Starting phenix.real_space_refine on Wed Jun 18 08:21:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8due_27719/06_2025/8due_27719.cif Found real_map, /net/cci-nas-00/data/ceres_data/8due_27719/06_2025/8due_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_27719/06_2025/8due_27719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8due_27719/06_2025/8due_27719.map" model { file = "/net/cci-nas-00/data/ceres_data/8due_27719/06_2025/8due_27719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8due_27719/06_2025/8due_27719.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.28, per 1000 atoms: 0.64 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: 5.34 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.80 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: 6.72 Time building geometry restraints manager: 6.26 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: 27699 1.14 - 2.29: 923 2.29 - 3.43: 209 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=" N PHE B 16 " pdb=" CA PHE B 16 " pdb=" C PHE B 16 " ideal model delta sigma weight residual 111.71 107.14 4.57 1.15e+00 7.56e-01 1.58e+01 angle pdb=" N ASP E 382 " pdb=" CA ASP E 382 " pdb=" C ASP E 382 " ideal model delta sigma weight residual 114.56 109.64 4.92 1.27e+00 6.20e-01 1.50e+01 angle pdb=" N SER F 30 " pdb=" CA SER F 30 " pdb=" C SER F 30 " ideal model delta sigma weight residual 113.01 108.60 4.41 1.20e+00 6.94e-01 1.35e+01 angle pdb=" N MET E 226 " pdb=" CA MET E 226 " pdb=" C MET E 226 " ideal model delta sigma weight residual 113.50 109.04 4.46 1.23e+00 6.61e-01 1.31e+01 ... (remaining 28893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 12670 35.99 - 71.99: 231 71.99 - 107.98: 6 107.98 - 143.97: 2 143.97 - 179.97: 2 Dihedral angle restraints: 12911 sinusoidal: 5297 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 12908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2345 0.039 - 0.079: 639 0.079 - 0.118: 232 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: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.170 Set scattering table: 0.190 Process input model: 48.580 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.090 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:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 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= 0.176 Angle : 0.535 5.720 28898 Z= 0.325 Chirality : 0.041 0.197 3238 Planarity : 0.003 0.040 3597 Dihedral : 13.298 179.966 7991 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.001 TRP E 162 HIS 0.002 0.001 HIS E 8 PHE 0.013 0.001 PHE F 417 TYR 0.009 0.001 TYR E 15 ARG 0.002 0.000 ARG F 101 Details of bonding type rmsd hydrogen bonds : bond 0.14678 ( 1054) hydrogen bonds : angle 6.20224 ( 3042) covalent geometry : bond 0.00297 (21324) covalent geometry : angle 0.53451 (28898) *********************** 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 : 2.308 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: 0.4433 (mpt) REVERT: A 155 MET cc_start: 0.6678 (tmm) cc_final: 0.6384 (tmm) REVERT: A 228 MET cc_start: 0.1530 (tpp) cc_final: 0.0638 (mtm) REVERT: A 241 MET cc_start: 0.1594 (mtm) cc_final: 0.1324 (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: 0.2699 (m-10) REVERT: A 315 ILE cc_start: 0.5531 (pt) cc_final: 0.5127 (pt) 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: 0.5252 (mm-40) REVERT: A 411 LYS cc_start: 0.4861 (ttmm) cc_final: 0.4516 (ttpp) REVERT: A 431 ILE cc_start: 0.4374 (tp) cc_final: 0.4039 (pt) REVERT: B 13 GLN cc_start: 0.5098 (tm-30) cc_final: 0.4744 (tp-100) REVERT: B 70 TYR cc_start: 0.6180 (t80) cc_final: 0.5711 (t80) REVERT: B 76 LEU cc_start: 0.5828 (mp) cc_final: 0.5518 (tt) REVERT: B 138 MET cc_start: 0.3359 (mtt) cc_final: 0.3149 (mtt) REVERT: B 177 ARG cc_start: 0.4499 (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: 0.6134 (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: 0.6075 (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: 0.2685 (mt) REVERT: C 308 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7072 (mt) REVERT: C 326 GLU cc_start: 0.5049 (tt0) cc_final: 0.4839 (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 92 LYS cc_start: 0.6759 (tmmt) cc_final: 0.6192 (mmmt) REVERT: D 93 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6085 (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: 0.6765 (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: 0.5762 (m-40) REVERT: D 295 ASN cc_start: 0.5535 (m110) cc_final: 0.5327 (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: 0.6344 (t) REVERT: E 86 ASP cc_start: 0.7200 (t0) cc_final: 0.6718 (t0) REVERT: E 92 LYS cc_start: 0.6422 (ttmt) cc_final: 0.5685 (mptp) REVERT: E 95 GLU cc_start: 0.6458 (tt0) cc_final: 0.6156 (tt0) REVERT: E 104 PHE cc_start: 0.6821 (t80) cc_final: 0.6385 (t80) REVERT: E 128 MET cc_start: 0.3086 (tmt) cc_final: 0.1513 (mtp) REVERT: E 156 ASP cc_start: 0.6572 (m-30) cc_final: 0.5998 (t0) REVERT: E 166 MET cc_start: 0.6687 (ptp) cc_final: 0.6363 (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: 0.7072 (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: 0.6459 (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: 0.1742 (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 155 MET cc_start: 0.1937 (OUTLIER) cc_final: 0.1465 (ttp) REVERT: F 184 LYS cc_start: 0.7105 (mmtp) cc_final: 0.6674 (mtmm) REVERT: F 226 MET cc_start: 0.6595 (mmt) cc_final: 0.5973 (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: 0.6542 (tt0) REVERT: F 312 TYR cc_start: 0.5321 (OUTLIER) cc_final: 0.3232 (m-80) REVERT: F 313 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.6035 (tt) REVERT: F 338 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6493 (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: 12 residues processed: 497 average time/residue: 1.2367 time to fit residues: 700.1168 Evaluate side-chains 296 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 271 time to evaluate : 2.149 ------------------------------------------------------------------------------- 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 315 ILE 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 155 MET 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 218 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 203 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 123 optimal weight: 0.4980 chunk 151 optimal weight: 7.9990 chunk 235 optimal weight: 7.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN C 279 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 ASN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 399 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.208060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.176342 restraints weight = 27238.436| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 2.68 r_work: 0.3875 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21324 Z= 0.210 Angle : 0.679 10.331 28898 Z= 0.359 Chirality : 0.046 0.225 3238 Planarity : 0.005 0.037 3597 Dihedral : 11.512 176.420 3022 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 5.45 % Allowed : 14.03 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.17), residues: 2580 helix: 0.98 (0.14), residues: 1306 sheet: -0.58 (0.30), residues: 326 loop : -1.52 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 20 HIS 0.007 0.002 HIS F 219 PHE 0.025 0.002 PHE F 417 TYR 0.023 0.002 TYR B 15 ARG 0.007 0.001 ARG C 267 Details of bonding type rmsd hydrogen bonds : bond 0.04264 ( 1054) hydrogen bonds : angle 5.35611 ( 3042) covalent geometry : bond 0.00482 (21324) covalent geometry : angle 0.67939 (28898) *********************** 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 406 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 284 time to evaluate : 2.415 Fit side-chains REVERT: A 19 VAL cc_start: 0.2953 (OUTLIER) cc_final: 0.2540 (m) REVERT: A 23 MET cc_start: 0.3496 (mtp) cc_final: 0.2754 (mmm) REVERT: A 113 ILE cc_start: 0.2254 (OUTLIER) cc_final: 0.1779 (tp) REVERT: A 228 MET cc_start: 0.2047 (tpp) cc_final: 0.1247 (tmm) REVERT: A 241 MET cc_start: 0.4486 (mtm) cc_final: 0.3624 (mtm) REVERT: A 298 LYS cc_start: 0.4342 (tptp) cc_final: 0.3971 (mtpm) REVERT: A 329 TYR cc_start: 0.3847 (m-80) cc_final: 0.3642 (m-80) REVERT: B 70 TYR cc_start: 0.6398 (t80) cc_final: 0.6069 (t80) REVERT: B 138 MET cc_start: 0.3248 (mtt) cc_final: 0.2806 (mmm) REVERT: B 177 ARG cc_start: 0.5064 (mtm110) cc_final: 0.4420 (mmt180) REVERT: B 205 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6540 (tp) REVERT: B 241 MET cc_start: 0.4094 (ptp) cc_final: 0.3547 (mtp) REVERT: B 249 ILE cc_start: 0.6606 (mm) cc_final: 0.6336 (mt) REVERT: B 267 ARG cc_start: 0.6264 (ttp-110) cc_final: 0.5635 (mmt-90) REVERT: B 304 VAL cc_start: 0.7151 (OUTLIER) cc_final: 0.6949 (p) REVERT: B 422 GLN cc_start: 0.6353 (OUTLIER) cc_final: 0.6152 (pt0) REVERT: C 3 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6811 (mt-10) REVERT: C 23 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7501 (mmp) REVERT: C 47 TYR cc_start: 0.5854 (OUTLIER) cc_final: 0.4885 (m-80) REVERT: C 50 VAL cc_start: 0.6530 (t) cc_final: 0.6230 (p) REVERT: C 103 MET cc_start: 0.7444 (tpp) cc_final: 0.6777 (tpp) REVERT: C 235 LYS cc_start: 0.7053 (tttt) cc_final: 0.6680 (ttmt) REVERT: C 290 PHE cc_start: 0.5991 (m-10) cc_final: 0.5752 (m-10) REVERT: C 293 LEU cc_start: 0.4764 (OUTLIER) cc_final: 0.3559 (tt) REVERT: C 294 LEU cc_start: 0.5264 (OUTLIER) cc_final: 0.5064 (tt) REVERT: C 365 ASP cc_start: 0.6772 (p0) cc_final: 0.5728 (t70) REVERT: C 421 VAL cc_start: 0.6597 (m) cc_final: 0.6332 (t) REVERT: D 4 ILE cc_start: 0.7311 (mp) cc_final: 0.7110 (mm) REVERT: D 36 THR cc_start: 0.8069 (t) cc_final: 0.7619 (m) REVERT: D 95 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7586 (mt-10) REVERT: D 177 ARG cc_start: 0.7311 (mtm110) cc_final: 0.6724 (mmm160) REVERT: D 226 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6714 (mmt) REVERT: D 288 ASN cc_start: 0.6611 (m-40) cc_final: 0.6385 (m-40) REVERT: D 295 ASN cc_start: 0.5773 (m110) cc_final: 0.5287 (m-40) REVERT: D 364 SER cc_start: 0.6689 (p) cc_final: 0.6079 (t) REVERT: D 368 MET cc_start: 0.7069 (ttp) cc_final: 0.6845 (ttm) REVERT: E 86 ASP cc_start: 0.7325 (t0) cc_final: 0.7069 (t70) REVERT: E 92 LYS cc_start: 0.7270 (ttmt) cc_final: 0.6526 (mptp) REVERT: E 95 GLU cc_start: 0.7336 (tt0) cc_final: 0.7052 (tt0) REVERT: E 101 ARG cc_start: 0.6619 (mmm-85) cc_final: 0.6231 (tpp-160) REVERT: E 128 MET cc_start: 0.4009 (tmt) cc_final: 0.3729 (tmt) REVERT: E 227 GLU cc_start: 0.4840 (mt-10) cc_final: 0.4609 (mt-10) REVERT: E 323 VAL cc_start: 0.3145 (OUTLIER) cc_final: 0.2800 (t) REVERT: E 397 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5662 (pp20) REVERT: E 419 MET cc_start: 0.7289 (tpt) cc_final: 0.7070 (tpp) REVERT: F 1 MET cc_start: 0.2613 (tmm) cc_final: 0.0383 (mmt) REVERT: F 114 GLN cc_start: 0.4953 (OUTLIER) cc_final: 0.4525 (mt0) REVERT: F 155 MET cc_start: 0.3625 (OUTLIER) cc_final: 0.3349 (tmt) REVERT: F 158 TYR cc_start: 0.6205 (p90) cc_final: 0.5901 (p90) REVERT: F 226 MET cc_start: 0.6491 (mmt) cc_final: 0.6152 (mmt) REVERT: F 368 MET cc_start: 0.6166 (OUTLIER) cc_final: 0.5648 (tmm) outliers start: 122 outliers final: 40 residues processed: 372 average time/residue: 1.2630 time to fit residues: 534.2119 Evaluate side-chains 287 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 232 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL 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 304 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 422 GLN 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 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 226 MET 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 397 GLU 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 138 MET Chi-restraints excluded: chain F residue 155 MET 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 142 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 41 optimal weight: 0.0170 chunk 155 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 120 optimal weight: 0.7980 chunk 7 optimal weight: 0.0010 chunk 165 optimal weight: 4.9990 overall best weight: 0.6626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN B 152 HIS ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN D 100 GLN 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 398 GLN F 288 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.210390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.179090 restraints weight = 27368.874| |-----------------------------------------------------------------------------| r_work (start): 0.4296 rms_B_bonded: 2.76 r_work: 0.3916 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.2328 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= 0.120 Angle : 0.557 9.755 28898 Z= 0.295 Chirality : 0.041 0.189 3238 Planarity : 0.003 0.038 3597 Dihedral : 10.673 175.778 3000 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.20 % Allowed : 16.67 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.17), residues: 2580 helix: 1.28 (0.15), residues: 1305 sheet: -0.54 (0.31), residues: 327 loop : -1.64 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 154 HIS 0.011 0.001 HIS B 152 PHE 0.024 0.001 PHE D 146 TYR 0.022 0.001 TYR B 15 ARG 0.004 0.000 ARG C 267 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 1054) hydrogen bonds : angle 4.95756 ( 3042) covalent geometry : bond 0.00251 (21324) covalent geometry : angle 0.55673 (28898) *********************** 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 349 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 255 time to evaluate : 2.143 Fit side-chains REVERT: A 19 VAL cc_start: 0.2769 (OUTLIER) cc_final: 0.2464 (m) REVERT: A 47 TYR cc_start: 0.3612 (t80) cc_final: 0.2551 (t80) REVERT: A 228 MET cc_start: 0.1813 (tpp) cc_final: 0.0955 (tmm) REVERT: A 241 MET cc_start: 0.4226 (mtm) cc_final: 0.3377 (mtm) REVERT: A 329 TYR cc_start: 0.3811 (m-80) cc_final: 0.3575 (m-80) REVERT: A 431 ILE cc_start: 0.4779 (OUTLIER) cc_final: 0.4307 (pt) REVERT: B 8 HIS cc_start: 0.6832 (m-70) cc_final: 0.6548 (m-70) REVERT: B 13 GLN cc_start: 0.5426 (tm-30) cc_final: 0.5211 (tp-100) REVERT: B 23 MET cc_start: 0.5804 (OUTLIER) cc_final: 0.5564 (tpp) REVERT: B 138 MET cc_start: 0.3211 (mtt) cc_final: 0.2774 (mmm) REVERT: B 177 ARG cc_start: 0.4942 (mtm110) cc_final: 0.4261 (mmt180) REVERT: B 249 ILE cc_start: 0.6518 (mm) cc_final: 0.6261 (mt) REVERT: B 253 HIS cc_start: 0.6379 (OUTLIER) cc_final: 0.6149 (t-90) REVERT: B 264 GLU cc_start: 0.5087 (mt-10) cc_final: 0.4795 (mt-10) REVERT: B 267 ARG cc_start: 0.6235 (ttp-110) cc_final: 0.5570 (mmt-90) REVERT: B 304 VAL cc_start: 0.7073 (OUTLIER) cc_final: 0.6867 (p) REVERT: C 3 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6579 (mt-10) REVERT: C 50 VAL cc_start: 0.6544 (t) cc_final: 0.6244 (p) REVERT: C 85 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.5866 (mp0) REVERT: C 103 MET cc_start: 0.7449 (tpp) cc_final: 0.6855 (tpp) REVERT: C 235 LYS cc_start: 0.7037 (tttt) cc_final: 0.6643 (ttmt) REVERT: C 293 LEU cc_start: 0.4567 (OUTLIER) cc_final: 0.4090 (tm) REVERT: C 312 TYR cc_start: 0.4815 (OUTLIER) cc_final: 0.4130 (t80) REVERT: C 365 ASP cc_start: 0.6777 (p0) cc_final: 0.5713 (t70) REVERT: C 421 VAL cc_start: 0.6585 (m) cc_final: 0.6260 (t) REVERT: D 4 ILE cc_start: 0.7247 (mp) cc_final: 0.7040 (mm) REVERT: D 36 THR cc_start: 0.8016 (t) cc_final: 0.7625 (m) REVERT: D 46 GLU cc_start: 0.7278 (tt0) cc_final: 0.6916 (mm-30) REVERT: D 92 LYS cc_start: 0.7277 (tmmt) cc_final: 0.6785 (mmmt) REVERT: D 95 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7246 (mt-10) REVERT: D 177 ARG cc_start: 0.7186 (mtm110) cc_final: 0.6668 (mmm160) REVERT: D 364 SER cc_start: 0.6613 (p) cc_final: 0.6046 (t) REVERT: E 86 ASP cc_start: 0.7204 (t0) cc_final: 0.6819 (t70) REVERT: E 92 LYS cc_start: 0.7271 (ttmt) cc_final: 0.6527 (mptp) REVERT: E 95 GLU cc_start: 0.7225 (tt0) cc_final: 0.7011 (tt0) REVERT: E 177 ARG cc_start: 0.7372 (mtm110) cc_final: 0.7151 (mtm110) REVERT: E 227 GLU cc_start: 0.4604 (mt-10) cc_final: 0.4315 (mt-10) REVERT: E 311 ASP cc_start: 0.6197 (OUTLIER) cc_final: 0.5925 (m-30) REVERT: E 323 VAL cc_start: 0.3223 (OUTLIER) cc_final: 0.2892 (t) REVERT: F 1 MET cc_start: 0.2651 (tmm) cc_final: 0.0312 (mmt) REVERT: F 114 GLN cc_start: 0.4900 (OUTLIER) cc_final: 0.4501 (mt0) REVERT: F 140 GLN cc_start: 0.5686 (tp40) cc_final: 0.5191 (tm-30) REVERT: F 158 TYR cc_start: 0.6102 (p90) cc_final: 0.5887 (p90) REVERT: F 166 MET cc_start: 0.7038 (mtt) cc_final: 0.6735 (mtm) REVERT: F 226 MET cc_start: 0.6491 (mmt) cc_final: 0.6232 (mmt) REVERT: F 263 MET cc_start: 0.7448 (mmm) cc_final: 0.7177 (mmm) REVERT: F 298 LYS cc_start: 0.7136 (tppp) cc_final: 0.6866 (tppt) REVERT: F 368 MET cc_start: 0.5690 (OUTLIER) cc_final: 0.5389 (tmm) outliers start: 94 outliers final: 28 residues processed: 317 average time/residue: 1.0844 time to fit residues: 399.7741 Evaluate side-chains 273 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 233 time to evaluate : 2.060 ------------------------------------------------------------------------------- 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 431 ILE Chi-restraints excluded: chain B residue 23 MET 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 253 HIS Chi-restraints excluded: chain B residue 304 VAL 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 65 PHE Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 176 LEU 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 312 TYR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain D residue 22 TYR 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 421 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 311 ASP 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 172 VAL 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 109 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 chunk 170 optimal weight: 0.0030 chunk 182 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 150 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 142 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 152 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.211002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.179895 restraints weight = 27661.070| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 2.82 r_work: 0.3928 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21324 Z= 0.113 Angle : 0.547 12.438 28898 Z= 0.288 Chirality : 0.041 0.160 3238 Planarity : 0.003 0.039 3597 Dihedral : 10.326 176.923 2993 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.24 % Allowed : 17.34 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.17), residues: 2580 helix: 1.42 (0.15), residues: 1298 sheet: -0.52 (0.30), residues: 328 loop : -1.68 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 20 HIS 0.010 0.001 HIS B 152 PHE 0.011 0.001 PHE D 417 TYR 0.022 0.001 TYR B 15 ARG 0.003 0.000 ARG C 267 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 1054) hydrogen bonds : angle 4.80821 ( 3042) covalent geometry : bond 0.00236 (21324) covalent geometry : angle 0.54652 (28898) *********************** 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 343 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 248 time to evaluate : 2.167 Fit side-chains REVERT: A 19 VAL cc_start: 0.2989 (OUTLIER) cc_final: 0.2678 (m) REVERT: A 41 LYS cc_start: 0.3933 (OUTLIER) cc_final: 0.3689 (tmtm) REVERT: A 47 TYR cc_start: 0.3603 (t80) cc_final: 0.2556 (t80) REVERT: A 138 MET cc_start: 0.4263 (mpt) cc_final: 0.3823 (mpt) REVERT: A 228 MET cc_start: 0.1827 (tpp) cc_final: 0.1608 (tpp) REVERT: A 241 MET cc_start: 0.4243 (mtm) cc_final: 0.3354 (mtm) REVERT: A 329 TYR cc_start: 0.3892 (m-80) cc_final: 0.3682 (m-80) REVERT: A 431 ILE cc_start: 0.4929 (tp) cc_final: 0.4474 (pt) REVERT: B 8 HIS cc_start: 0.6776 (m-70) cc_final: 0.6398 (m-70) REVERT: B 138 MET cc_start: 0.3103 (mtt) cc_final: 0.2584 (mmm) REVERT: B 177 ARG cc_start: 0.4865 (mtm110) cc_final: 0.4245 (mmp-170) REVERT: B 249 ILE cc_start: 0.6515 (mm) cc_final: 0.6264 (mt) REVERT: B 264 GLU cc_start: 0.4957 (mt-10) cc_final: 0.4686 (mt-10) REVERT: B 267 ARG cc_start: 0.6111 (ttp-110) cc_final: 0.5835 (tpt-90) REVERT: B 425 ASN cc_start: 0.5146 (t0) cc_final: 0.4851 (t0) REVERT: C 3 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6639 (mt-10) REVERT: C 50 VAL cc_start: 0.6561 (t) cc_final: 0.6238 (p) REVERT: C 103 MET cc_start: 0.7342 (tpp) cc_final: 0.6722 (tpp) REVERT: C 235 LYS cc_start: 0.6959 (tttt) cc_final: 0.6575 (ttmt) REVERT: C 293 LEU cc_start: 0.4799 (OUTLIER) cc_final: 0.4446 (tm) REVERT: C 312 TYR cc_start: 0.4694 (OUTLIER) cc_final: 0.4073 (t80) REVERT: C 365 ASP cc_start: 0.6752 (p0) cc_final: 0.5719 (t70) REVERT: C 421 VAL cc_start: 0.6510 (m) cc_final: 0.6205 (t) REVERT: C 425 ASN cc_start: 0.4901 (m110) cc_final: 0.4262 (m-40) REVERT: D 26 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6897 (mt-10) REVERT: D 36 THR cc_start: 0.7975 (t) cc_final: 0.7605 (m) REVERT: D 46 GLU cc_start: 0.7049 (tt0) cc_final: 0.6752 (mm-30) REVERT: D 92 LYS cc_start: 0.7366 (tmmt) cc_final: 0.6925 (mmmt) REVERT: D 95 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7311 (mt-10) REVERT: D 177 ARG cc_start: 0.7223 (mtm110) cc_final: 0.6742 (mmm160) REVERT: D 364 SER cc_start: 0.6658 (p) cc_final: 0.6090 (t) REVERT: E 86 ASP cc_start: 0.7166 (t0) cc_final: 0.6791 (t70) REVERT: E 92 LYS cc_start: 0.7262 (ttmt) cc_final: 0.6550 (mptp) REVERT: E 95 GLU cc_start: 0.7241 (tt0) cc_final: 0.7040 (tt0) REVERT: E 128 MET cc_start: 0.3995 (tmt) cc_final: 0.3757 (ppp) REVERT: E 227 GLU cc_start: 0.4664 (mt-10) cc_final: 0.4420 (mt-10) REVERT: E 311 ASP cc_start: 0.6109 (OUTLIER) cc_final: 0.5906 (m-30) REVERT: E 323 VAL cc_start: 0.3227 (OUTLIER) cc_final: 0.2858 (t) REVERT: E 384 MET cc_start: 0.7688 (mtm) cc_final: 0.7453 (mtm) REVERT: E 419 MET cc_start: 0.7151 (tpt) cc_final: 0.6949 (tpp) REVERT: F 1 MET cc_start: 0.2409 (tmm) cc_final: 0.0199 (mmm) REVERT: F 114 GLN cc_start: 0.4927 (OUTLIER) cc_final: 0.4526 (mt0) REVERT: F 166 MET cc_start: 0.7025 (mtt) cc_final: 0.6721 (mtm) REVERT: F 226 MET cc_start: 0.6467 (mmt) cc_final: 0.6111 (mmt) REVERT: F 263 MET cc_start: 0.7489 (mmm) cc_final: 0.7282 (mmm) REVERT: F 294 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7266 (mt) REVERT: F 298 LYS cc_start: 0.7085 (tppp) cc_final: 0.6824 (tppt) REVERT: F 368 MET cc_start: 0.5663 (OUTLIER) cc_final: 0.5330 (tmm) REVERT: F 384 MET cc_start: 0.7052 (mtm) cc_final: 0.6699 (ttm) outliers start: 95 outliers final: 34 residues processed: 316 average time/residue: 1.1614 time to fit residues: 424.5570 Evaluate side-chains 279 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 235 time to evaluate : 2.259 ------------------------------------------------------------------------------- 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 41 LYS Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 150 VAL 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 98 VAL 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 387 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 137 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 312 TYR 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 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 83 SER Chi-restraints excluded: chain E residue 311 ASP 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 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 294 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 82 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 chunk 171 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 152 HIS B 288 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 = 0.4588 r_free = 0.4588 target = 0.208835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.177401 restraints weight = 27928.661| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 2.72 r_work: 0.3902 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.2774 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= 0.134 Angle : 0.577 15.177 28898 Z= 0.302 Chirality : 0.042 0.155 3238 Planarity : 0.003 0.036 3597 Dihedral : 10.307 177.954 2992 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.75 % Allowed : 18.41 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.17), residues: 2580 helix: 1.30 (0.14), residues: 1306 sheet: -0.52 (0.30), residues: 328 loop : -1.74 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 20 HIS 0.012 0.001 HIS B 152 PHE 0.016 0.002 PHE F 417 TYR 0.022 0.001 TYR B 15 ARG 0.004 0.000 ARG E 177 Details of bonding type rmsd hydrogen bonds : bond 0.03233 ( 1054) hydrogen bonds : angle 4.79850 ( 3042) covalent geometry : bond 0.00296 (21324) covalent geometry : angle 0.57719 (28898) *********************** 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 322 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 238 time to evaluate : 2.158 Fit side-chains revert: symmetry clash REVERT: A 19 VAL cc_start: 0.2996 (OUTLIER) cc_final: 0.2710 (m) REVERT: A 41 LYS cc_start: 0.3897 (OUTLIER) cc_final: 0.3643 (tmtm) REVERT: A 47 TYR cc_start: 0.3618 (t80) cc_final: 0.2651 (t80) REVERT: A 138 MET cc_start: 0.4314 (mpt) cc_final: 0.4002 (mpp) REVERT: A 203 LYS cc_start: 0.4390 (mmtm) cc_final: 0.3166 (mppt) REVERT: A 241 MET cc_start: 0.4238 (mtm) cc_final: 0.3509 (mtm) REVERT: A 431 ILE cc_start: 0.4845 (OUTLIER) cc_final: 0.4403 (pt) REVERT: B 8 HIS cc_start: 0.6728 (m-70) cc_final: 0.6375 (m-70) REVERT: B 15 TYR cc_start: 0.6147 (t80) cc_final: 0.5871 (t80) REVERT: B 138 MET cc_start: 0.3112 (mtt) cc_final: 0.2825 (mmm) REVERT: B 177 ARG cc_start: 0.4852 (mtm110) cc_final: 0.4214 (mmt180) REVERT: B 226 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6229 (mtt) REVERT: B 249 ILE cc_start: 0.6497 (mm) cc_final: 0.6255 (mt) REVERT: B 264 GLU cc_start: 0.5014 (mt-10) cc_final: 0.4763 (mt-10) REVERT: B 267 ARG cc_start: 0.6095 (ttp-110) cc_final: 0.5841 (tpt-90) REVERT: B 384 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.6512 (mtt) REVERT: B 425 ASN cc_start: 0.5456 (t0) cc_final: 0.5082 (t0) REVERT: C 3 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6655 (mt-10) REVERT: C 50 VAL cc_start: 0.6452 (t) cc_final: 0.6128 (p) REVERT: C 103 MET cc_start: 0.7397 (tpp) cc_final: 0.6797 (tpp) REVERT: C 158 TYR cc_start: 0.6139 (p90) cc_final: 0.5924 (p90) REVERT: C 235 LYS cc_start: 0.6818 (tttt) cc_final: 0.6445 (ttmt) REVERT: C 365 ASP cc_start: 0.6686 (p0) cc_final: 0.5669 (t70) REVERT: C 421 VAL cc_start: 0.6558 (m) cc_final: 0.6276 (t) REVERT: C 425 ASN cc_start: 0.4947 (m110) cc_final: 0.4358 (m-40) REVERT: D 26 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6902 (mt-10) REVERT: D 36 THR cc_start: 0.8044 (t) cc_final: 0.7662 (m) REVERT: D 46 GLU cc_start: 0.7088 (tt0) cc_final: 0.6835 (mm-30) REVERT: D 92 LYS cc_start: 0.7343 (tmmt) cc_final: 0.6951 (mmmt) REVERT: D 177 ARG cc_start: 0.7191 (mtm110) cc_final: 0.6706 (mmm160) REVERT: D 364 SER cc_start: 0.6780 (p) cc_final: 0.6188 (t) REVERT: E 86 ASP cc_start: 0.7195 (t0) cc_final: 0.6814 (t70) REVERT: E 92 LYS cc_start: 0.7303 (ttmt) cc_final: 0.6552 (mptp) REVERT: E 95 GLU cc_start: 0.7177 (tt0) cc_final: 0.6891 (tt0) REVERT: E 128 MET cc_start: 0.4056 (tmt) cc_final: 0.3808 (ppp) REVERT: E 227 GLU cc_start: 0.4840 (mt-10) cc_final: 0.4598 (mt-10) REVERT: E 311 ASP cc_start: 0.6179 (OUTLIER) cc_final: 0.5962 (m-30) REVERT: E 323 VAL cc_start: 0.3178 (OUTLIER) cc_final: 0.2807 (t) REVERT: E 384 MET cc_start: 0.7812 (mtm) cc_final: 0.7502 (mtm) REVERT: F 1 MET cc_start: 0.2418 (tmm) cc_final: 0.0252 (mmm) REVERT: F 114 GLN cc_start: 0.4978 (OUTLIER) cc_final: 0.4616 (mt0) REVERT: F 166 MET cc_start: 0.7018 (mtt) cc_final: 0.6705 (mtm) REVERT: F 226 MET cc_start: 0.6551 (mmt) cc_final: 0.6161 (mmt) REVERT: F 263 MET cc_start: 0.7524 (mmm) cc_final: 0.7293 (mmm) REVERT: F 368 MET cc_start: 0.5710 (OUTLIER) cc_final: 0.5321 (tmm) outliers start: 84 outliers final: 39 residues processed: 303 average time/residue: 1.1397 time to fit residues: 402.7393 Evaluate side-chains 277 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 228 time to evaluate : 2.446 ------------------------------------------------------------------------------- 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 41 LYS Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 431 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 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 88 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 255 SER 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 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 83 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 311 ASP 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 172 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 98 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 255 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 169 optimal weight: 0.9980 chunk 249 optimal weight: 5.9990 chunk 209 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 229 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.208065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.176567 restraints weight = 27186.471| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 2.65 r_work: 0.3874 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21324 Z= 0.222 Angle : 0.713 17.220 28898 Z= 0.371 Chirality : 0.047 0.199 3238 Planarity : 0.005 0.047 3597 Dihedral : 10.731 177.540 2990 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.47 % Allowed : 18.36 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.16), residues: 2580 helix: 0.79 (0.14), residues: 1298 sheet: -0.58 (0.31), residues: 315 loop : -1.83 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 154 HIS 0.012 0.002 HIS B 152 PHE 0.028 0.002 PHE F 417 TYR 0.027 0.002 TYR D 22 ARG 0.006 0.001 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 1054) hydrogen bonds : angle 5.20157 ( 3042) covalent geometry : bond 0.00511 (21324) covalent geometry : angle 0.71251 (28898) *********************** 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 327 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 227 time to evaluate : 2.160 Fit side-chains REVERT: A 19 VAL cc_start: 0.3037 (OUTLIER) cc_final: 0.2695 (m) REVERT: A 41 LYS cc_start: 0.3871 (OUTLIER) cc_final: 0.3594 (tmtm) REVERT: A 138 MET cc_start: 0.4423 (mpt) cc_final: 0.3776 (mpp) REVERT: A 228 MET cc_start: 0.2549 (tpp) cc_final: 0.1341 (tmm) REVERT: A 241 MET cc_start: 0.4369 (mtm) cc_final: 0.3550 (mtm) REVERT: A 398 GLN cc_start: 0.2825 (mt0) cc_final: 0.2549 (pt0) REVERT: B 8 HIS cc_start: 0.6792 (m-70) cc_final: 0.6375 (m-70) REVERT: B 138 MET cc_start: 0.3147 (mtt) cc_final: 0.2928 (mmt) REVERT: B 177 ARG cc_start: 0.4819 (mtm110) cc_final: 0.4288 (mmt180) REVERT: B 184 LYS cc_start: 0.6631 (OUTLIER) cc_final: 0.6226 (mttp) REVERT: B 226 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6059 (mtt) REVERT: B 249 ILE cc_start: 0.6601 (mm) cc_final: 0.6368 (mm) REVERT: B 253 HIS cc_start: 0.6545 (OUTLIER) cc_final: 0.6251 (t-90) REVERT: B 264 GLU cc_start: 0.5130 (mt-10) cc_final: 0.4883 (mt-10) REVERT: B 267 ARG cc_start: 0.6197 (ttp-110) cc_final: 0.5521 (mpt90) REVERT: B 384 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.6875 (mtt) REVERT: B 425 ASN cc_start: 0.5346 (t0) cc_final: 0.4960 (t0) REVERT: C 48 HIS cc_start: 0.4809 (m90) cc_final: 0.4397 (m170) REVERT: C 49 SER cc_start: 0.4996 (p) cc_final: 0.4606 (t) REVERT: C 50 VAL cc_start: 0.6598 (t) cc_final: 0.6205 (p) REVERT: C 103 MET cc_start: 0.7538 (tpp) cc_final: 0.6895 (tpp) REVERT: C 235 LYS cc_start: 0.6901 (tttt) cc_final: 0.6570 (ttmt) REVERT: C 365 ASP cc_start: 0.6592 (p0) cc_final: 0.5626 (t70) REVERT: C 421 VAL cc_start: 0.6550 (m) cc_final: 0.6348 (t) REVERT: D 22 TYR cc_start: 0.4773 (m-80) cc_final: 0.4447 (m-80) REVERT: D 26 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6924 (mt-10) REVERT: D 36 THR cc_start: 0.8014 (t) cc_final: 0.7594 (m) REVERT: D 177 ARG cc_start: 0.7191 (mtm110) cc_final: 0.6692 (mmm160) REVERT: D 364 SER cc_start: 0.6875 (p) cc_final: 0.6228 (t) REVERT: E 86 ASP cc_start: 0.7197 (t0) cc_final: 0.6825 (t70) REVERT: E 92 LYS cc_start: 0.7306 (ttmt) cc_final: 0.6504 (mptp) REVERT: E 95 GLU cc_start: 0.7322 (tt0) cc_final: 0.7007 (tt0) REVERT: E 101 ARG cc_start: 0.6543 (mmm-85) cc_final: 0.6189 (tpp-160) REVERT: E 128 MET cc_start: 0.4028 (OUTLIER) cc_final: 0.3777 (ppp) REVERT: E 227 GLU cc_start: 0.4951 (mt-10) cc_final: 0.4742 (mt-10) REVERT: F 1 MET cc_start: 0.2709 (tmm) cc_final: 0.0785 (tpp) REVERT: F 114 GLN cc_start: 0.5144 (OUTLIER) cc_final: 0.4692 (mt0) REVERT: F 166 MET cc_start: 0.7082 (mtt) cc_final: 0.6751 (mtm) REVERT: F 227 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6887 (pt0) REVERT: F 368 MET cc_start: 0.6226 (OUTLIER) cc_final: 0.5690 (tmm) outliers start: 100 outliers final: 44 residues processed: 300 average time/residue: 1.1772 time to fit residues: 406.2294 Evaluate side-chains 264 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 209 time to evaluate : 2.202 ------------------------------------------------------------------------------- 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 68 THR Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 404 ILE 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 367 ASN Chi-restraints excluded: chain B residue 384 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 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 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 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 421 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 128 MET 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 114 GLN Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 227 GLU 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 67 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 192 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 224 optimal weight: 0.7980 chunk 222 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 250 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 177 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN B 13 GLN B 425 ASN C 200 ASN D 200 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.210140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.178926 restraints weight = 27546.638| |-----------------------------------------------------------------------------| r_work (start): 0.4291 rms_B_bonded: 2.46 r_work: 0.3926 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21324 Z= 0.119 Angle : 0.576 16.113 28898 Z= 0.302 Chirality : 0.042 0.210 3238 Planarity : 0.003 0.033 3597 Dihedral : 10.164 170.916 2990 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.53 % Allowed : 19.71 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.17), residues: 2580 helix: 1.16 (0.14), residues: 1302 sheet: -0.61 (0.31), residues: 323 loop : -1.80 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 20 HIS 0.010 0.001 HIS B 152 PHE 0.013 0.001 PHE D 417 TYR 0.014 0.001 TYR D 22 ARG 0.006 0.000 ARG E 177 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 1054) hydrogen bonds : angle 4.83960 ( 3042) covalent geometry : bond 0.00254 (21324) covalent geometry : angle 0.57647 (28898) *********************** 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 317 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 238 time to evaluate : 2.369 Fit side-chains revert: symmetry clash REVERT: A 19 VAL cc_start: 0.2936 (OUTLIER) cc_final: 0.2624 (m) REVERT: A 41 LYS cc_start: 0.3837 (OUTLIER) cc_final: 0.3606 (tmtm) REVERT: A 138 MET cc_start: 0.4222 (mpt) cc_final: 0.3846 (mpp) REVERT: A 228 MET cc_start: 0.2616 (tpp) cc_final: 0.1296 (tmm) REVERT: A 430 GLU cc_start: 0.4131 (OUTLIER) cc_final: 0.3134 (mm-30) REVERT: B 8 HIS cc_start: 0.6777 (m-70) cc_final: 0.6380 (m-70) REVERT: B 15 TYR cc_start: 0.6209 (t80) cc_final: 0.5803 (t80) REVERT: B 23 MET cc_start: 0.5715 (tpp) cc_final: 0.5466 (tpp) REVERT: B 138 MET cc_start: 0.2985 (mtt) cc_final: 0.2754 (mmm) REVERT: B 177 ARG cc_start: 0.4883 (mtm110) cc_final: 0.4307 (mmt180) REVERT: B 226 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6086 (mtt) REVERT: B 249 ILE cc_start: 0.6606 (mm) cc_final: 0.6366 (mm) REVERT: B 264 GLU cc_start: 0.4888 (mt-10) cc_final: 0.4651 (mt-10) REVERT: B 267 ARG cc_start: 0.6063 (ttp-110) cc_final: 0.5380 (mpt90) REVERT: B 384 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.6551 (mtt) REVERT: B 425 ASN cc_start: 0.4936 (OUTLIER) cc_final: 0.4691 (t0) REVERT: C 48 HIS cc_start: 0.4768 (m90) cc_final: 0.4434 (m170) REVERT: C 49 SER cc_start: 0.5026 (p) cc_final: 0.4648 (t) REVERT: C 50 VAL cc_start: 0.6531 (t) cc_final: 0.6130 (p) REVERT: C 103 MET cc_start: 0.7351 (tpp) cc_final: 0.6740 (tpp) REVERT: C 235 LYS cc_start: 0.6858 (tttt) cc_final: 0.6501 (ttmt) REVERT: C 293 LEU cc_start: 0.4960 (OUTLIER) cc_final: 0.4192 (tm) REVERT: C 297 LEU cc_start: 0.4680 (OUTLIER) cc_final: 0.3963 (tp) REVERT: C 365 ASP cc_start: 0.6678 (p0) cc_final: 0.5680 (t70) REVERT: C 421 VAL cc_start: 0.6574 (OUTLIER) cc_final: 0.6300 (t) REVERT: D 26 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6861 (mt-10) REVERT: D 36 THR cc_start: 0.7960 (t) cc_final: 0.7550 (m) REVERT: D 46 GLU cc_start: 0.7165 (tt0) cc_final: 0.6850 (mm-30) REVERT: D 177 ARG cc_start: 0.7108 (mtm110) cc_final: 0.6643 (mmm160) REVERT: D 364 SER cc_start: 0.6824 (p) cc_final: 0.6149 (t) REVERT: D 368 MET cc_start: 0.6925 (ttt) cc_final: 0.6296 (tpp) REVERT: E 86 ASP cc_start: 0.7114 (t0) cc_final: 0.6789 (t70) REVERT: E 92 LYS cc_start: 0.7267 (ttmt) cc_final: 0.6502 (mptp) REVERT: E 95 GLU cc_start: 0.7233 (tt0) cc_final: 0.6900 (tt0) REVERT: E 128 MET cc_start: 0.4003 (OUTLIER) cc_final: 0.3752 (ppp) REVERT: E 323 VAL cc_start: 0.3204 (OUTLIER) cc_final: 0.2845 (t) REVERT: F 1 MET cc_start: 0.2597 (tmm) cc_final: 0.0759 (tpp) REVERT: F 114 GLN cc_start: 0.5096 (OUTLIER) cc_final: 0.4668 (mt0) REVERT: F 227 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6655 (pt0) REVERT: F 298 LYS cc_start: 0.7015 (tppp) cc_final: 0.6755 (tppt) REVERT: F 368 MET cc_start: 0.5944 (OUTLIER) cc_final: 0.5507 (tmm) outliers start: 79 outliers final: 29 residues processed: 293 average time/residue: 1.1514 time to fit residues: 389.2302 Evaluate side-chains 271 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 227 time to evaluate : 2.124 ------------------------------------------------------------------------------- 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 68 THR Chi-restraints excluded: chain A residue 150 VAL 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 205 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 350 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 B residue 384 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 137 ILE 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 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 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 128 MET 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 F residue 114 GLN Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 316 CYS Chi-restraints excluded: chain F residue 368 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 173 optimal weight: 5.9990 chunk 238 optimal weight: 0.9980 chunk 243 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 208 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 234 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 425 ASN C 200 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.209687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.177972 restraints weight = 27412.524| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 2.67 r_work: 0.3904 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21324 Z= 0.170 Angle : 0.634 16.179 28898 Z= 0.331 Chirality : 0.044 0.164 3238 Planarity : 0.004 0.036 3597 Dihedral : 10.324 174.696 2990 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.71 % Allowed : 19.75 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.17), residues: 2580 helix: 1.03 (0.14), residues: 1302 sheet: -0.54 (0.31), residues: 317 loop : -1.85 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 89 HIS 0.009 0.001 HIS B 152 PHE 0.021 0.002 PHE E 146 TYR 0.026 0.002 TYR D 22 ARG 0.004 0.000 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 1054) hydrogen bonds : angle 4.92744 ( 3042) covalent geometry : bond 0.00386 (21324) covalent geometry : angle 0.63436 (28898) *********************** 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 300 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 217 time to evaluate : 2.207 Fit side-chains revert: symmetry clash REVERT: A 19 VAL cc_start: 0.2993 (OUTLIER) cc_final: 0.2654 (m) REVERT: A 41 LYS cc_start: 0.3881 (OUTLIER) cc_final: 0.3629 (tmtm) REVERT: A 89 TRP cc_start: 0.4843 (t60) cc_final: 0.4115 (t60) REVERT: A 114 GLN cc_start: 0.2413 (mt0) cc_final: 0.1693 (tp40) REVERT: A 138 MET cc_start: 0.4284 (mpt) cc_final: 0.3957 (mpp) REVERT: A 228 MET cc_start: 0.2236 (tpp) cc_final: 0.1041 (tmm) REVERT: A 430 GLU cc_start: 0.4149 (OUTLIER) cc_final: 0.3127 (mm-30) REVERT: B 8 HIS cc_start: 0.6775 (m-70) cc_final: 0.6357 (m-70) REVERT: B 23 MET cc_start: 0.5661 (tpp) cc_final: 0.5371 (tpp) REVERT: B 155 MET cc_start: 0.6526 (tpp) cc_final: 0.4403 (mpp) REVERT: B 177 ARG cc_start: 0.4832 (mtm110) cc_final: 0.4314 (mmt180) REVERT: B 184 LYS cc_start: 0.6625 (OUTLIER) cc_final: 0.6201 (mttp) REVERT: B 226 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6059 (mtt) REVERT: B 249 ILE cc_start: 0.6698 (mm) cc_final: 0.6467 (mm) REVERT: B 264 GLU cc_start: 0.4982 (mt-10) cc_final: 0.4771 (mt-10) REVERT: B 267 ARG cc_start: 0.6065 (ttp-110) cc_final: 0.5334 (mpt90) REVERT: B 384 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.6821 (mtt) REVERT: C 48 HIS cc_start: 0.4830 (m90) cc_final: 0.4452 (m170) REVERT: C 49 SER cc_start: 0.5031 (p) cc_final: 0.4655 (t) REVERT: C 50 VAL cc_start: 0.6535 (t) cc_final: 0.6141 (p) REVERT: C 103 MET cc_start: 0.7541 (tpp) cc_final: 0.6906 (tpp) REVERT: C 235 LYS cc_start: 0.6902 (tttt) cc_final: 0.6559 (ttmt) REVERT: C 293 LEU cc_start: 0.5079 (OUTLIER) cc_final: 0.4135 (tm) REVERT: C 297 LEU cc_start: 0.4683 (OUTLIER) cc_final: 0.3951 (tp) REVERT: C 365 ASP cc_start: 0.6637 (p0) cc_final: 0.5642 (t70) REVERT: C 421 VAL cc_start: 0.6653 (OUTLIER) cc_final: 0.6386 (t) REVERT: D 26 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6891 (mt-10) REVERT: D 36 THR cc_start: 0.8007 (t) cc_final: 0.7611 (m) REVERT: D 46 GLU cc_start: 0.7262 (tt0) cc_final: 0.6893 (mm-30) REVERT: D 177 ARG cc_start: 0.7157 (mtm110) cc_final: 0.6665 (mmm160) REVERT: E 70 TYR cc_start: 0.3756 (OUTLIER) cc_final: 0.2917 (t80) REVERT: E 86 ASP cc_start: 0.7130 (t0) cc_final: 0.6795 (t70) REVERT: E 92 LYS cc_start: 0.7319 (ttmt) cc_final: 0.6529 (mptp) REVERT: E 95 GLU cc_start: 0.7266 (tt0) cc_final: 0.6906 (tt0) REVERT: E 101 ARG cc_start: 0.6569 (mmm-85) cc_final: 0.6223 (tpp-160) REVERT: E 128 MET cc_start: 0.4020 (OUTLIER) cc_final: 0.3762 (ppp) REVERT: F 1 MET cc_start: 0.2722 (tmm) cc_final: 0.0769 (tpp) REVERT: F 114 GLN cc_start: 0.5181 (OUTLIER) cc_final: 0.4718 (mt0) REVERT: F 166 MET cc_start: 0.7117 (mtt) cc_final: 0.6766 (mtm) REVERT: F 368 MET cc_start: 0.6042 (OUTLIER) cc_final: 0.5510 (tmm) outliers start: 83 outliers final: 37 residues processed: 278 average time/residue: 1.1697 time to fit residues: 376.1746 Evaluate side-chains 262 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 211 time to evaluate : 2.168 ------------------------------------------------------------------------------- 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 68 THR Chi-restraints excluded: chain A residue 150 VAL 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 60 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 137 ILE 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 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 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 70 TYR Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 128 MET 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 13 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 240 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 80 optimal weight: 0.0970 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS A 398 GLN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN C 200 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.209490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.176858 restraints weight = 27376.122| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 2.67 r_work: 0.3907 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21324 Z= 0.177 Angle : 0.653 16.868 28898 Z= 0.341 Chirality : 0.044 0.196 3238 Planarity : 0.004 0.037 3597 Dihedral : 10.342 161.213 2990 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.75 % Allowed : 19.66 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.17), residues: 2580 helix: 0.93 (0.14), residues: 1301 sheet: -0.64 (0.31), residues: 317 loop : -1.87 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 89 HIS 0.009 0.001 HIS B 152 PHE 0.032 0.002 PHE B 16 TYR 0.029 0.002 TYR D 22 ARG 0.004 0.001 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 1054) hydrogen bonds : angle 4.99267 ( 3042) covalent geometry : bond 0.00405 (21324) covalent geometry : angle 0.65306 (28898) *********************** 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 299 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 215 time to evaluate : 2.384 Fit side-chains revert: symmetry clash REVERT: A 19 VAL cc_start: 0.2996 (OUTLIER) cc_final: 0.2631 (m) REVERT: A 41 LYS cc_start: 0.3824 (OUTLIER) cc_final: 0.3558 (tmtm) REVERT: A 89 TRP cc_start: 0.4616 (t60) cc_final: 0.3904 (t60) REVERT: A 114 GLN cc_start: 0.2413 (mt0) cc_final: 0.1687 (tp40) REVERT: A 138 MET cc_start: 0.4292 (mpt) cc_final: 0.4031 (mpp) REVERT: A 228 MET cc_start: 0.2091 (tpp) cc_final: 0.1008 (tmm) REVERT: A 430 GLU cc_start: 0.4220 (OUTLIER) cc_final: 0.3201 (mm-30) REVERT: B 8 HIS cc_start: 0.6756 (m-70) cc_final: 0.6310 (m-70) REVERT: B 15 TYR cc_start: 0.6180 (t80) cc_final: 0.5850 (t80) REVERT: B 23 MET cc_start: 0.5606 (tpp) cc_final: 0.5368 (tpp) REVERT: B 155 MET cc_start: 0.6498 (tpp) cc_final: 0.4434 (mpp) REVERT: B 177 ARG cc_start: 0.4721 (mtm110) cc_final: 0.4301 (mmt180) REVERT: B 184 LYS cc_start: 0.6607 (OUTLIER) cc_final: 0.6195 (mttp) REVERT: B 226 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6043 (mtt) REVERT: B 249 ILE cc_start: 0.6789 (mm) cc_final: 0.6543 (mm) REVERT: B 267 ARG cc_start: 0.6045 (ttp-110) cc_final: 0.5340 (mpt90) REVERT: B 384 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.6873 (mtt) REVERT: C 1 MET cc_start: 0.7469 (ptm) cc_final: 0.7105 (ttt) REVERT: C 48 HIS cc_start: 0.4731 (m90) cc_final: 0.4379 (m170) REVERT: C 49 SER cc_start: 0.4928 (p) cc_final: 0.4588 (t) REVERT: C 50 VAL cc_start: 0.6577 (t) cc_final: 0.6202 (p) REVERT: C 103 MET cc_start: 0.7493 (tpp) cc_final: 0.6880 (tpp) REVERT: C 235 LYS cc_start: 0.6803 (tttt) cc_final: 0.6476 (ttmt) REVERT: C 293 LEU cc_start: 0.5132 (OUTLIER) cc_final: 0.4392 (tm) REVERT: C 297 LEU cc_start: 0.4603 (OUTLIER) cc_final: 0.3930 (tp) REVERT: C 365 ASP cc_start: 0.6627 (p0) cc_final: 0.5652 (t70) REVERT: C 421 VAL cc_start: 0.6650 (OUTLIER) cc_final: 0.6380 (t) REVERT: D 22 TYR cc_start: 0.4661 (m-80) cc_final: 0.4448 (m-80) REVERT: D 26 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6867 (mt-10) REVERT: D 36 THR cc_start: 0.8006 (t) cc_final: 0.7599 (m) REVERT: D 46 GLU cc_start: 0.7275 (tt0) cc_final: 0.6916 (mm-30) REVERT: D 177 ARG cc_start: 0.7117 (mtm110) cc_final: 0.6637 (mmm160) REVERT: D 299 LEU cc_start: 0.6890 (pp) cc_final: 0.6623 (pp) REVERT: E 70 TYR cc_start: 0.3761 (OUTLIER) cc_final: 0.2891 (t80) REVERT: E 86 ASP cc_start: 0.7142 (t0) cc_final: 0.6801 (t70) REVERT: E 92 LYS cc_start: 0.7306 (ttmt) cc_final: 0.6558 (mptp) REVERT: E 95 GLU cc_start: 0.7298 (tt0) cc_final: 0.6978 (tt0) REVERT: E 101 ARG cc_start: 0.6584 (mmm-85) cc_final: 0.6233 (tpp-160) REVERT: E 128 MET cc_start: 0.4069 (OUTLIER) cc_final: 0.3815 (ppp) REVERT: F 1 MET cc_start: 0.2483 (tmm) cc_final: 0.2248 (ptm) REVERT: F 114 GLN cc_start: 0.5251 (OUTLIER) cc_final: 0.4748 (mt0) REVERT: F 166 MET cc_start: 0.7109 (mtt) cc_final: 0.6783 (mtm) REVERT: F 368 MET cc_start: 0.6068 (OUTLIER) cc_final: 0.5552 (tmm) outliers start: 84 outliers final: 43 residues processed: 272 average time/residue: 1.1802 time to fit residues: 369.4536 Evaluate side-chains 264 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 207 time to evaluate : 2.131 ------------------------------------------------------------------------------- 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 68 THR Chi-restraints excluded: chain A residue 150 VAL 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 60 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 137 ILE 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 348 THR 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 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 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 58 VAL Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 128 MET 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 137 ILE Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 196 MET 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 401 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 66 optimal weight: 0.9990 chunk 235 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 186 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN C 200 ASN C 355 GLN D 200 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.209437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.177722 restraints weight = 27364.468| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 2.64 r_work: 0.3911 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.3733 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= 0.177 Angle : 0.661 17.015 28898 Z= 0.345 Chirality : 0.044 0.196 3238 Planarity : 0.004 0.039 3597 Dihedral : 10.323 153.694 2990 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.08 % Allowed : 20.73 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.17), residues: 2580 helix: 0.91 (0.14), residues: 1301 sheet: -0.71 (0.31), residues: 318 loop : -1.88 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 89 HIS 0.009 0.001 HIS B 152 PHE 0.027 0.002 PHE B 16 TYR 0.033 0.002 TYR A 97 ARG 0.004 0.001 ARG C 236 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 1054) hydrogen bonds : angle 5.02468 ( 3042) covalent geometry : bond 0.00405 (21324) covalent geometry : angle 0.66076 (28898) ********************** 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 283 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 214 time to evaluate : 2.344 Fit side-chains revert: symmetry clash REVERT: A 19 VAL cc_start: 0.3122 (OUTLIER) cc_final: 0.2746 (m) REVERT: A 41 LYS cc_start: 0.3824 (OUTLIER) cc_final: 0.3537 (tmtm) REVERT: A 89 TRP cc_start: 0.4859 (t60) cc_final: 0.4058 (t60) REVERT: A 114 GLN cc_start: 0.2407 (mt0) cc_final: 0.1680 (tp40) REVERT: A 138 MET cc_start: 0.4281 (mpt) cc_final: 0.4033 (mpp) REVERT: A 228 MET cc_start: 0.2210 (tpp) cc_final: 0.1167 (tmm) REVERT: A 430 GLU cc_start: 0.4225 (OUTLIER) cc_final: 0.3154 (mm-30) REVERT: B 8 HIS cc_start: 0.6727 (m-70) cc_final: 0.6290 (m-70) REVERT: B 15 TYR cc_start: 0.6259 (t80) cc_final: 0.5809 (t80) REVERT: B 23 MET cc_start: 0.5616 (tpp) cc_final: 0.5360 (tpp) REVERT: B 177 ARG cc_start: 0.4659 (mtm110) cc_final: 0.4267 (mmt180) REVERT: B 184 LYS cc_start: 0.6574 (OUTLIER) cc_final: 0.6150 (mttp) REVERT: B 226 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6037 (mtt) REVERT: B 249 ILE cc_start: 0.6880 (mm) cc_final: 0.6658 (mm) REVERT: B 384 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.6827 (mtt) REVERT: C 1 MET cc_start: 0.7429 (ptm) cc_final: 0.7109 (ttt) REVERT: C 48 HIS cc_start: 0.4867 (m90) cc_final: 0.4489 (m170) REVERT: C 49 SER cc_start: 0.4940 (p) cc_final: 0.4592 (t) REVERT: C 50 VAL cc_start: 0.6595 (t) cc_final: 0.6213 (p) REVERT: C 103 MET cc_start: 0.7486 (tpp) cc_final: 0.6863 (tpp) REVERT: C 235 LYS cc_start: 0.6809 (tttt) cc_final: 0.6474 (ttmt) REVERT: C 293 LEU cc_start: 0.5186 (OUTLIER) cc_final: 0.4444 (tm) REVERT: C 297 LEU cc_start: 0.4453 (OUTLIER) cc_final: 0.3903 (tp) REVERT: C 365 ASP cc_start: 0.6515 (p0) cc_final: 0.5547 (t70) REVERT: C 421 VAL cc_start: 0.6652 (OUTLIER) cc_final: 0.6384 (t) REVERT: D 22 TYR cc_start: 0.4653 (m-80) cc_final: 0.4437 (m-10) REVERT: D 26 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6878 (mt-10) REVERT: D 36 THR cc_start: 0.7991 (t) cc_final: 0.7585 (m) REVERT: D 46 GLU cc_start: 0.7313 (tt0) cc_final: 0.6982 (mm-30) REVERT: D 177 ARG cc_start: 0.7087 (mtm110) cc_final: 0.6634 (mmm160) REVERT: D 299 LEU cc_start: 0.6968 (pp) cc_final: 0.6698 (pp) REVERT: E 70 TYR cc_start: 0.3701 (OUTLIER) cc_final: 0.2841 (t80) REVERT: E 86 ASP cc_start: 0.7159 (t0) cc_final: 0.6820 (t70) REVERT: E 92 LYS cc_start: 0.7323 (ttmt) cc_final: 0.6565 (mptp) REVERT: E 95 GLU cc_start: 0.7270 (tt0) cc_final: 0.6952 (tt0) REVERT: E 101 ARG cc_start: 0.6590 (mmm-85) cc_final: 0.6238 (tpp-160) REVERT: E 128 MET cc_start: 0.4073 (OUTLIER) cc_final: 0.3812 (ppp) REVERT: F 114 GLN cc_start: 0.5335 (OUTLIER) cc_final: 0.4799 (mt0) REVERT: F 166 MET cc_start: 0.7083 (mtt) cc_final: 0.6762 (mtm) REVERT: F 368 MET cc_start: 0.6085 (OUTLIER) cc_final: 0.5582 (tmm) outliers start: 69 outliers final: 44 residues processed: 262 average time/residue: 1.2099 time to fit residues: 364.8011 Evaluate side-chains 269 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 211 time to evaluate : 2.426 ------------------------------------------------------------------------------- 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 68 THR Chi-restraints excluded: chain A residue 150 VAL 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 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 88 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 276 ILE 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 355 GLN 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 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 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 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 103 MET Chi-restraints excluded: chain E residue 128 MET 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 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 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 401 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 188 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 189 optimal weight: 0.9980 chunk 236 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 242 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN C 200 ASN D 200 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.209548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.178649 restraints weight = 27390.458| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 2.61 r_work: 0.3903 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.153 21324 Z= 0.190 Angle : 0.808 59.200 28898 Z= 0.447 Chirality : 0.043 0.184 3238 Planarity : 0.004 0.039 3597 Dihedral : 10.316 153.466 2990 Min Nonbonded Distance : 1.592 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.04 % Allowed : 21.00 % Favored : 75.96 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.17), residues: 2580 helix: 0.92 (0.14), residues: 1300 sheet: -0.71 (0.31), residues: 318 loop : -1.88 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 89 HIS 0.008 0.001 HIS B 152 PHE 0.019 0.002 PHE F 417 TYR 0.028 0.002 TYR A 97 ARG 0.028 0.001 ARG B 267 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 1054) hydrogen bonds : angle 5.02884 ( 3042) covalent geometry : bond 0.00419 (21324) covalent geometry : angle 0.80776 (28898) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13476.39 seconds wall clock time: 230 minutes 50.48 seconds (13850.48 seconds total)