Starting phenix.real_space_refine on Sun Sep 13 04:55:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8due_27719/09_2026/8due_27719.cif Found real_map, /net/cci-nas-00/data/ceres_data/8due_27719/09_2026/8due_27719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8due_27719/09_2026/8due_27719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8due_27719/09_2026/8due_27719.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8due_27719/09_2026/8due_27719.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8due_27719/09_2026/8due_27719.cif" model { file = "/net/cci-nas-00/data/ceres_data/8due_27719/09_2026/8due_27719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8due_27719/09_2026/8due_27719.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 25 5.49 5 Mg 5 5.21 5 S 119 5.16 5 C 13224 2.51 5 N 3465 2.21 5 O 4066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20904 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "B" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "C" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "D" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "E" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "F" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "M" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 200 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.69, per 1000 atoms: 0.22 Number of scatterers: 20904 At special positions: 0 Unit cell: (115.92, 135.792, 154.836, 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 119 16.00 P 25 15.00 Mg 5 11.99 O 4066 8.00 N 3465 7.00 C 13224 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: 1.67 Conformation dependent library (CDL) restraints added in 850.9 milliseconds 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4920 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 11 sheets defined 55.7% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 3.780A pdb=" N ILE A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 19 removed outlier: 3.639A pdb=" N VAL A 19 " --> pdb=" O TYR A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 28 removed outlier: 4.119A pdb=" N PHE A 28 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 47 Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.673A pdb=" N ASN A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 78 Processing helix chain 'A' and resid 86 through 119 removed outlier: 3.627A pdb=" N LEU A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 133 through 143 removed outlier: 4.007A pdb=" N ILE A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 203 through 217 removed outlier: 3.722A pdb=" N LEU A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 243 Processing helix chain 'A' and resid 245 through 252 removed outlier: 3.666A pdb=" N ILE A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 268 Processing helix chain 'A' and resid 288 through 300 removed outlier: 3.576A pdb=" N LYS A 300 " --> pdb=" O GLU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 347 Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.808A pdb=" N ILE A 371 " --> pdb=" O MET A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.652A pdb=" N THR A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 396 Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 12 through 20 Processing helix chain 'B' and resid 24 through 28 removed outlier: 4.149A pdb=" N PHE B 28 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 48 removed outlier: 3.649A pdb=" N ASN B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 58 Processing helix chain 'B' and resid 66 through 79 removed outlier: 3.567A pdb=" N GLY B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 119 Processing helix chain 'B' and resid 130 through 133 Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 176 through 184 Processing helix chain 'B' and resid 204 through 217 Processing helix chain 'B' and resid 229 through 242 Processing helix chain 'B' and resid 245 through 250 removed outlier: 3.887A pdb=" N ASP B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 269 removed outlier: 3.564A pdb=" N LYS B 269 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 Processing helix chain 'B' and resid 327 through 347 removed outlier: 3.685A pdb=" N THR B 331 " --> pdb=" O ASN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 363 removed outlier: 4.099A pdb=" N ASP B 362 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 363 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.728A pdb=" N THR B 380 " --> pdb=" O GLY B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 396 Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 13 through 19 Processing helix chain 'C' and resid 31 through 47 removed outlier: 3.609A pdb=" N ASN C 35 " --> pdb=" O GLY C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 63 Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 86 through 118 Processing helix chain 'C' and resid 120 through 124 removed outlier: 3.783A pdb=" N ARG C 124 " --> pdb=" O PRO C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 133 through 143 removed outlier: 3.656A pdb=" N ILE C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 229 through 242 Processing helix chain 'C' and resid 245 through 251 removed outlier: 3.744A pdb=" N ASP C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 269 removed outlier: 3.507A pdb=" N LYS C 269 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 302 removed outlier: 3.604A pdb=" N LEU C 293 " --> pdb=" O THR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 327 through 347 Processing helix chain 'C' and resid 357 through 361 removed outlier: 3.719A pdb=" N TRP C 361 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 381 removed outlier: 3.857A pdb=" N ALA C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 396 Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 13 through 19 Processing helix chain 'D' and resid 24 through 28 removed outlier: 4.062A pdb=" N PHE D 28 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 48 Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 66 through 80 Processing helix chain 'D' and resid 86 through 119 Processing helix chain 'D' and resid 130 through 133 Processing helix chain 'D' and resid 134 through 141 removed outlier: 3.657A pdb=" N ALA D 141 " --> pdb=" O ILE D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 168 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 229 through 242 Processing helix chain 'D' and resid 245 through 252 removed outlier: 3.553A pdb=" N ILE D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP D 250 " --> pdb=" O LEU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 268 Processing helix chain 'D' and resid 286 through 301 Processing helix chain 'D' and resid 327 through 347 Processing helix chain 'D' and resid 357 through 361 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 375 through 381 removed outlier: 3.840A pdb=" N ALA D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 396 Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 13 through 18 removed outlier: 4.052A pdb=" N SER E 17 " --> pdb=" O GLN E 13 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 13 through 18' Processing helix chain 'E' and resid 24 through 29 removed outlier: 3.953A pdb=" N PHE E 28 " --> pdb=" O ASP E 24 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU E 29 " --> pdb=" O SER E 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 24 through 29' Processing helix chain 'E' and resid 31 through 47 removed outlier: 3.627A pdb=" N ASN E 35 " --> pdb=" O GLY E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 63 Processing helix chain 'E' and resid 66 through 77 Processing helix chain 'E' and resid 86 through 119 removed outlier: 3.588A pdb=" N GLU E 118 " --> pdb=" O GLN E 114 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU E 119 " --> pdb=" O THR E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 133 through 143 removed outlier: 4.196A pdb=" N ILE E 137 " --> pdb=" O ALA E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 166 Processing helix chain 'E' and resid 176 through 184 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 229 through 243 Processing helix chain 'E' and resid 245 through 251 Processing helix chain 'E' and resid 255 through 269 Processing helix chain 'E' and resid 286 through 301 removed outlier: 3.503A pdb=" N LYS E 301 " --> pdb=" O LEU E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 347 removed outlier: 5.768A pdb=" N LYS E 333 " --> pdb=" O TYR E 329 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA E 334 " --> pdb=" O THR E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 361 Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 390 through 397 Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 13 through 19 removed outlier: 3.583A pdb=" N VAL F 19 " --> pdb=" O TYR F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 48 removed outlier: 3.851A pdb=" N ASN F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 63 Processing helix chain 'F' and resid 66 through 80 Processing helix chain 'F' and resid 89 through 119 removed outlier: 4.022A pdb=" N ASN F 116 " --> pdb=" O GLU F 112 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU F 119 " --> pdb=" O THR F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 132 No H-bonds generated for 'chain 'F' and resid 130 through 132' Processing helix chain 'F' and resid 133 through 143 Processing helix chain 'F' and resid 154 through 156 No H-bonds generated for 'chain 'F' and resid 154 through 156' Processing helix chain 'F' and resid 157 through 168 removed outlier: 4.570A pdb=" N LEU F 163 " --> pdb=" O GLU F 159 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN F 167 " --> pdb=" O LEU F 163 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS F 168 " --> pdb=" O SER F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 183 Processing helix chain 'F' and resid 202 through 216 Processing helix chain 'F' and resid 229 through 243 removed outlier: 3.526A pdb=" N ASP F 243 " --> pdb=" O ALA F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 251 Processing helix chain 'F' and resid 255 through 269 removed outlier: 3.778A pdb=" N LYS F 269 " --> pdb=" O LYS F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 300 Processing helix chain 'F' and resid 327 through 347 Processing helix chain 'F' and resid 357 through 361 Processing helix chain 'F' and resid 367 through 371 removed outlier: 3.585A pdb=" N ASP F 370 " --> pdb=" O ASN F 367 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE F 371 " --> pdb=" O MET F 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 367 through 371' Processing helix chain 'F' and resid 375 through 381 removed outlier: 3.854A pdb=" N ALA F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153 removed outlier: 4.234A pdb=" N ALA B 353 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 383 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 275 through 279 removed outlier: 6.561A pdb=" N VAL A 221 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LYS A 278 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TYR A 223 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA A 353 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU A 385 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL A 194 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL A 387 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N MET A 196 " --> pdb=" O VAL A 387 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.815A pdb=" N HIS B 152 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL C 221 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LYS C 278 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TYR C 223 " --> pdb=" O LYS C 278 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN C 220 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE C 309 " --> pdb=" O ASN C 220 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU C 222 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA C 353 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASN C 193 " --> pdb=" O THR C 352 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ALA C 354 " --> pdb=" O ASN C 193 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU C 195 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU C 192 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU C 385 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL C 194 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL C 387 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N MET C 196 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA C 386 " --> pdb=" O GLN C 403 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N GLN C 403 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE C 388 " --> pdb=" O ILE C 401 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE C 401 " --> pdb=" O ILE C 388 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 171 through 172 removed outlier: 3.733A pdb=" N ALA B 187 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 152 through 153 removed outlier: 6.812A pdb=" N VAL D 221 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA D 353 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE D 383 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS D 405 " --> pdb=" O MET D 384 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ALA D 386 " --> pdb=" O GLN D 403 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLN D 403 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE D 388 " --> pdb=" O ILE D 401 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ILE D 401 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS D 427 " --> pdb=" O GLN D 422 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 152 through 153 removed outlier: 6.421A pdb=" N ASN E 220 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ILE E 309 " --> pdb=" O ASN E 220 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU E 222 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THR E 191 " --> pdb=" O LEU E 350 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR E 352 " --> pdb=" O THR E 191 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASN E 193 " --> pdb=" O THR E 352 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ALA E 354 " --> pdb=" O ASN E 193 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU E 195 " --> pdb=" O ALA E 354 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE E 383 " --> pdb=" O LEU E 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 152 through 153 removed outlier: 6.215A pdb=" N LEU F 222 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 171 through 172 Processing sheet with id=AA9, first strand: chain 'F' and resid 171 through 172 Processing sheet with id=AB1, first strand: chain 'F' and resid 350 through 355 Processing sheet with id=AB2, first strand: chain 'F' and resid 420 through 422 1054 hydrogen bonds defined for protein. 3042 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: 3.43 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 6754 1.36 - 1.51: 5720 1.51 - 1.65: 8641 1.65 - 1.80: 137 1.80 - 1.95: 72 Bond restraints: 21324 Sorted by residual: bond pdb=" N VAL C 304 " pdb=" CA VAL C 304 " ideal model delta sigma weight residual 1.457 1.492 -0.035 9.00e-03 1.23e+04 1.54e+01 bond pdb=" N VAL B 19 " pdb=" CA VAL B 19 " ideal model delta sigma weight residual 1.460 1.492 -0.032 8.60e-03 1.35e+04 1.39e+01 bond pdb=" N LYS C 301 " pdb=" CA LYS C 301 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.22e-02 6.72e+03 9.42e+00 bond pdb=" N SER C 292 " pdb=" CA SER C 292 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.08e+00 bond pdb=" N VAL E 232 " pdb=" CA VAL E 232 " ideal model delta sigma weight residual 1.460 1.494 -0.033 1.19e-02 7.06e+03 7.90e+00 ... (remaining 21319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 27661 1.14 - 2.29: 936 2.29 - 3.43: 234 3.43 - 4.58: 41 4.58 - 5.72: 26 Bond angle restraints: 28898 Sorted by residual: angle pdb=" N LYS C 298 " pdb=" CA LYS C 298 " pdb=" C LYS C 298 " ideal model delta sigma weight residual 111.28 105.70 5.58 1.09e+00 8.42e-01 2.62e+01 angle pdb=" N3 DT M 12 " pdb=" C4 DT M 12 " pdb=" O4 DT M 12 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT M 16 " pdb=" C4 DT M 16 " pdb=" O4 DT M 16 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT M 14 " pdb=" C4 DT M 14 " pdb=" O4 DT M 14 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT M 10 " pdb=" C4 DT M 10 " pdb=" O4 DT M 10 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 ... (remaining 28893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 12644 35.99 - 71.99: 202 71.99 - 107.98: 6 107.98 - 143.97: 2 143.97 - 179.97: 2 Dihedral angle restraints: 12856 sinusoidal: 5242 harmonic: 7614 Sorted by residual: dihedral pdb=" CA VAL E 19 " pdb=" C VAL E 19 " pdb=" N TRP E 20 " pdb=" CA TRP E 20 " ideal model delta harmonic sigma weight residual 180.00 153.47 26.53 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA VAL C 19 " pdb=" C VAL C 19 " pdb=" N TRP C 20 " pdb=" CA TRP C 20 " ideal model delta harmonic sigma weight residual 180.00 156.56 23.44 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" O1A AGS D 501 " pdb=" O3A AGS D 501 " pdb=" PA AGS D 501 " pdb=" PB AGS D 501 " ideal model delta sinusoidal sigma weight residual -67.73 112.24 -179.97 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2333 0.039 - 0.079: 643 0.079 - 0.118: 240 0.118 - 0.158: 16 0.158 - 0.197: 6 Chirality restraints: 3238 Sorted by residual: chirality pdb=" CA VAL F 150 " pdb=" N VAL F 150 " pdb=" C VAL F 150 " pdb=" CB VAL F 150 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CA LEU C 294 " pdb=" N LEU C 294 " pdb=" C LEU C 294 " pdb=" CB LEU C 294 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.18e-01 chirality pdb=" CA LEU C 299 " pdb=" N LEU C 299 " pdb=" C LEU C 299 " pdb=" CB LEU C 299 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.18e-01 ... (remaining 3235 not shown) Planarity restraints: 3597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 225 " -0.020 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C SER E 225 " 0.069 2.00e-02 2.50e+03 pdb=" O SER E 225 " -0.026 2.00e-02 2.50e+03 pdb=" N MET E 226 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 227 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.06e+00 pdb=" C GLU E 227 " 0.046 2.00e-02 2.50e+03 pdb=" O GLU E 227 " -0.017 2.00e-02 2.50e+03 pdb=" N MET E 228 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 16 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C PHE B 16 " 0.028 2.00e-02 2.50e+03 pdb=" O PHE B 16 " -0.011 2.00e-02 2.50e+03 pdb=" N SER B 17 " -0.010 2.00e-02 2.50e+03 ... (remaining 3594 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 212 2.52 - 3.12: 16489 3.12 - 3.71: 34033 3.71 - 4.31: 46791 4.31 - 4.90: 77922 Nonbonded interactions: 175447 Sorted by model distance: nonbonded pdb=" O2B AGS D 501 " pdb="MG MG D 502 " model vdw 1.926 2.170 nonbonded pdb=" O3B AGS B 501 " pdb="MG MG B 502 " model vdw 1.963 2.170 nonbonded pdb=" O3B AGS D 501 " pdb="MG MG D 502 " model vdw 1.972 2.170 nonbonded pdb=" O3A AGS C 501 " pdb="MG MG C 502 " model vdw 1.990 2.170 nonbonded pdb=" O1A AGS C 501 " pdb="MG MG C 502 " model vdw 1.998 2.170 ... (remaining 175442 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 432) selection = (chain 'C' and resid 1 through 432) selection = (chain 'D' and resid 1 through 432) selection = (chain 'E' and resid 1 through 432) selection = (chain 'F' and resid 1 through 432) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.620 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 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 : 0.003 0.037 21324 Z= 0.189 Angle : 0.542 5.720 28898 Z= 0.346 Chirality : 0.041 0.197 3238 Planarity : 0.003 0.040 3597 Dihedral : 12.978 179.966 7936 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.40 % Allowed : 8.98 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.17), residues: 2580 helix: 1.55 (0.15), residues: 1274 sheet: -0.32 (0.31), residues: 307 loop : -1.51 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 101 TYR 0.009 0.001 TYR E 15 PHE 0.013 0.001 PHE F 417 TRP 0.013 0.001 TRP E 162 HIS 0.002 0.001 HIS E 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.19 (21324) covalent geometry : angle 0.54169 / 0.35 (28898) hydrogen bonds : bond 0.14678 / 9.81 ( 1054) hydrogen bonds : angle 6.20224 / 4.35 ( 3042) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 446 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.3989 (pm20) cc_final: 0.3118 (pt0) REVERT: A 138 MET cc_start: 0.4909 (mpp) cc_final: 0.4431 (mpt) REVERT: A 155 MET cc_start: 0.6678 (tmm) cc_final: 0.6383 (tmm) REVERT: A 228 MET cc_start: 0.1530 (tpp) cc_final: 0.0637 (mtm) REVERT: A 241 MET cc_start: 0.1594 (mtm) cc_final: 0.1322 (mtm) REVERT: A 296 GLU cc_start: 0.2610 (OUTLIER) cc_final: 0.2379 (pt0) REVERT: A 298 LYS cc_start: 0.4106 (tptp) cc_final: 0.3714 (mtpm) REVERT: A 312 TYR cc_start: 0.2929 (OUTLIER) cc_final: 0.1514 (t80) REVERT: A 325 SER cc_start: 0.4461 (t) cc_final: 0.4172 (p) REVERT: A 329 TYR cc_start: 0.3597 (m-80) cc_final: 0.3392 (m-80) REVERT: A 355 GLN cc_start: 0.5519 (mm110) cc_final: 0.5208 (mm-40) REVERT: A 411 LYS cc_start: 0.4861 (ttmm) cc_final: 0.4529 (ttpp) REVERT: A 431 ILE cc_start: 0.4374 (tp) cc_final: 0.4040 (pt) REVERT: B 13 GLN cc_start: 0.5098 (tm-30) cc_final: 0.4743 (tp-100) REVERT: B 70 TYR cc_start: 0.6180 (t80) cc_final: 0.5712 (t80) REVERT: B 76 LEU cc_start: 0.5828 (mp) cc_final: 0.5519 (tt) REVERT: B 138 MET cc_start: 0.3359 (mtt) cc_final: 0.3150 (mtt) REVERT: B 177 ARG cc_start: 0.4500 (mtm110) cc_final: 0.3706 (tpp-160) REVERT: B 241 MET cc_start: 0.4009 (ptp) cc_final: 0.2631 (mtp) REVERT: B 249 ILE cc_start: 0.6041 (mm) cc_final: 0.5695 (mt) REVERT: B 265 LYS cc_start: 0.5955 (pttp) cc_final: 0.5745 (ptpt) REVERT: B 267 ARG cc_start: 0.6511 (ttp-110) cc_final: 0.5456 (mmt-90) REVERT: B 304 VAL cc_start: 0.7196 (OUTLIER) cc_final: 0.6995 (p) REVERT: B 348 THR cc_start: 0.8075 (p) cc_final: 0.7594 (t) REVERT: B 384 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7064 (mtt) REVERT: C 1 MET cc_start: 0.7077 (ptm) cc_final: 0.6786 (ptm) REVERT: C 29 GLU cc_start: 0.6497 (tp30) cc_final: 0.6125 (mt-10) REVERT: C 93 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7215 (mm-30) REVERT: C 103 MET cc_start: 0.6971 (tpp) cc_final: 0.6074 (tpp) REVERT: C 113 ILE cc_start: 0.6473 (mt) cc_final: 0.6253 (mp) REVERT: C 235 LYS cc_start: 0.6264 (tttt) cc_final: 0.5687 (ttmt) REVERT: C 243 ASP cc_start: 0.6115 (t0) cc_final: 0.5888 (t0) REVERT: C 247 ASP cc_start: 0.4178 (OUTLIER) cc_final: 0.3701 (m-30) REVERT: C 274 ARG cc_start: 0.3695 (mpp-170) cc_final: 0.3283 (ttm170) REVERT: C 293 LEU cc_start: 0.3922 (OUTLIER) cc_final: 0.2686 (mt) REVERT: C 308 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7071 (mt) REVERT: C 326 GLU cc_start: 0.5049 (tt0) cc_final: 0.4838 (mp0) REVERT: C 356 VAL cc_start: 0.7535 (m) cc_final: 0.7297 (p) REVERT: C 368 MET cc_start: 0.5758 (ttm) cc_final: 0.5473 (ttp) REVERT: D 36 THR cc_start: 0.7595 (t) cc_final: 0.7349 (m) REVERT: D 46 GLU cc_start: 0.7142 (tt0) cc_final: 0.6884 (tt0) REVERT: D 92 LYS cc_start: 0.6759 (tmmt) cc_final: 0.6192 (mmmt) REVERT: D 93 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6086 (tp30) REVERT: D 139 ARG cc_start: 0.5877 (ptp90) cc_final: 0.5313 (ptt-90) REVERT: D 140 GLN cc_start: 0.6385 (mt0) cc_final: 0.5848 (pt0) REVERT: D 177 ARG cc_start: 0.7168 (mtm110) cc_final: 0.6886 (mtp-110) REVERT: D 184 LYS cc_start: 0.7569 (mmtp) cc_final: 0.7001 (mtpt) REVERT: D 231 GLU cc_start: 0.6390 (mp0) cc_final: 0.6114 (mp0) REVERT: D 288 ASN cc_start: 0.6166 (m-40) cc_final: 0.5760 (m-40) REVERT: D 295 ASN cc_start: 0.5535 (m110) cc_final: 0.5326 (m110) REVERT: D 347 GLU cc_start: 0.6661 (mm-30) cc_final: 0.6374 (mm-30) REVERT: D 364 SER cc_start: 0.6473 (p) cc_final: 0.5998 (t) REVERT: D 387 VAL cc_start: 0.6553 (t) cc_final: 0.6342 (t) REVERT: E 86 ASP cc_start: 0.7200 (t0) cc_final: 0.6719 (t0) REVERT: E 92 LYS cc_start: 0.6422 (ttmt) cc_final: 0.5701 (mptp) REVERT: E 95 GLU cc_start: 0.6458 (tt0) cc_final: 0.6157 (tt0) REVERT: E 104 PHE cc_start: 0.6821 (t80) cc_final: 0.6387 (t80) REVERT: E 128 MET cc_start: 0.3086 (tmt) cc_final: 0.1510 (mtp) REVERT: E 156 ASP cc_start: 0.6573 (m-30) cc_final: 0.5997 (t0) REVERT: E 166 MET cc_start: 0.6687 (ptp) cc_final: 0.6364 (ptt) REVERT: E 226 MET cc_start: 0.6666 (mmm) cc_final: 0.5426 (mpp) REVERT: E 292 SER cc_start: 0.7576 (t) cc_final: 0.7073 (p) REVERT: E 323 VAL cc_start: 0.3218 (OUTLIER) cc_final: 0.2805 (t) REVERT: E 373 GLU cc_start: 0.6682 (mt-10) cc_final: 0.6460 (mt-10) REVERT: E 384 MET cc_start: 0.7874 (mtm) cc_final: 0.7524 (mtt) REVERT: E 389 GLU cc_start: 0.5406 (tt0) cc_final: 0.5078 (tp30) REVERT: F 1 MET cc_start: 0.2564 (tmm) cc_final: 0.1741 (mmt) REVERT: F 114 GLN cc_start: 0.4700 (OUTLIER) cc_final: 0.4477 (mt0) REVERT: F 123 LYS cc_start: 0.3431 (OUTLIER) cc_final: 0.3151 (ptpt) REVERT: F 184 LYS cc_start: 0.7105 (mmtp) cc_final: 0.6673 (mtmm) REVERT: F 226 MET cc_start: 0.6595 (mmt) cc_final: 0.5972 (mmt) REVERT: F 265 LYS cc_start: 0.6706 (ttmm) cc_final: 0.6387 (ttmt) REVERT: F 279 GLN cc_start: 0.6854 (tt0) cc_final: 0.6558 (tt0) REVERT: F 312 TYR cc_start: 0.5321 (OUTLIER) cc_final: 0.3227 (m-80) REVERT: F 313 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.6033 (tt) REVERT: F 338 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6561 (mp0) REVERT: F 368 MET cc_start: 0.5453 (tpt) cc_final: 0.5021 (tmm) REVERT: F 384 MET cc_start: 0.6275 (mtm) cc_final: 0.5710 (ttm) REVERT: F 407 ARG cc_start: 0.7002 (tmm-80) cc_final: 0.6709 (ttt180) REVERT: F 427 LYS cc_start: 0.6338 (ttpt) cc_final: 0.6105 (ttmt) outliers start: 76 outliers final: 11 residues processed: 497 average time/residue: 0.5653 time to fit residues: 320.4012 Evaluate side-chains 294 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 271 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 312 TYR Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 316 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 258 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 ASN A 48 HIS A 355 GLN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 HIS B 13 GLN B 295 ASN C 62 ASN C 200 ASN C 279 GLN C 355 GLN D 200 ASN ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 ASN ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 GLN E 253 HIS E 398 GLN F 288 ASN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 399 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.208349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.176701 restraints weight = 27237.749| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 2.71 r_work: 0.3899 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21324 Z= 0.198 Angle : 0.668 10.146 28898 Z= 0.352 Chirality : 0.045 0.230 3238 Planarity : 0.004 0.036 3597 Dihedral : 10.794 176.088 2962 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 5.45 % Allowed : 13.90 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.16 (0.17), residues: 2580 helix: 1.04 (0.14), residues: 1306 sheet: -0.67 (0.30), residues: 331 loop : -1.48 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 267 TYR 0.024 0.002 TYR B 15 PHE 0.024 0.002 PHE F 417 TRP 0.019 0.002 TRP B 20 HIS 0.007 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (21324) covalent geometry : angle 0.66760 / 0.35 (28898) hydrogen bonds : bond 0.04108 / 2.72 ( 1054) hydrogen bonds : angle 5.27395 / 3.75 ( 3042) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 280 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 19 VAL cc_start: 0.2997 (OUTLIER) cc_final: 0.2581 (m) REVERT: A 23 MET cc_start: 0.3479 (mtp) cc_final: 0.2738 (mmm) REVERT: A 41 LYS cc_start: 0.3968 (OUTLIER) cc_final: 0.3675 (tmtm) REVERT: A 113 ILE cc_start: 0.2277 (OUTLIER) cc_final: 0.1810 (tp) REVERT: A 228 MET cc_start: 0.2065 (tpp) cc_final: 0.1259 (tmm) REVERT: A 241 MET cc_start: 0.4550 (mtm) cc_final: 0.3655 (mtm) REVERT: A 278 LYS cc_start: 0.4587 (OUTLIER) cc_final: 0.4139 (tppp) REVERT: A 298 LYS cc_start: 0.4332 (tptp) cc_final: 0.3982 (mtpm) REVERT: A 329 TYR cc_start: 0.3929 (m-80) cc_final: 0.3727 (m-80) REVERT: A 411 LYS cc_start: 0.6316 (ttmm) cc_final: 0.6076 (ttpt) REVERT: B 70 TYR cc_start: 0.6405 (t80) cc_final: 0.6054 (t80) REVERT: B 138 MET cc_start: 0.3325 (mtt) cc_final: 0.2865 (mmm) REVERT: B 177 ARG cc_start: 0.4968 (mtm110) cc_final: 0.4364 (mmt180) REVERT: B 205 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6524 (tp) REVERT: B 241 MET cc_start: 0.4234 (ptp) cc_final: 0.3719 (mtp) REVERT: B 249 ILE cc_start: 0.6588 (mm) cc_final: 0.6331 (mt) REVERT: B 267 ARG cc_start: 0.6206 (ttp-110) cc_final: 0.5642 (mmt-90) REVERT: C 3 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6725 (mt-10) REVERT: C 23 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7498 (mmp) REVERT: C 47 TYR cc_start: 0.5804 (OUTLIER) cc_final: 0.4832 (m-80) REVERT: C 50 VAL cc_start: 0.6497 (t) cc_final: 0.6202 (p) REVERT: C 103 MET cc_start: 0.7382 (tpp) cc_final: 0.6744 (tpp) REVERT: C 170 ARG cc_start: 0.6485 (mtm110) cc_final: 0.6276 (mtp-110) REVERT: C 205 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7203 (tp) REVERT: C 235 LYS cc_start: 0.7104 (tttt) cc_final: 0.6734 (ttmt) REVERT: C 290 PHE cc_start: 0.6012 (m-10) cc_final: 0.5771 (m-10) REVERT: C 293 LEU cc_start: 0.4645 (OUTLIER) cc_final: 0.3548 (tt) REVERT: C 294 LEU cc_start: 0.5313 (OUTLIER) cc_final: 0.4943 (tt) REVERT: C 365 ASP cc_start: 0.6746 (p0) cc_final: 0.5741 (t70) REVERT: C 421 VAL cc_start: 0.6510 (m) cc_final: 0.6267 (t) REVERT: D 4 ILE cc_start: 0.7294 (mp) cc_final: 0.7087 (mm) REVERT: D 36 THR cc_start: 0.8049 (t) cc_final: 0.7617 (m) REVERT: D 95 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7596 (mt-10) REVERT: D 177 ARG cc_start: 0.7232 (mtm110) cc_final: 0.6773 (mmm160) REVERT: D 288 ASN cc_start: 0.6569 (m-40) cc_final: 0.6366 (m-40) REVERT: D 364 SER cc_start: 0.6694 (p) cc_final: 0.6090 (t) REVERT: D 368 MET cc_start: 0.7034 (ttp) cc_final: 0.6814 (ttm) REVERT: E 86 ASP cc_start: 0.7299 (t0) cc_final: 0.7091 (t70) REVERT: E 92 LYS cc_start: 0.7279 (ttmt) cc_final: 0.6596 (mptp) REVERT: E 95 GLU cc_start: 0.7331 (tt0) cc_final: 0.7059 (tt0) REVERT: E 101 ARG cc_start: 0.6498 (mmm-85) cc_final: 0.6243 (tpp-160) REVERT: E 128 MET cc_start: 0.4011 (tmt) cc_final: 0.3737 (tmt) REVERT: E 227 GLU cc_start: 0.4745 (mt-10) cc_final: 0.4539 (mt-10) REVERT: E 323 VAL cc_start: 0.3071 (OUTLIER) cc_final: 0.2718 (t) REVERT: F 1 MET cc_start: 0.2545 (tmm) cc_final: 0.0403 (mmm) REVERT: F 114 GLN cc_start: 0.4909 (OUTLIER) cc_final: 0.4469 (mt0) REVERT: F 226 MET cc_start: 0.6543 (mmt) cc_final: 0.6265 (mmt) REVERT: F 368 MET cc_start: 0.6060 (OUTLIER) cc_final: 0.5538 (tmm) outliers start: 122 outliers final: 38 residues processed: 371 average time/residue: 0.5631 time to fit residues: 238.8648 Evaluate side-chains 281 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 230 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 316 CYS Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 368 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 0.0010 chunk 121 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 232 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 chunk 4 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN B 422 GLN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN C 279 GLN D 167 ASN D 200 ASN ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS E 279 GLN F 288 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.209483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.177400 restraints weight = 27673.054| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 2.76 r_work: 0.3904 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21324 Z= 0.128 Angle : 0.570 10.443 28898 Z= 0.301 Chirality : 0.041 0.194 3238 Planarity : 0.003 0.038 3597 Dihedral : 10.220 178.338 2941 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.60 % Allowed : 16.35 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.17), residues: 2580 helix: 1.22 (0.14), residues: 1306 sheet: -0.67 (0.30), residues: 328 loop : -1.62 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 267 TYR 0.022 0.001 TYR B 15 PHE 0.020 0.001 PHE D 146 TRP 0.023 0.001 TRP A 154 HIS 0.009 0.001 HIS B 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (21324) covalent geometry : angle 0.56979 / 0.30 (28898) hydrogen bonds : bond 0.03497 / 2.33 ( 1054) hydrogen bonds : angle 5.00283 / 3.56 ( 3042) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 249 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 19 VAL cc_start: 0.2831 (OUTLIER) cc_final: 0.2527 (m) REVERT: A 47 TYR cc_start: 0.3506 (t80) cc_final: 0.2344 (t80) REVERT: A 113 ILE cc_start: 0.2237 (OUTLIER) cc_final: 0.1732 (tp) REVERT: A 228 MET cc_start: 0.1859 (tpp) cc_final: 0.1085 (tmm) REVERT: A 241 MET cc_start: 0.4298 (mtm) cc_final: 0.3375 (mtm) REVERT: A 298 LYS cc_start: 0.4260 (tptp) cc_final: 0.3953 (mtpm) REVERT: A 329 TYR cc_start: 0.3816 (m-80) cc_final: 0.3598 (m-80) REVERT: A 431 ILE cc_start: 0.4766 (tp) cc_final: 0.4284 (pt) REVERT: B 8 HIS cc_start: 0.6793 (m-70) cc_final: 0.6569 (m-70) REVERT: B 13 GLN cc_start: 0.5475 (tm-30) cc_final: 0.5262 (tp-100) REVERT: B 138 MET cc_start: 0.3172 (mtt) cc_final: 0.2724 (mmm) REVERT: B 177 ARG cc_start: 0.4927 (mtm110) cc_final: 0.4305 (mmp-170) REVERT: B 249 ILE cc_start: 0.6537 (mm) cc_final: 0.6297 (mt) REVERT: B 253 HIS cc_start: 0.6399 (OUTLIER) cc_final: 0.6169 (t-90) REVERT: B 264 GLU cc_start: 0.5089 (mt-10) cc_final: 0.4797 (mt-10) REVERT: B 267 ARG cc_start: 0.6249 (ttp-110) cc_final: 0.5616 (mmt-90) REVERT: B 384 MET cc_start: 0.7647 (mtp) cc_final: 0.7306 (mtt) REVERT: B 425 ASN cc_start: 0.5236 (t0) cc_final: 0.5015 (t0) REVERT: C 3 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6606 (mt-10) REVERT: C 23 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7479 (mmp) REVERT: C 47 TYR cc_start: 0.5710 (OUTLIER) cc_final: 0.4723 (m-80) REVERT: C 50 VAL cc_start: 0.6516 (t) cc_final: 0.6217 (p) REVERT: C 85 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.5877 (mp0) REVERT: C 103 MET cc_start: 0.7430 (tpp) cc_final: 0.6781 (tpp) REVERT: C 235 LYS cc_start: 0.7006 (tttt) cc_final: 0.6608 (ttmt) REVERT: C 293 LEU cc_start: 0.4448 (OUTLIER) cc_final: 0.3690 (tm) REVERT: C 312 TYR cc_start: 0.4989 (OUTLIER) cc_final: 0.4185 (t80) REVERT: C 365 ASP cc_start: 0.6642 (p0) cc_final: 0.5647 (t70) REVERT: C 421 VAL cc_start: 0.6655 (m) cc_final: 0.6353 (t) REVERT: D 4 ILE cc_start: 0.7160 (mp) cc_final: 0.6948 (mm) REVERT: D 36 THR cc_start: 0.8043 (t) cc_final: 0.7646 (m) REVERT: D 92 LYS cc_start: 0.7320 (tmmt) cc_final: 0.6806 (mmmt) REVERT: D 95 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7228 (mt-10) REVERT: D 177 ARG cc_start: 0.7218 (mtm110) cc_final: 0.6794 (mmm160) REVERT: D 364 SER cc_start: 0.6645 (p) cc_final: 0.6080 (t) REVERT: E 86 ASP cc_start: 0.7275 (t0) cc_final: 0.7037 (t70) REVERT: E 92 LYS cc_start: 0.7265 (ttmt) cc_final: 0.6527 (mptp) REVERT: E 95 GLU cc_start: 0.7172 (tt0) cc_final: 0.6888 (tt0) REVERT: E 128 MET cc_start: 0.3956 (tmt) cc_final: 0.3723 (ppp) REVERT: E 226 MET cc_start: 0.6706 (OUTLIER) cc_final: 0.6311 (mmm) REVERT: E 227 GLU cc_start: 0.4678 (mt-10) cc_final: 0.4436 (mt-10) REVERT: E 323 VAL cc_start: 0.3163 (OUTLIER) cc_final: 0.2850 (t) REVERT: F 1 MET cc_start: 0.2561 (tmm) cc_final: 0.0269 (mmt) REVERT: F 114 GLN cc_start: 0.4922 (OUTLIER) cc_final: 0.4516 (mt0) REVERT: F 140 GLN cc_start: 0.5697 (tp40) cc_final: 0.5251 (tm-30) REVERT: F 166 MET cc_start: 0.7013 (mtt) cc_final: 0.6697 (mtm) REVERT: F 226 MET cc_start: 0.6517 (mmt) cc_final: 0.6226 (mmt) REVERT: F 263 MET cc_start: 0.7476 (mmm) cc_final: 0.7219 (mmm) REVERT: F 368 MET cc_start: 0.5821 (OUTLIER) cc_final: 0.5432 (tmm) outliers start: 103 outliers final: 37 residues processed: 322 average time/residue: 0.5174 time to fit residues: 192.7540 Evaluate side-chains 278 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 229 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 265 LYS Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 316 CYS Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 368 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 189 optimal weight: 0.0070 chunk 52 optimal weight: 10.0000 chunk 225 optimal weight: 20.0000 chunk 79 optimal weight: 0.0050 chunk 161 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 164 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 191 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 overall best weight: 3.2018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN D 200 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.208243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.176637 restraints weight = 27398.443| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 2.67 r_work: 0.3868 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 21324 Z= 0.207 Angle : 0.676 12.606 28898 Z= 0.354 Chirality : 0.046 0.210 3238 Planarity : 0.004 0.036 3597 Dihedral : 10.407 176.939 2937 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 5.36 % Allowed : 16.93 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.45 (0.16), residues: 2580 helix: 0.84 (0.14), residues: 1298 sheet: -0.70 (0.30), residues: 323 loop : -1.72 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 177 TYR 0.024 0.002 TYR B 15 PHE 0.024 0.002 PHE F 417 TRP 0.019 0.002 TRP B 20 HIS 0.009 0.002 HIS B 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (21324) covalent geometry : angle 0.67561 / 0.35 (28898) hydrogen bonds : bond 0.03878 / 2.58 ( 1054) hydrogen bonds : angle 5.19812 / 3.70 ( 3042) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 244 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 VAL cc_start: 0.2995 (OUTLIER) cc_final: 0.2658 (m) REVERT: A 47 TYR cc_start: 0.3582 (t80) cc_final: 0.2562 (t80) REVERT: A 228 MET cc_start: 0.1878 (tpp) cc_final: 0.0895 (tmm) REVERT: A 241 MET cc_start: 0.4369 (mtm) cc_final: 0.3563 (mtm) REVERT: A 312 TYR cc_start: 0.3089 (OUTLIER) cc_final: 0.2678 (m-10) REVERT: A 329 TYR cc_start: 0.3795 (m-80) cc_final: 0.3591 (m-80) REVERT: A 355 GLN cc_start: 0.5511 (mm110) cc_final: 0.4942 (mp10) REVERT: B 8 HIS cc_start: 0.6887 (m-70) cc_final: 0.6545 (m-70) REVERT: B 138 MET cc_start: 0.3314 (mtt) cc_final: 0.2954 (mmm) REVERT: B 177 ARG cc_start: 0.4966 (mtm110) cc_final: 0.4322 (mmt180) REVERT: B 205 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6515 (tp) REVERT: B 226 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6048 (mtt) REVERT: B 249 ILE cc_start: 0.6514 (mm) cc_final: 0.6253 (mt) REVERT: B 253 HIS cc_start: 0.6485 (OUTLIER) cc_final: 0.6218 (t-90) REVERT: B 264 GLU cc_start: 0.5204 (mt-10) cc_final: 0.4941 (mt-10) REVERT: B 267 ARG cc_start: 0.6187 (ttp-110) cc_final: 0.5487 (mpt90) REVERT: B 425 ASN cc_start: 0.5495 (t0) cc_final: 0.5140 (t0) REVERT: C 3 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6845 (mt-10) REVERT: C 23 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7632 (mmp) REVERT: C 50 VAL cc_start: 0.6543 (t) cc_final: 0.6230 (p) REVERT: C 103 MET cc_start: 0.7562 (tpp) cc_final: 0.6926 (tpp) REVERT: C 235 LYS cc_start: 0.6983 (tttt) cc_final: 0.6672 (ttmt) REVERT: C 365 ASP cc_start: 0.6815 (p0) cc_final: 0.5779 (t70) REVERT: C 421 VAL cc_start: 0.6717 (m) cc_final: 0.6431 (t) REVERT: D 4 ILE cc_start: 0.7200 (mp) cc_final: 0.6985 (mm) REVERT: D 26 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7117 (mt-10) REVERT: D 36 THR cc_start: 0.8045 (t) cc_final: 0.7572 (m) REVERT: D 95 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7394 (mt-10) REVERT: D 177 ARG cc_start: 0.7215 (mtm110) cc_final: 0.6762 (mmm160) REVERT: D 364 SER cc_start: 0.6805 (p) cc_final: 0.6220 (t) REVERT: E 86 ASP cc_start: 0.7246 (t0) cc_final: 0.6823 (t70) REVERT: E 92 LYS cc_start: 0.7304 (ttmt) cc_final: 0.6566 (mptp) REVERT: E 95 GLU cc_start: 0.7380 (tt0) cc_final: 0.7128 (tt0) REVERT: E 227 GLU cc_start: 0.5114 (mt-10) cc_final: 0.4755 (mt-10) REVERT: E 317 LYS cc_start: 0.6589 (OUTLIER) cc_final: 0.6175 (ptmm) REVERT: E 323 VAL cc_start: 0.3290 (OUTLIER) cc_final: 0.2916 (t) REVERT: E 384 MET cc_start: 0.7879 (mtm) cc_final: 0.7654 (mtm) REVERT: F 1 MET cc_start: 0.2715 (tmm) cc_final: 0.0561 (mmm) REVERT: F 114 GLN cc_start: 0.5021 (OUTLIER) cc_final: 0.4564 (mt0) REVERT: F 166 MET cc_start: 0.7151 (mtt) cc_final: 0.6806 (mtm) REVERT: F 263 MET cc_start: 0.7594 (mmm) cc_final: 0.7352 (mmm) REVERT: F 298 LYS cc_start: 0.7133 (tppp) cc_final: 0.6802 (tppt) REVERT: F 368 MET cc_start: 0.6238 (OUTLIER) cc_final: 0.5694 (tmm) REVERT: F 384 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.6778 (ttm) outliers start: 120 outliers final: 42 residues processed: 327 average time/residue: 0.4958 time to fit residues: 188.8829 Evaluate side-chains 284 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 230 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 316 CYS Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain F residue 384 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 184 optimal weight: 6.9990 chunk 188 optimal weight: 0.3980 chunk 195 optimal weight: 3.9990 chunk 189 optimal weight: 0.9990 chunk 236 optimal weight: 5.9990 chunk 221 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 234 optimal weight: 5.9990 chunk 224 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 227 optimal weight: 0.0050 overall best weight: 1.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN B 13 GLN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN B 422 GLN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN D 200 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.209027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.180206 restraints weight = 27493.340| |-----------------------------------------------------------------------------| r_work (start): 0.4304 rms_B_bonded: 2.51 r_work: 0.3899 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21324 Z= 0.140 Angle : 0.588 13.965 28898 Z= 0.311 Chirality : 0.042 0.163 3238 Planarity : 0.003 0.034 3597 Dihedral : 10.135 175.391 2937 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.51 % Allowed : 18.59 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.33 (0.17), residues: 2580 helix: 1.05 (0.14), residues: 1304 sheet: -0.82 (0.30), residues: 329 loop : -1.79 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 177 TYR 0.019 0.001 TYR D 22 PHE 0.019 0.002 PHE B 16 TRP 0.022 0.001 TRP B 20 HIS 0.008 0.001 HIS B 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (21324) covalent geometry : angle 0.58811 / 0.31 (28898) hydrogen bonds : bond 0.03358 / 2.23 ( 1054) hydrogen bonds : angle 4.98099 / 3.55 ( 3042) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 244 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 VAL cc_start: 0.2951 (OUTLIER) cc_final: 0.2648 (m) REVERT: A 138 MET cc_start: 0.3939 (OUTLIER) cc_final: 0.3462 (mpt) REVERT: A 203 LYS cc_start: 0.4392 (OUTLIER) cc_final: 0.4041 (pmtt) REVERT: A 228 MET cc_start: 0.1728 (tpp) cc_final: 0.0712 (tmm) REVERT: A 241 MET cc_start: 0.4286 (mtm) cc_final: 0.3472 (mtm) REVERT: A 312 TYR cc_start: 0.3066 (OUTLIER) cc_final: 0.2710 (m-10) REVERT: A 329 TYR cc_start: 0.3765 (m-80) cc_final: 0.3553 (m-80) REVERT: A 355 GLN cc_start: 0.5687 (mm110) cc_final: 0.5065 (mp10) REVERT: A 430 GLU cc_start: 0.4285 (OUTLIER) cc_final: 0.3219 (mm-30) REVERT: B 8 HIS cc_start: 0.6747 (m-70) cc_final: 0.6301 (m-70) REVERT: B 15 TYR cc_start: 0.6254 (t80) cc_final: 0.5897 (t80) REVERT: B 138 MET cc_start: 0.3096 (mtt) cc_final: 0.2844 (mmm) REVERT: B 177 ARG cc_start: 0.4875 (mtm110) cc_final: 0.4265 (mmt180) REVERT: B 226 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6093 (mtt) REVERT: B 249 ILE cc_start: 0.6562 (mm) cc_final: 0.6351 (mm) REVERT: B 253 HIS cc_start: 0.6389 (OUTLIER) cc_final: 0.6101 (t-90) REVERT: B 264 GLU cc_start: 0.5120 (mt-10) cc_final: 0.4854 (mt-10) REVERT: B 267 ARG cc_start: 0.6115 (ttp-110) cc_final: 0.5505 (mpt180) REVERT: B 425 ASN cc_start: 0.5426 (t0) cc_final: 0.5046 (t0) REVERT: C 23 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7488 (mmp) REVERT: C 48 HIS cc_start: 0.4759 (m90) cc_final: 0.4426 (m170) REVERT: C 50 VAL cc_start: 0.6523 (t) cc_final: 0.6230 (p) REVERT: C 85 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.5979 (mp0) REVERT: C 103 MET cc_start: 0.7469 (tpp) cc_final: 0.6890 (tpp) REVERT: C 205 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7099 (tp) REVERT: C 235 LYS cc_start: 0.6893 (tttt) cc_final: 0.6548 (ttmt) REVERT: C 365 ASP cc_start: 0.6620 (p0) cc_final: 0.5667 (t70) REVERT: C 421 VAL cc_start: 0.6621 (m) cc_final: 0.6346 (t) REVERT: D 26 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6875 (mt-10) REVERT: D 36 THR cc_start: 0.8042 (t) cc_final: 0.7609 (m) REVERT: D 92 LYS cc_start: 0.7417 (tmmt) cc_final: 0.6933 (mmmt) REVERT: D 95 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7303 (mt-10) REVERT: D 177 ARG cc_start: 0.7055 (mtm110) cc_final: 0.6715 (mmm160) REVERT: D 364 SER cc_start: 0.6800 (p) cc_final: 0.6178 (t) REVERT: E 86 ASP cc_start: 0.7248 (t0) cc_final: 0.6844 (t70) REVERT: E 92 LYS cc_start: 0.7220 (ttmt) cc_final: 0.6523 (mptp) REVERT: E 95 GLU cc_start: 0.7245 (tt0) cc_final: 0.6974 (tt0) REVERT: E 128 MET cc_start: 0.4123 (OUTLIER) cc_final: 0.3601 (tmt) REVERT: E 227 GLU cc_start: 0.4650 (mt-10) cc_final: 0.4371 (mt-10) REVERT: E 317 LYS cc_start: 0.6526 (OUTLIER) cc_final: 0.6066 (ptmm) REVERT: E 323 VAL cc_start: 0.3231 (OUTLIER) cc_final: 0.2872 (t) REVERT: E 384 MET cc_start: 0.7787 (mtm) cc_final: 0.7525 (mtm) REVERT: E 397 GLU cc_start: 0.6037 (OUTLIER) cc_final: 0.5755 (pp20) REVERT: F 1 MET cc_start: 0.2629 (tmm) cc_final: 0.0527 (mmm) REVERT: F 114 GLN cc_start: 0.5080 (OUTLIER) cc_final: 0.4609 (mt0) REVERT: F 166 MET cc_start: 0.7089 (mtt) cc_final: 0.6735 (mtm) REVERT: F 263 MET cc_start: 0.7475 (mmm) cc_final: 0.7271 (mmm) REVERT: F 298 LYS cc_start: 0.7105 (tppp) cc_final: 0.6797 (tppt) REVERT: F 368 MET cc_start: 0.5933 (OUTLIER) cc_final: 0.5433 (tmm) REVERT: F 384 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6751 (ttm) outliers start: 101 outliers final: 46 residues processed: 314 average time/residue: 0.5128 time to fit residues: 186.0391 Evaluate side-chains 297 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 233 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 316 CYS Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 384 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 211 optimal weight: 4.9990 chunk 19 optimal weight: 0.3980 chunk 234 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 120 optimal weight: 0.3980 chunk 213 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN B 116 ASN B 288 ASN B 355 GLN B 422 GLN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 200 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.208439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.177323 restraints weight = 27752.327| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 2.72 r_work: 0.3894 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21324 Z= 0.135 Angle : 0.582 16.073 28898 Z= 0.306 Chirality : 0.042 0.157 3238 Planarity : 0.003 0.033 3597 Dihedral : 9.971 173.018 2937 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.87 % Allowed : 18.45 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.27 (0.17), residues: 2580 helix: 1.12 (0.14), residues: 1304 sheet: -0.79 (0.30), residues: 331 loop : -1.79 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 177 TYR 0.018 0.001 TYR D 22 PHE 0.014 0.001 PHE F 417 TRP 0.020 0.001 TRP B 20 HIS 0.007 0.001 HIS B 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (21324) covalent geometry : angle 0.58193 / 0.31 (28898) hydrogen bonds : bond 0.03247 / 2.16 ( 1054) hydrogen bonds : angle 4.89346 / 3.49 ( 3042) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 239 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 VAL cc_start: 0.2979 (OUTLIER) cc_final: 0.2660 (m) REVERT: A 89 TRP cc_start: 0.4517 (t60) cc_final: 0.3941 (t60) REVERT: A 138 MET cc_start: 0.3962 (OUTLIER) cc_final: 0.3692 (mpt) REVERT: A 203 LYS cc_start: 0.4232 (OUTLIER) cc_final: 0.3922 (pmtt) REVERT: A 228 MET cc_start: 0.1618 (tpp) cc_final: 0.1411 (tpp) REVERT: A 241 MET cc_start: 0.4188 (mtm) cc_final: 0.3471 (mtm) REVERT: A 288 ASN cc_start: 0.4227 (t0) cc_final: 0.3874 (t0) REVERT: A 312 TYR cc_start: 0.3133 (OUTLIER) cc_final: 0.2763 (m-10) REVERT: A 320 ARG cc_start: 0.4000 (mtm180) cc_final: 0.3621 (mtp180) REVERT: A 355 GLN cc_start: 0.5690 (mm110) cc_final: 0.5100 (mp10) REVERT: A 430 GLU cc_start: 0.4226 (OUTLIER) cc_final: 0.3234 (mm-30) REVERT: B 8 HIS cc_start: 0.6715 (m-70) cc_final: 0.6344 (m-70) REVERT: B 15 TYR cc_start: 0.6207 (t80) cc_final: 0.5798 (t80) REVERT: B 23 MET cc_start: 0.5647 (tpp) cc_final: 0.5297 (tpp) REVERT: B 138 MET cc_start: 0.2980 (mtt) cc_final: 0.2763 (mmm) REVERT: B 155 MET cc_start: 0.6533 (tpp) cc_final: 0.4294 (mpp) REVERT: B 177 ARG cc_start: 0.4867 (mtm110) cc_final: 0.4257 (mmt180) REVERT: B 184 LYS cc_start: 0.6715 (OUTLIER) cc_final: 0.6237 (mttp) REVERT: B 226 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6116 (mtt) REVERT: B 249 ILE cc_start: 0.6626 (mm) cc_final: 0.6399 (mm) REVERT: B 253 HIS cc_start: 0.6471 (OUTLIER) cc_final: 0.6158 (t-90) REVERT: B 264 GLU cc_start: 0.5011 (mt-10) cc_final: 0.4762 (mt-10) REVERT: B 267 ARG cc_start: 0.6050 (ttp-110) cc_final: 0.5412 (mpt90) REVERT: B 425 ASN cc_start: 0.5325 (t0) cc_final: 0.4990 (t0) REVERT: C 3 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7250 (pm20) REVERT: C 23 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7688 (mmp) REVERT: C 48 HIS cc_start: 0.4778 (m90) cc_final: 0.4471 (m170) REVERT: C 49 SER cc_start: 0.4917 (p) cc_final: 0.4546 (t) REVERT: C 50 VAL cc_start: 0.6519 (t) cc_final: 0.6128 (p) REVERT: C 103 MET cc_start: 0.7483 (tpp) cc_final: 0.6834 (tpp) REVERT: C 205 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.7045 (tp) REVERT: C 235 LYS cc_start: 0.6871 (tttt) cc_final: 0.6514 (ttmt) REVERT: C 365 ASP cc_start: 0.6640 (p0) cc_final: 0.5645 (t70) REVERT: C 400 LEU cc_start: 0.7292 (tt) cc_final: 0.7087 (tp) REVERT: C 421 VAL cc_start: 0.6568 (m) cc_final: 0.6295 (t) REVERT: D 26 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6861 (mt-10) REVERT: D 36 THR cc_start: 0.8042 (t) cc_final: 0.7597 (m) REVERT: D 92 LYS cc_start: 0.7373 (tmmt) cc_final: 0.6883 (mmmt) REVERT: D 95 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7317 (mt-10) REVERT: D 177 ARG cc_start: 0.7130 (mtm110) cc_final: 0.6687 (mmm160) REVERT: D 248 ASP cc_start: 0.7223 (m-30) cc_final: 0.7022 (m-30) REVERT: D 364 SER cc_start: 0.6861 (p) cc_final: 0.6205 (t) REVERT: E 3 GLU cc_start: 0.6850 (mp0) cc_final: 0.6541 (mm-30) REVERT: E 86 ASP cc_start: 0.7222 (t0) cc_final: 0.6817 (t70) REVERT: E 92 LYS cc_start: 0.7206 (ttmt) cc_final: 0.6499 (mptp) REVERT: E 95 GLU cc_start: 0.7241 (tt0) cc_final: 0.6898 (tt0) REVERT: E 101 ARG cc_start: 0.6544 (mmm-85) cc_final: 0.6186 (tpp-160) REVERT: E 323 VAL cc_start: 0.3280 (OUTLIER) cc_final: 0.2909 (t) REVERT: F 1 MET cc_start: 0.2580 (tmm) cc_final: 0.0722 (tpp) REVERT: F 114 GLN cc_start: 0.5150 (OUTLIER) cc_final: 0.4711 (mt0) REVERT: F 166 MET cc_start: 0.7067 (mtt) cc_final: 0.6733 (mtm) REVERT: F 263 MET cc_start: 0.7494 (mmm) cc_final: 0.7288 (mmm) REVERT: F 298 LYS cc_start: 0.7004 (tppp) cc_final: 0.6770 (tppt) REVERT: F 368 MET cc_start: 0.5806 (OUTLIER) cc_final: 0.5291 (tmm) REVERT: F 384 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6790 (ttm) outliers start: 109 outliers final: 43 residues processed: 315 average time/residue: 0.5844 time to fit residues: 213.0916 Evaluate side-chains 291 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 233 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 316 CYS Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 384 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 254 optimal weight: 8.9990 chunk 177 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 228 optimal weight: 0.9980 chunk 216 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN D 200 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.207959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.176508 restraints weight = 27484.788| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 2.71 r_work: 0.3857 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 21324 Z= 0.231 Angle : 0.715 16.496 28898 Z= 0.372 Chirality : 0.047 0.237 3238 Planarity : 0.005 0.040 3597 Dihedral : 10.310 166.050 2937 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 5.23 % Allowed : 18.10 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.16), residues: 2580 helix: 0.67 (0.14), residues: 1305 sheet: -0.91 (0.30), residues: 320 loop : -1.89 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 407 TYR 0.027 0.002 TYR D 22 PHE 0.026 0.002 PHE F 417 TRP 0.019 0.002 TRP B 89 HIS 0.008 0.002 HIS F 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.23 (21324) covalent geometry : angle 0.71507 / 0.37 (28898) hydrogen bonds : bond 0.03917 / 2.59 ( 1054) hydrogen bonds : angle 5.22626 / 3.73 ( 3042) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 235 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 VAL cc_start: 0.3147 (OUTLIER) cc_final: 0.2790 (m) REVERT: A 89 TRP cc_start: 0.4501 (t60) cc_final: 0.3828 (t60) REVERT: A 114 GLN cc_start: 0.2261 (mt0) cc_final: 0.1550 (tp40) REVERT: A 138 MET cc_start: 0.4114 (OUTLIER) cc_final: 0.3743 (mpt) REVERT: A 203 LYS cc_start: 0.4287 (OUTLIER) cc_final: 0.3869 (pmtt) REVERT: A 228 MET cc_start: 0.1599 (tpp) cc_final: 0.0478 (tmm) REVERT: A 241 MET cc_start: 0.4363 (mtm) cc_final: 0.3635 (mtm) REVERT: A 312 TYR cc_start: 0.3252 (OUTLIER) cc_final: 0.2858 (m-10) REVERT: A 320 ARG cc_start: 0.4024 (mtm180) cc_final: 0.3703 (mtm180) REVERT: A 355 GLN cc_start: 0.5600 (mm110) cc_final: 0.5003 (mp10) REVERT: A 430 GLU cc_start: 0.4200 (OUTLIER) cc_final: 0.3144 (mm-30) REVERT: B 8 HIS cc_start: 0.6752 (m-70) cc_final: 0.6340 (m-70) REVERT: B 177 ARG cc_start: 0.4890 (mtm110) cc_final: 0.4329 (mmt180) REVERT: B 184 LYS cc_start: 0.6636 (OUTLIER) cc_final: 0.6231 (mttp) REVERT: B 226 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6072 (mtt) REVERT: B 249 ILE cc_start: 0.6646 (mm) cc_final: 0.6412 (mm) REVERT: B 264 GLU cc_start: 0.5359 (mt-10) cc_final: 0.5104 (mt-10) REVERT: B 267 ARG cc_start: 0.6086 (ttp-110) cc_final: 0.5483 (mpt180) REVERT: B 384 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6445 (mtm) REVERT: B 425 ASN cc_start: 0.5442 (t0) cc_final: 0.5041 (t0) REVERT: C 3 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7342 (pm20) REVERT: C 48 HIS cc_start: 0.4666 (m90) cc_final: 0.4292 (m170) REVERT: C 49 SER cc_start: 0.4998 (p) cc_final: 0.4636 (t) REVERT: C 50 VAL cc_start: 0.6660 (t) cc_final: 0.6285 (p) REVERT: C 85 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6095 (mp0) REVERT: C 103 MET cc_start: 0.7571 (tpp) cc_final: 0.6909 (tpp) REVERT: C 235 LYS cc_start: 0.6939 (tttt) cc_final: 0.6605 (ttmt) REVERT: C 365 ASP cc_start: 0.6631 (p0) cc_final: 0.5640 (t70) REVERT: C 400 LEU cc_start: 0.7540 (tt) cc_final: 0.7338 (tp) REVERT: C 421 VAL cc_start: 0.6639 (OUTLIER) cc_final: 0.6414 (t) REVERT: D 22 TYR cc_start: 0.4991 (m-80) cc_final: 0.4752 (m-10) REVERT: D 26 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7074 (mt-10) REVERT: D 36 THR cc_start: 0.8073 (t) cc_final: 0.7603 (m) REVERT: D 39 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7911 (mp) REVERT: D 46 GLU cc_start: 0.7463 (tt0) cc_final: 0.7089 (mm-30) REVERT: D 95 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7275 (mt-10) REVERT: D 177 ARG cc_start: 0.7177 (mtm110) cc_final: 0.6734 (mmm160) REVERT: E 86 ASP cc_start: 0.7259 (t0) cc_final: 0.6946 (t70) REVERT: E 92 LYS cc_start: 0.7293 (ttmt) cc_final: 0.6477 (mptp) REVERT: E 95 GLU cc_start: 0.7401 (tt0) cc_final: 0.7075 (tt0) REVERT: E 101 ARG cc_start: 0.6611 (mmm-85) cc_final: 0.6249 (tpp-160) REVERT: E 128 MET cc_start: 0.4582 (ppp) cc_final: 0.2529 (mtm) REVERT: F 1 MET cc_start: 0.2488 (tmm) cc_final: 0.2053 (ptm) REVERT: F 114 GLN cc_start: 0.5241 (OUTLIER) cc_final: 0.4730 (mt0) REVERT: F 200 ASN cc_start: 0.7719 (OUTLIER) cc_final: 0.7409 (m110) REVERT: F 263 MET cc_start: 0.7641 (mmm) cc_final: 0.7385 (mmm) REVERT: F 368 MET cc_start: 0.6266 (OUTLIER) cc_final: 0.5722 (tmm) outliers start: 117 outliers final: 54 residues processed: 317 average time/residue: 0.5817 time to fit residues: 212.7617 Evaluate side-chains 288 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 219 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 422 GLN Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain F residue 200 ASN Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 316 CYS Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain F residue 382 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 99 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 204 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 179 optimal weight: 10.0000 chunk 252 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 HIS A 398 GLN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN D 200 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 GLN ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.208177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.177084 restraints weight = 27295.889| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 2.67 r_work: 0.3859 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21324 Z= 0.217 Angle : 0.706 17.245 28898 Z= 0.370 Chirality : 0.046 0.196 3238 Planarity : 0.004 0.038 3597 Dihedral : 10.410 173.267 2935 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.92 % Allowed : 18.72 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.16), residues: 2580 helix: 0.56 (0.14), residues: 1310 sheet: -1.01 (0.30), residues: 320 loop : -1.99 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 101 TYR 0.023 0.002 TYR D 22 PHE 0.030 0.002 PHE B 16 TRP 0.021 0.002 TRP B 89 HIS 0.007 0.001 HIS B 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.22 (21324) covalent geometry : angle 0.70600 / 0.37 (28898) hydrogen bonds : bond 0.03855 / 2.55 ( 1054) hydrogen bonds : angle 5.26224 / 3.75 ( 3042) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 229 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 VAL cc_start: 0.3117 (OUTLIER) cc_final: 0.2737 (m) REVERT: A 89 TRP cc_start: 0.4716 (t60) cc_final: 0.4015 (t60) REVERT: A 114 GLN cc_start: 0.2277 (mt0) cc_final: 0.1558 (tp40) REVERT: A 138 MET cc_start: 0.3924 (OUTLIER) cc_final: 0.3550 (mpt) REVERT: A 203 LYS cc_start: 0.4300 (OUTLIER) cc_final: 0.4014 (pmtt) REVERT: A 228 MET cc_start: 0.1706 (tpp) cc_final: 0.0578 (tmm) REVERT: A 241 MET cc_start: 0.4375 (mtm) cc_final: 0.3605 (mtm) REVERT: A 320 ARG cc_start: 0.3849 (mtm180) cc_final: 0.3611 (mtm180) REVERT: A 355 GLN cc_start: 0.5631 (mm110) cc_final: 0.5049 (mp10) REVERT: B 8 HIS cc_start: 0.6796 (m-70) cc_final: 0.6309 (m-70) REVERT: B 177 ARG cc_start: 0.4874 (mtm110) cc_final: 0.4292 (mmt180) REVERT: B 184 LYS cc_start: 0.6634 (OUTLIER) cc_final: 0.6210 (mttp) REVERT: B 226 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6047 (mtt) REVERT: B 249 ILE cc_start: 0.6794 (mm) cc_final: 0.6549 (mm) REVERT: B 264 GLU cc_start: 0.5310 (mt-10) cc_final: 0.5093 (mt-10) REVERT: B 384 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.6386 (mtm) REVERT: B 425 ASN cc_start: 0.5346 (t0) cc_final: 0.4959 (t0) REVERT: C 3 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7291 (pm20) REVERT: C 7 SER cc_start: 0.7898 (p) cc_final: 0.7234 (m) REVERT: C 48 HIS cc_start: 0.4798 (m90) cc_final: 0.4418 (m170) REVERT: C 49 SER cc_start: 0.4982 (p) cc_final: 0.4621 (t) REVERT: C 50 VAL cc_start: 0.6684 (t) cc_final: 0.6339 (p) REVERT: C 85 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6000 (mp0) REVERT: C 103 MET cc_start: 0.7556 (tpp) cc_final: 0.6902 (tpp) REVERT: C 205 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6570 (tp) REVERT: C 235 LYS cc_start: 0.6905 (tttt) cc_final: 0.6572 (ttmt) REVERT: C 365 ASP cc_start: 0.6554 (p0) cc_final: 0.5590 (t70) REVERT: C 421 VAL cc_start: 0.6649 (OUTLIER) cc_final: 0.6430 (t) REVERT: D 22 TYR cc_start: 0.4935 (m-80) cc_final: 0.4633 (m-10) REVERT: D 26 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7074 (mt-10) REVERT: D 36 THR cc_start: 0.8085 (t) cc_final: 0.7617 (m) REVERT: D 39 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.8005 (mp) REVERT: D 95 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7266 (mt-10) REVERT: D 177 ARG cc_start: 0.7157 (mtm110) cc_final: 0.6717 (mmm160) REVERT: D 248 ASP cc_start: 0.7398 (m-30) cc_final: 0.7101 (m-30) REVERT: D 299 LEU cc_start: 0.6951 (pp) cc_final: 0.6722 (pp) REVERT: D 368 MET cc_start: 0.6973 (ttt) cc_final: 0.6410 (tpp) REVERT: E 70 TYR cc_start: 0.3855 (OUTLIER) cc_final: 0.2886 (t80) REVERT: E 86 ASP cc_start: 0.7278 (t0) cc_final: 0.6906 (t70) REVERT: E 92 LYS cc_start: 0.7305 (ttmt) cc_final: 0.6496 (mptp) REVERT: E 95 GLU cc_start: 0.7315 (tt0) cc_final: 0.6987 (tt0) REVERT: E 101 ARG cc_start: 0.6665 (mmm-85) cc_final: 0.6307 (tpp-160) REVERT: E 128 MET cc_start: 0.4484 (ppp) cc_final: 0.2472 (mtm) REVERT: E 279 GLN cc_start: 0.6875 (OUTLIER) cc_final: 0.6235 (tp-100) REVERT: F 1 MET cc_start: 0.2500 (tmm) cc_final: 0.2207 (ptm) REVERT: F 114 GLN cc_start: 0.5291 (OUTLIER) cc_final: 0.4778 (mt0) REVERT: F 140 GLN cc_start: 0.5655 (tp40) cc_final: 0.5314 (tm-30) REVERT: F 166 MET cc_start: 0.7176 (mtt) cc_final: 0.6821 (mtm) REVERT: F 200 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7440 (m110) REVERT: F 263 MET cc_start: 0.7616 (mmm) cc_final: 0.7395 (mmm) outliers start: 110 outliers final: 58 residues processed: 308 average time/residue: 0.5403 time to fit residues: 193.6598 Evaluate side-chains 292 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 219 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 422 GLN Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 200 ASN Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 316 CYS Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain F residue 401 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 247 optimal weight: 0.0670 chunk 136 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 236 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN A 422 GLN B 13 GLN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN D 200 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 GLN F 200 ASN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.210874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.179243 restraints weight = 27157.114| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 2.57 r_work: 0.3930 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21324 Z= 0.126 Angle : 0.608 16.096 28898 Z= 0.318 Chirality : 0.042 0.200 3238 Planarity : 0.004 0.039 3597 Dihedral : 10.021 176.837 2935 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.53 % Allowed : 20.24 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.17), residues: 2580 helix: 0.98 (0.14), residues: 1311 sheet: -0.94 (0.30), residues: 328 loop : -1.92 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 267 TYR 0.019 0.001 TYR A 97 PHE 0.020 0.001 PHE E 146 TRP 0.023 0.001 TRP B 20 HIS 0.011 0.001 HIS B 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (21324) covalent geometry : angle 0.60834 / 0.32 (28898) hydrogen bonds : bond 0.03214 / 2.15 ( 1054) hydrogen bonds : angle 4.95213 / 3.52 ( 3042) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 248 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3984 (ttm) cc_final: 0.3322 (mmt) REVERT: A 19 VAL cc_start: 0.3002 (OUTLIER) cc_final: 0.2641 (m) REVERT: A 89 TRP cc_start: 0.4862 (t60) cc_final: 0.4057 (t60) REVERT: A 114 GLN cc_start: 0.2301 (mt0) cc_final: 0.1614 (tp40) REVERT: A 203 LYS cc_start: 0.4263 (OUTLIER) cc_final: 0.3887 (pmtt) REVERT: A 228 MET cc_start: 0.1588 (tpp) cc_final: 0.0426 (tmm) REVERT: A 312 TYR cc_start: 0.3281 (OUTLIER) cc_final: 0.2923 (m-10) REVERT: A 355 GLN cc_start: 0.5576 (mm110) cc_final: 0.5050 (mp10) REVERT: A 430 GLU cc_start: 0.4225 (OUTLIER) cc_final: 0.3106 (mm-30) REVERT: B 8 HIS cc_start: 0.6679 (m-70) cc_final: 0.6303 (m-70) REVERT: B 15 TYR cc_start: 0.6175 (t80) cc_final: 0.5819 (t80) REVERT: B 155 MET cc_start: 0.6605 (tpp) cc_final: 0.4519 (mpp) REVERT: B 177 ARG cc_start: 0.4747 (mtm110) cc_final: 0.4193 (mmt180) REVERT: B 184 LYS cc_start: 0.6548 (OUTLIER) cc_final: 0.6145 (mttp) REVERT: B 226 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6103 (mtt) REVERT: B 249 ILE cc_start: 0.6795 (mm) cc_final: 0.6557 (mm) REVERT: B 267 ARG cc_start: 0.6375 (tpm170) cc_final: 0.5845 (mmt-90) REVERT: B 384 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.6279 (mtm) REVERT: B 425 ASN cc_start: 0.5072 (t0) cc_final: 0.4757 (t0) REVERT: C 1 MET cc_start: 0.7377 (ptm) cc_final: 0.7134 (ttt) REVERT: C 3 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7155 (pm20) REVERT: C 7 SER cc_start: 0.7806 (p) cc_final: 0.7144 (m) REVERT: C 48 HIS cc_start: 0.4884 (m90) cc_final: 0.4512 (m170) REVERT: C 49 SER cc_start: 0.4932 (p) cc_final: 0.4594 (t) REVERT: C 50 VAL cc_start: 0.6584 (t) cc_final: 0.6220 (p) REVERT: C 85 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6009 (mp0) REVERT: C 103 MET cc_start: 0.7443 (tpp) cc_final: 0.6784 (tpp) REVERT: C 235 LYS cc_start: 0.6845 (tttt) cc_final: 0.6503 (ttmt) REVERT: C 297 LEU cc_start: 0.4678 (OUTLIER) cc_final: 0.3943 (tp) REVERT: C 338 GLU cc_start: 0.6204 (tt0) cc_final: 0.5232 (mt-10) REVERT: C 365 ASP cc_start: 0.6505 (p0) cc_final: 0.5569 (t70) REVERT: C 421 VAL cc_start: 0.6606 (OUTLIER) cc_final: 0.6329 (t) REVERT: D 26 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6849 (mt-10) REVERT: D 36 THR cc_start: 0.8026 (t) cc_final: 0.7602 (m) REVERT: D 46 GLU cc_start: 0.7324 (tt0) cc_final: 0.6960 (mm-30) REVERT: D 95 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7244 (mt-10) REVERT: D 177 ARG cc_start: 0.7022 (mtm110) cc_final: 0.6608 (mmm160) REVERT: D 299 LEU cc_start: 0.6912 (pp) cc_final: 0.6688 (pp) REVERT: D 368 MET cc_start: 0.6841 (ttt) cc_final: 0.6391 (tpp) REVERT: E 86 ASP cc_start: 0.7185 (t0) cc_final: 0.6813 (t70) REVERT: E 92 LYS cc_start: 0.7258 (ttmt) cc_final: 0.6487 (mptp) REVERT: E 95 GLU cc_start: 0.7226 (tt0) cc_final: 0.6861 (tt0) REVERT: E 101 ARG cc_start: 0.6627 (mmm-85) cc_final: 0.6219 (tpp-160) REVERT: E 128 MET cc_start: 0.4367 (ppp) cc_final: 0.2382 (mtm) REVERT: E 323 VAL cc_start: 0.3209 (OUTLIER) cc_final: 0.2858 (t) REVERT: F 1 MET cc_start: 0.2471 (tmm) cc_final: 0.2180 (ptm) REVERT: F 114 GLN cc_start: 0.5203 (OUTLIER) cc_final: 0.4761 (mt0) REVERT: F 166 MET cc_start: 0.7058 (mtt) cc_final: 0.6732 (mtm) REVERT: F 263 MET cc_start: 0.7481 (mmm) cc_final: 0.7258 (mmm) REVERT: F 384 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.6887 (ttm) outliers start: 79 outliers final: 39 residues processed: 302 average time/residue: 0.5776 time to fit residues: 201.0799 Evaluate side-chains 280 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 227 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 125 ASN Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 316 CYS Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 384 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 80 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 210 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN D 200 ASN E 43 HIS ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 GLN F 200 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.209323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.177935 restraints weight = 27336.361| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 2.62 r_work: 0.3887 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21324 Z= 0.165 Angle : 0.656 17.093 28898 Z= 0.341 Chirality : 0.044 0.249 3238 Planarity : 0.004 0.038 3597 Dihedral : 10.006 163.822 2935 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.22 % Allowed : 21.27 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.17), residues: 2580 helix: 0.87 (0.14), residues: 1312 sheet: -0.83 (0.30), residues: 320 loop : -1.95 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 320 TYR 0.023 0.002 TYR B 324 PHE 0.029 0.002 PHE B 16 TRP 0.028 0.002 TRP B 89 HIS 0.010 0.001 HIS B 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (21324) covalent geometry : angle 0.65601 / 0.34 (28898) hydrogen bonds : bond 0.03453 / 2.30 ( 1054) hydrogen bonds : angle 5.02442 / 3.58 ( 3042) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 226 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3812 (ttm) cc_final: 0.3195 (mmt) REVERT: A 19 VAL cc_start: 0.3122 (OUTLIER) cc_final: 0.2747 (m) REVERT: A 89 TRP cc_start: 0.4769 (t60) cc_final: 0.3955 (t60) REVERT: A 114 GLN cc_start: 0.2411 (mt0) cc_final: 0.1693 (tp40) REVERT: A 203 LYS cc_start: 0.4316 (OUTLIER) cc_final: 0.3882 (pmtt) REVERT: A 228 MET cc_start: 0.1625 (tpp) cc_final: 0.0548 (tmm) REVERT: A 312 TYR cc_start: 0.3388 (OUTLIER) cc_final: 0.3019 (m-10) REVERT: A 355 GLN cc_start: 0.5746 (mm110) cc_final: 0.5170 (mp10) REVERT: A 430 GLU cc_start: 0.4204 (OUTLIER) cc_final: 0.3110 (mm-30) REVERT: B 8 HIS cc_start: 0.6726 (m-70) cc_final: 0.6428 (m-70) REVERT: B 15 TYR cc_start: 0.6147 (t80) cc_final: 0.5780 (t80) REVERT: B 177 ARG cc_start: 0.4761 (mtm110) cc_final: 0.4287 (mmt180) REVERT: B 184 LYS cc_start: 0.6629 (OUTLIER) cc_final: 0.6218 (mttp) REVERT: B 226 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6041 (mtt) REVERT: B 249 ILE cc_start: 0.6874 (mm) cc_final: 0.6672 (mm) REVERT: B 267 ARG cc_start: 0.6591 (tpm170) cc_final: 0.5949 (mmt-90) REVERT: B 384 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.6400 (mtm) REVERT: B 425 ASN cc_start: 0.5220 (t0) cc_final: 0.4834 (t0) REVERT: C 1 MET cc_start: 0.7441 (ptm) cc_final: 0.7206 (ttt) REVERT: C 3 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7205 (pm20) REVERT: C 7 SER cc_start: 0.7854 (p) cc_final: 0.7195 (m) REVERT: C 48 HIS cc_start: 0.4710 (m90) cc_final: 0.4367 (m170) REVERT: C 49 SER cc_start: 0.4990 (p) cc_final: 0.4633 (t) REVERT: C 50 VAL cc_start: 0.6626 (t) cc_final: 0.6260 (p) REVERT: C 85 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6071 (mp0) REVERT: C 103 MET cc_start: 0.7564 (tpp) cc_final: 0.6854 (tpp) REVERT: C 235 LYS cc_start: 0.6858 (tttt) cc_final: 0.6531 (ttmt) REVERT: C 297 LEU cc_start: 0.4586 (OUTLIER) cc_final: 0.4315 (tp) REVERT: C 365 ASP cc_start: 0.6634 (p0) cc_final: 0.5615 (t70) REVERT: C 421 VAL cc_start: 0.6655 (OUTLIER) cc_final: 0.6387 (t) REVERT: D 26 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7147 (mt-10) REVERT: D 36 THR cc_start: 0.8040 (t) cc_final: 0.7564 (m) REVERT: D 46 GLU cc_start: 0.7618 (tt0) cc_final: 0.7251 (mm-30) REVERT: D 95 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7304 (mt-10) REVERT: D 177 ARG cc_start: 0.7117 (mtm110) cc_final: 0.6709 (mmm160) REVERT: D 299 LEU cc_start: 0.6941 (pp) cc_final: 0.6612 (pp) REVERT: D 368 MET cc_start: 0.6924 (ttt) cc_final: 0.6438 (tpp) REVERT: D 387 VAL cc_start: 0.7551 (OUTLIER) cc_final: 0.7315 (t) REVERT: E 86 ASP cc_start: 0.7209 (t0) cc_final: 0.6871 (t70) REVERT: E 92 LYS cc_start: 0.7349 (ttmt) cc_final: 0.6515 (mptp) REVERT: E 95 GLU cc_start: 0.7374 (tt0) cc_final: 0.7031 (tt0) REVERT: E 101 ARG cc_start: 0.6695 (mmm-85) cc_final: 0.6346 (tpp-160) REVERT: E 128 MET cc_start: 0.4510 (ppp) cc_final: 0.2473 (mtm) REVERT: F 114 GLN cc_start: 0.5350 (OUTLIER) cc_final: 0.4800 (mt0) REVERT: F 166 MET cc_start: 0.7134 (mtt) cc_final: 0.6794 (mtm) REVERT: F 263 MET cc_start: 0.7569 (mmm) cc_final: 0.7351 (mmm) REVERT: F 368 MET cc_start: 0.6244 (tpp) cc_final: 0.5874 (tmm) REVERT: F 384 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.6936 (ttm) outliers start: 72 outliers final: 42 residues processed: 275 average time/residue: 0.5559 time to fit residues: 177.8255 Evaluate side-chains 276 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 220 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 316 CYS Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain F residue 401 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 65 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 71 optimal weight: 0.0040 chunk 170 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 245 optimal weight: 1.9990 chunk 240 optimal weight: 8.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN D 200 ASN E 43 HIS ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 GLN F 200 ASN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.210511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.178763 restraints weight = 27327.875| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 2.57 r_work: 0.3923 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21324 Z= 0.141 Angle : 0.626 16.667 28898 Z= 0.326 Chirality : 0.043 0.190 3238 Planarity : 0.004 0.041 3597 Dihedral : 9.852 165.224 2935 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.31 % Allowed : 21.27 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.47 (0.17), residues: 2580 helix: 0.99 (0.14), residues: 1314 sheet: -0.93 (0.30), residues: 328 loop : -1.96 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 320 TYR 0.018 0.001 TYR B 324 PHE 0.029 0.002 PHE B 16 TRP 0.026 0.002 TRP B 89 HIS 0.010 0.001 HIS B 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (21324) covalent geometry : angle 0.62592 / 0.33 (28898) hydrogen bonds : bond 0.03258 / 2.17 ( 1054) hydrogen bonds : angle 4.93073 / 3.50 ( 3042) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6402.06 seconds wall clock time: 110 minutes 25.21 seconds (6625.21 seconds total)