVERT: C 123 MET cc_start: 0.7190 (mmm) cc_final: 0.6692 (mmm) REVERT: C 160 LYS cc_start: 0.8930 (tptp) cc_final: 0.8539 (ptpp) REVERT: C 162 ARG cc_start: 0.8113 (mtm-85) cc_final: 0.7479 (mtp85) REVERT: C 222 GLN cc_start: 0.8526 (mm110) cc_final: 0.8163 (mm110) REVERT: C 238 LYS cc_start: 0.8224 (ttmt) cc_final: 0.7796 (ttpp) REVERT: C 322 GLN cc_start: 0.8299 (tt0) cc_final: 0.7685 (mm-40) outliers start: 46 outliers final: 17 residues processed: 189 average time/residue: 0.6203 time to fit residues: 124.9448 Evaluate side-chains 164 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 391 ARG Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 297 ARG Chi-restraints excluded: chain C residue 299 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 109 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 60 optimal weight: 0.0670 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 334 GLN C 35 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.104649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.081558 restraints weight = 13142.322| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.32 r_work: 0.2895 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9512 Z= 0.169 Angle : 0.542 6.297 12901 Z= 0.284 Chirality : 0.044 0.160 1419 Planarity : 0.004 0.042 1670 Dihedral : 10.507 173.946 1353 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.49 % Favored : 97.42 % Rotamer: Outliers : 4.24 % Allowed : 22.41 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.25), residues: 1163 helix: 1.95 (0.23), residues: 519 sheet: 0.91 (0.36), residues: 204 loop : -0.01 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 213 TYR 0.012 0.001 TYR B 425 PHE 0.019 0.001 PHE C 117 TRP 0.013 0.001 TRP A 21 HIS 0.004 0.001 HIS A 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 9512) covalent geometry : angle 0.54152 / 0.28 (12901) hydrogen bonds : bond 0.04582 / 3.09 ( 462) hydrogen bonds : angle 4.08976 / 2.99 ( 1386) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8901 (mm-30) REVERT: A 91 GLN cc_start: 0.8719 (mt0) cc_final: 0.8479 (mt0) REVERT: A 155 GLU cc_start: 0.8278 (tt0) cc_final: 0.7848 (mt-10) REVERT: A 191 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8215 (p) REVERT: A 254 GLU cc_start: 0.8334 (tt0) cc_final: 0.7933 (mt-10) REVERT: A 282 TYR cc_start: 0.8792 (m-80) cc_final: 0.8396 (m-10) REVERT: A 337 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8073 (p) REVERT: A 339 ARG cc_start: 0.8524 (tpp-160) cc_final: 0.8282 (mmt180) REVERT: A 411 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: B 88 ASP cc_start: 0.9250 (m-30) cc_final: 0.8962 (m-30) REVERT: B 156 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.7384 (tpm170) REVERT: B 213 ARG cc_start: 0.8345 (ttp-110) cc_final: 0.8082 (ttp-110) REVERT: B 257 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8636 (mmm) REVERT: B 280 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8497 (pm20) REVERT: B 320 ARG cc_start: 0.8462 (mtp85) cc_final: 0.7982 (mmt-90) REVERT: B 328 GLU cc_start: 0.8789 (tt0) cc_final: 0.8427 (tt0) REVERT: B 332 ASN cc_start: 0.8280 (t0) cc_final: 0.7967 (m-40) REVERT: B 424 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8402 (tm-30) REVERT: C 29 LYS cc_start: 0.8019 (mtpp) cc_final: 0.7656 (mptp) REVERT: C 60 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8305 (tp30) REVERT: C 123 MET cc_start: 0.7211 (mmm) cc_final: 0.6477 (mmm) REVERT: C 160 LYS cc_start: 0.8924 (tptp) cc_final: 0.8500 (mptt) REVERT: C 162 ARG cc_start: 0.8180 (mtm-85) cc_final: 0.7557 (mtp85) REVERT: C 238 LYS cc_start: 0.8271 (ttmt) cc_final: 0.7841 (ttpp) outliers start: 43 outliers final: 22 residues processed: 171 average time/residue: 0.5826 time to fit residues: 106.5736 Evaluate side-chains 169 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 297 ARG Chi-restraints excluded: chain C residue 299 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 26 optimal weight: 0.0670 chunk 11 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN C 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.104494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.080866 restraints weight = 12992.899| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.34 r_work: 0.2837 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9512 Z= 0.137 Angle : 0.519 6.215 12901 Z= 0.271 Chirality : 0.043 0.152 1419 Planarity : 0.004 0.040 1670 Dihedral : 10.468 174.576 1353 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.24 % Favored : 97.68 % Rotamer: Outliers : 3.46 % Allowed : 23.40 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.25), residues: 1163 helix: 2.03 (0.24), residues: 518 sheet: 0.88 (0.36), residues: 205 loop : 0.07 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 215 TYR 0.010 0.001 TYR B 425 PHE 0.019 0.001 PHE C 117 TRP 0.014 0.001 TRP A 21 HIS 0.003 0.001 HIS A 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 9512) covalent geometry : angle 0.51883 / 0.27 (12901) hydrogen bonds : bond 0.04259 / 2.86 ( 462) hydrogen bonds : angle 4.02069 / 2.94 ( 1386) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9303 (t) cc_final: 0.9030 (m) REVERT: A 90 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8954 (mm-30) REVERT: A 91 GLN cc_start: 0.8719 (mt0) cc_final: 0.8503 (mt0) REVERT: A 155 GLU cc_start: 0.8315 (tt0) cc_final: 0.7914 (mt-10) REVERT: A 191 THR cc_start: 0.8591 (t) cc_final: 0.8248 (p) REVERT: A 254 GLU cc_start: 0.8358 (tt0) cc_final: 0.7967 (mt-10) REVERT: A 282 TYR cc_start: 0.8757 (m-80) cc_final: 0.8326 (m-10) REVERT: A 337 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8080 (p) REVERT: A 411 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8371 (mp0) REVERT: B 88 ASP cc_start: 0.9247 (m-30) cc_final: 0.8977 (m-30) REVERT: B 156 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.7496 (tpm170) REVERT: B 257 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8753 (mmm) REVERT: B 280 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8550 (pm20) REVERT: B 320 ARG cc_start: 0.8509 (mtp85) cc_final: 0.8057 (mmt-90) REVERT: B 328 GLU cc_start: 0.8805 (tt0) cc_final: 0.8481 (tt0) REVERT: B 332 ASN cc_start: 0.8320 (t0) cc_final: 0.8021 (m-40) REVERT: B 391 ARG cc_start: 0.9304 (OUTLIER) cc_final: 0.6876 (mtm180) REVERT: B 424 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8447 (tm-30) REVERT: C 29 LYS cc_start: 0.8021 (mtpp) cc_final: 0.7653 (mptp) REVERT: C 60 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8312 (tp30) REVERT: C 63 TYR cc_start: 0.8378 (t80) cc_final: 0.7891 (t80) REVERT: C 123 MET cc_start: 0.7242 (mmm) cc_final: 0.6673 (mmm) REVERT: C 160 LYS cc_start: 0.8931 (tptp) cc_final: 0.8530 (mptt) REVERT: C 162 ARG cc_start: 0.8228 (mtm-85) cc_final: 0.7628 (mtp85) REVERT: C 238 LYS cc_start: 0.8355 (ttmt) cc_final: 0.7941 (ttpp) REVERT: C 300 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.7677 (tpt) outliers start: 35 outliers final: 21 residues processed: 163 average time/residue: 0.6143 time to fit residues: 106.7373 Evaluate side-chains 166 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 391 ARG Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 297 ARG Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 300 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 57 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.102296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.078710 restraints weight = 13040.267| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.33 r_work: 0.2801 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9512 Z= 0.178 Angle : 0.548 6.557 12901 Z= 0.286 Chirality : 0.044 0.171 1419 Planarity : 0.004 0.045 1670 Dihedral : 10.633 177.033 1353 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.41 % Favored : 97.51 % Rotamer: Outliers : 4.05 % Allowed : 23.20 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.25), residues: 1163 helix: 1.96 (0.24), residues: 520 sheet: 0.81 (0.36), residues: 205 loop : 0.05 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 215 TYR 0.012 0.001 TYR B 425 PHE 0.019 0.001 PHE C 117 TRP 0.013 0.001 TRP A 21 HIS 0.004 0.001 HIS A 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 9512) covalent geometry : angle 0.54819 / 0.29 (12901) hydrogen bonds : bond 0.04763 / 3.22 ( 462) hydrogen bonds : angle 4.11550 / 3.00 ( 1386) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 GLU cc_start: 0.8313 (tt0) cc_final: 0.7885 (mt-10) REVERT: A 191 THR cc_start: 0.8595 (t) cc_final: 0.8233 (p) REVERT: A 254 GLU cc_start: 0.8425 (tt0) cc_final: 0.7969 (tt0) REVERT: A 282 TYR cc_start: 0.8754 (m-80) cc_final: 0.8311 (m-10) REVERT: A 337 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8147 (p) REVERT: A 411 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8356 (mp0) REVERT: B 88 ASP cc_start: 0.9249 (m-30) cc_final: 0.8991 (m-30) REVERT: B 156 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.7455 (tpm170) REVERT: B 213 ARG cc_start: 0.8383 (ttp-110) cc_final: 0.8087 (ttp-110) REVERT: B 320 ARG cc_start: 0.8495 (mtp85) cc_final: 0.8031 (mmt-90) REVERT: B 328 GLU cc_start: 0.8807 (tt0) cc_final: 0.8473 (tt0) REVERT: B 332 ASN cc_start: 0.8354 (t0) cc_final: 0.8062 (m-40) REVERT: B 391 ARG cc_start: 0.9333 (OUTLIER) cc_final: 0.6934 (mtm180) REVERT: B 424 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8435 (tm-30) REVERT: C 29 LYS cc_start: 0.7999 (mtpp) cc_final: 0.7591 (mptp) REVERT: C 60 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8359 (tp30) REVERT: C 63 TYR cc_start: 0.8426 (t80) cc_final: 0.8099 (t80) REVERT: C 123 MET cc_start: 0.7292 (mmm) cc_final: 0.6472 (mmm) REVERT: C 160 LYS cc_start: 0.8948 (tptp) cc_final: 0.8540 (mptt) REVERT: C 162 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.7670 (mtp85) REVERT: C 238 LYS cc_start: 0.8369 (ttmt) cc_final: 0.7952 (ttpp) REVERT: C 300 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.7700 (tpt) outliers start: 41 outliers final: 25 residues processed: 166 average time/residue: 0.6123 time to fit residues: 108.2575 Evaluate side-chains 164 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 391 ARG Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 297 ARG Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 300 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 9 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 96 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.103616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.079932 restraints weight = 12899.712| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.34 r_work: 0.2820 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9512 Z= 0.149 Angle : 0.532 6.238 12901 Z= 0.278 Chirality : 0.043 0.165 1419 Planarity : 0.004 0.042 1670 Dihedral : 10.592 177.634 1353 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.32 % Favored : 97.59 % Rotamer: Outliers : 3.46 % Allowed : 23.69 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.25), residues: 1163 helix: 1.99 (0.24), residues: 520 sheet: 0.82 (0.36), residues: 205 loop : 0.07 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 215 TYR 0.010 0.001 TYR B 425 PHE 0.018 0.001 PHE C 117 TRP 0.015 0.001 TRP A 21 HIS 0.003 0.001 HIS A 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 9512) covalent geometry : angle 0.53196 / 0.28 (12901) hydrogen bonds : bond 0.04388 / 2.96 ( 462) hydrogen bonds : angle 4.06150 / 2.97 ( 1386) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 SER cc_start: 0.9121 (OUTLIER) cc_final: 0.8909 (m) REVERT: A 155 GLU cc_start: 0.8304 (tt0) cc_final: 0.7883 (mt-10) REVERT: A 191 THR cc_start: 0.8580 (t) cc_final: 0.8252 (p) REVERT: A 254 GLU cc_start: 0.8420 (tt0) cc_final: 0.7964 (tt0) REVERT: A 282 TYR cc_start: 0.8760 (m-80) cc_final: 0.8315 (m-10) REVERT: A 337 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8129 (p) REVERT: A 411 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8352 (mp0) REVERT: B 88 ASP cc_start: 0.9245 (m-30) cc_final: 0.8986 (m-30) REVERT: B 156 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.7461 (tpm170) REVERT: B 209 ASP cc_start: 0.8367 (t0) cc_final: 0.8151 (t0) REVERT: B 320 ARG cc_start: 0.8503 (mtp85) cc_final: 0.8020 (mmt-90) REVERT: B 328 GLU cc_start: 0.8796 (tt0) cc_final: 0.8456 (tt0) REVERT: B 332 ASN cc_start: 0.8333 (t0) cc_final: 0.8047 (m-40) REVERT: B 391 ARG cc_start: 0.9318 (OUTLIER) cc_final: 0.6921 (mtm180) REVERT: B 424 GLN cc_start: 0.8889 (tm-30) cc_final: 0.8465 (tm-30) REVERT: C 60 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8338 (tp30) REVERT: C 63 TYR cc_start: 0.8417 (t80) cc_final: 0.8153 (t80) REVERT: C 123 MET cc_start: 0.7297 (mmm) cc_final: 0.6458 (mmm) REVERT: C 160 LYS cc_start: 0.8951 (tptp) cc_final: 0.8535 (mptt) REVERT: C 162 ARG cc_start: 0.8265 (mtm-85) cc_final: 0.7685 (mtp85) REVERT: C 238 LYS cc_start: 0.8359 (ttmt) cc_final: 0.7939 (ttpp) REVERT: C 300 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.7725 (tpt) outliers start: 35 outliers final: 24 residues processed: 165 average time/residue: 0.5740 time to fit residues: 101.3464 Evaluate side-chains 169 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 391 ARG Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 297 ARG Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 300 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 101 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 105 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN ** A 101 ASN ** 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 = 0.3335 r_free = 0.3335 target = 0.104967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.081379 restraints weight = 12809.277| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.33 r_work: 0.2847 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9512 Z= 0.124 Angle : 0.527 6.579 12901 Z= 0.273 Chirality : 0.043 0.157 1419 Planarity : 0.004 0.041 1670 Dihedral : 10.465 176.746 1353 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.24 % Favored : 97.68 % Rotamer: Outliers : 3.36 % Allowed : 24.38 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.25), residues: 1163 helix: 2.04 (0.24), residues: 520 sheet: 0.88 (0.36), residues: 205 loop : 0.06 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 215 TYR 0.009 0.001 TYR C 279 PHE 0.018 0.001 PHE B 92 TRP 0.015 0.001 TRP A 21 HIS 0.003 0.001 HIS C 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 9512) covalent geometry : angle 0.52744 / 0.27 (12901) hydrogen bonds : bond 0.04051 / 2.72 ( 462) hydrogen bonds : angle 3.99559 / 2.93 ( 1386) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9304 (t) cc_final: 0.9047 (m) REVERT: A 155 GLU cc_start: 0.8276 (tt0) cc_final: 0.7841 (mt-10) REVERT: A 191 THR cc_start: 0.8552 (t) cc_final: 0.8237 (p) REVERT: A 254 GLU cc_start: 0.8384 (tt0) cc_final: 0.7915 (tt0) REVERT: A 282 TYR cc_start: 0.8744 (m-80) cc_final: 0.8302 (m-10) REVERT: A 337 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8090 (p) REVERT: A 411 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8359 (mp0) REVERT: B 88 ASP cc_start: 0.9243 (m-30) cc_final: 0.8982 (m-30) REVERT: B 156 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.7268 (tpm170) REVERT: B 257 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8769 (mmm) REVERT: B 320 ARG cc_start: 0.8503 (mtp85) cc_final: 0.8011 (mmt-90) REVERT: B 328 GLU cc_start: 0.8767 (tt0) cc_final: 0.8444 (tt0) REVERT: B 332 ASN cc_start: 0.8312 (t0) cc_final: 0.8051 (m-40) REVERT: B 391 ARG cc_start: 0.9306 (OUTLIER) cc_final: 0.6892 (mtm180) REVERT: B 424 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8412 (tm-30) REVERT: C 29 LYS cc_start: 0.8142 (mtpp) cc_final: 0.7584 (mptp) REVERT: C 60 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8312 (tp30) REVERT: C 63 TYR cc_start: 0.8384 (t80) cc_final: 0.8183 (t80) REVERT: C 123 MET cc_start: 0.7297 (mmm) cc_final: 0.6450 (mmm) REVERT: C 160 LYS cc_start: 0.8959 (tptp) cc_final: 0.8533 (mptt) REVERT: C 162 ARG cc_start: 0.8246 (mtm-85) cc_final: 0.7679 (mtp85) REVERT: C 238 LYS cc_start: 0.8347 (ttmt) cc_final: 0.7932 (ttpp) REVERT: C 300 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.7643 (tpt) outliers start: 34 outliers final: 22 residues processed: 166 average time/residue: 0.5578 time to fit residues: 99.1263 Evaluate side-chains 172 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 391 ARG Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 297 ARG Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 300 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 83 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.101095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.077422 restraints weight = 13112.805| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.34 r_work: 0.2778 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9512 Z= 0.217 Angle : 0.586 6.953 12901 Z= 0.305 Chirality : 0.045 0.172 1419 Planarity : 0.004 0.048 1670 Dihedral : 10.780 178.926 1353 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.32 % Favored : 97.59 % Rotamer: Outliers : 3.55 % Allowed : 24.38 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.25), residues: 1163 helix: 2.01 (0.23), residues: 513 sheet: 0.77 (0.36), residues: 205 loop : -0.04 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 213 TYR 0.015 0.001 TYR B 425 PHE 0.018 0.002 PHE C 117 TRP 0.011 0.001 TRP A 21 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 ( 9512) covalent geometry : angle 0.58583 / 0.31 (12901) hydrogen bonds : bond 0.05132 / 3.48 ( 462) hydrogen bonds : angle 4.19258 / 3.06 ( 1386) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 SER cc_start: 0.9123 (OUTLIER) cc_final: 0.8919 (m) REVERT: A 155 GLU cc_start: 0.8317 (tt0) cc_final: 0.7886 (mt-10) REVERT: A 191 THR cc_start: 0.8561 (t) cc_final: 0.8244 (p) REVERT: A 254 GLU cc_start: 0.8535 (tt0) cc_final: 0.8109 (tt0) REVERT: A 282 TYR cc_start: 0.8768 (m-80) cc_final: 0.8374 (m-80) REVERT: A 337 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8204 (p) REVERT: A 411 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8346 (mp0) REVERT: B 88 ASP cc_start: 0.9231 (m-30) cc_final: 0.8986 (m-30) REVERT: B 156 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.7377 (tpm170) REVERT: B 297 LYS cc_start: 0.9096 (mppt) cc_final: 0.8804 (mtpt) REVERT: B 320 ARG cc_start: 0.8486 (mtp85) cc_final: 0.7989 (mmt-90) REVERT: B 328 GLU cc_start: 0.8831 (tt0) cc_final: 0.8495 (tt0) REVERT: B 332 ASN cc_start: 0.8346 (t0) cc_final: 0.7940 (m-40) REVERT: B 336 LYS cc_start: 0.8160 (mptp) cc_final: 0.7709 (mptt) REVERT: B 391 ARG cc_start: 0.9346 (OUTLIER) cc_final: 0.6980 (mtm180) REVERT: B 424 GLN cc_start: 0.8904 (tm-30) cc_final: 0.8446 (tm-30) REVERT: C 29 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7581 (mptp) REVERT: C 60 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8348 (tp30) REVERT: C 123 MET cc_start: 0.7349 (mmm) cc_final: 0.6470 (mmm) REVERT: C 160 LYS cc_start: 0.8951 (tptp) cc_final: 0.8547 (mptt) REVERT: C 162 ARG cc_start: 0.8319 (mtm-85) cc_final: 0.7729 (mtp85) REVERT: C 178 GLU cc_start: 0.7947 (mp0) cc_final: 0.7440 (pm20) REVERT: C 238 LYS cc_start: 0.8404 (ttmt) cc_final: 0.7985 (tttm) REVERT: C 300 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.7667 (tpt) outliers start: 36 outliers final: 24 residues processed: 167 average time/residue: 0.5882 time to fit residues: 104.9896 Evaluate side-chains 168 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 391 ARG Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 297 ARG Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 300 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 14 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** 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 = 0.3301 r_free = 0.3301 target = 0.102553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.079220 restraints weight = 12871.558| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.24 r_work: 0.2812 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9512 Z= 0.159 Angle : 0.555 6.306 12901 Z= 0.289 Chirality : 0.044 0.162 1419 Planarity : 0.004 0.048 1670 Dihedral : 10.696 178.604 1353 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.24 % Favored : 97.68 % Rotamer: Outliers : 3.16 % Allowed : 24.58 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.25), residues: 1163 helix: 1.97 (0.23), residues: 520 sheet: 0.80 (0.36), residues: 205 loop : -0.07 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 215 TYR 0.021 0.001 TYR C 63 PHE 0.017 0.001 PHE C 117 TRP 0.015 0.001 TRP A 21 HIS 0.003 0.001 HIS A 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 9512) covalent geometry : angle 0.55503 / 0.29 (12901) hydrogen bonds : bond 0.04556 / 3.08 ( 462) hydrogen bonds : angle 4.10847 / 3.00 ( 1386) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3614.84 seconds wall clock time: 62 minutes 28.82 seconds (3748.82 seconds total)