Starting phenix.real_space_refine on Sun Sep 29 21:39:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvi_27739/09_2024/8dvi_27739.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvi_27739/09_2024/8dvi_27739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvi_27739/09_2024/8dvi_27739.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvi_27739/09_2024/8dvi_27739.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvi_27739/09_2024/8dvi_27739.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvi_27739/09_2024/8dvi_27739.cif" } resolution = 3.2 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= 0.004 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 32 5.49 5 Mg 5 5.21 5 S 132 5.16 5 C 14995 2.51 5 N 3943 2.21 5 O 4586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23693 Number of models: 1 Model: "" Number of chains: 14 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: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "H" Number of atoms: 2644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2644 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain breaks: 1 Chain: "T" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} 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: 14.08, per 1000 atoms: 0.59 Number of scatterers: 23693 At special positions: 0 Unit cell: (134.136, 130.824, 142.416, 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 132 16.00 P 32 15.00 Mg 5 11.99 O 4586 8.00 N 3943 7.00 C 14995 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: 5.43 Conformation dependent library (CDL) restraints added in 2.6 seconds 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5530 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 20 sheets defined 53.8% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 24 through 28 Processing helix chain 'A' and resid 31 through 47 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 66 through 79 Processing helix chain 'A' and resid 86 through 118 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 Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 176 through 183 Processing helix chain 'A' and resid 202 through 217 removed outlier: 4.527A pdb=" N GLY A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.709A 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: 3.520A pdb=" N ILE A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 269 removed outlier: 3.550A pdb=" N LYS A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 301 Processing helix chain 'A' and resid 328 through 347 Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 390 through 396 Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 12 through 20 Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 24 through 28 removed outlier: 3.542A pdb=" N TYR B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE B 28 " --> pdb=" O SER B 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 24 through 28' Processing helix chain 'B' and resid 31 through 48 Processing helix chain 'B' and resid 52 through 58 Processing helix chain 'B' and resid 66 through 80 Processing helix chain 'B' and resid 88 through 119 removed outlier: 3.529A pdb=" N LEU B 119 " --> pdb=" O THR B 115 " (cutoff:3.500A) 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 removed outlier: 3.512A pdb=" N ILE B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 217 Processing helix chain 'B' and resid 229 through 243 removed outlier: 3.568A pdb=" N ASP B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 Processing helix chain 'B' and resid 255 through 269 removed outlier: 3.842A 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: 3.589A pdb=" N THR B 331 " --> pdb=" O ASN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 391 through 396 removed outlier: 3.628A pdb=" N ALA B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 13 through 20 Processing helix chain 'C' and resid 24 through 28 removed outlier: 3.769A pdb=" N PHE C 28 " --> pdb=" O SER C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 52 through 63 Processing helix chain 'C' and resid 66 through 77 removed outlier: 4.001A pdb=" N GLY C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 119 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 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 203 through 217 Processing helix chain 'C' and resid 229 through 242 Processing helix chain 'C' and resid 245 through 252 Processing helix chain 'C' and resid 255 through 268 Processing helix chain 'C' and resid 286 through 301 Processing helix chain 'C' and resid 312 through 316 removed outlier: 3.640A pdb=" N ILE C 315 " --> pdb=" O TYR C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 347 Processing helix chain 'C' and resid 357 through 361 removed outlier: 3.653A pdb=" N TRP C 361 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 375 through 381 removed outlier: 3.957A pdb=" N ALA C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 395 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 12 through 20 removed outlier: 3.607A pdb=" N LYS D 18 " --> pdb=" O ALA D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.502A pdb=" N TYR D 27 " --> pdb=" O ASP D 24 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE D 28 " --> pdb=" O SER D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 28' Processing helix chain 'D' and resid 31 through 48 removed outlier: 3.671A pdb=" N PHE D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) 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 118 Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 143 removed outlier: 3.936A pdb=" N ILE D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'D' and resid 245 through 252 Processing helix chain 'D' and resid 255 through 268 Processing helix chain 'D' and resid 286 through 301 Processing helix chain 'D' and resid 312 through 316 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 380 removed outlier: 4.004A 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 12 through 20 removed outlier: 3.594A pdb=" N LYS E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 28 removed outlier: 3.560A pdb=" N PHE E 28 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 47 Processing helix chain 'E' and resid 52 through 63 Processing helix chain 'E' and resid 66 through 79 Processing helix chain 'E' and resid 86 through 118 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 141 removed outlier: 3.534A pdb=" N ALA E 141 " --> pdb=" O ILE E 137 " (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 246 through 251 removed outlier: 3.587A pdb=" N ASP E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 269 Processing helix chain 'E' and resid 286 through 301 Processing helix chain 'E' and resid 327 through 347 removed outlier: 3.842A pdb=" N LYS E 333 " --> pdb=" O TYR E 329 " (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 20 Processing helix chain 'F' and resid 21 through 23 No H-bonds generated for 'chain 'F' and resid 21 through 23' Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 31 through 48 removed outlier: 3.760A pdb=" N ASN F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 62 Processing helix chain 'F' and resid 66 through 80 Processing helix chain 'F' and resid 88 through 118 removed outlier: 3.903A pdb=" N LYS F 92 " --> pdb=" O SER F 88 " (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 142 removed outlier: 3.660A pdb=" N LEU F 142 " --> pdb=" O MET F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 167 Processing helix chain 'F' and resid 176 through 184 Processing helix chain 'F' and resid 202 through 216 Processing helix chain 'F' and resid 229 through 243 Processing helix chain 'F' and resid 245 through 252 Processing helix chain 'F' and resid 255 through 269 removed outlier: 3.706A pdb=" N LYS F 269 " --> pdb=" O LYS F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 302 Processing helix chain 'F' and resid 327 through 347 Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'H' and resid 4 through 18 removed outlier: 3.547A pdb=" N ASP H 8 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG H 14 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS H 18 " --> pdb=" O ARG H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 82 Processing helix chain 'H' and resid 82 through 96 removed outlier: 3.858A pdb=" N GLU H 88 " --> pdb=" O ASP H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 143 Processing helix chain 'H' and resid 146 through 152 removed outlier: 4.001A pdb=" N LYS H 151 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 167 Processing helix chain 'H' and resid 221 through 225 Processing helix chain 'H' and resid 237 through 242 removed outlier: 3.606A pdb=" N PHE H 241 " --> pdb=" O ASP H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 274 through 287 Processing helix chain 'H' and resid 303 through 312 removed outlier: 3.606A pdb=" N GLY H 312 " --> pdb=" O ILE H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 325 removed outlier: 3.738A pdb=" N ILE H 318 " --> pdb=" O THR H 314 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS H 323 " --> pdb=" O MET H 319 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN H 324 " --> pdb=" O GLU H 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153 removed outlier: 6.565A pdb=" N VAL B 221 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LYS B 278 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR B 223 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B 222 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA B 353 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 383 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS B 405 " --> pdb=" O MET B 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 427 through 429 removed outlier: 6.511A pdb=" N MET A 384 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU A 192 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N LEU A 385 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 194 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL A 387 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N MET A 196 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR A 191 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N THR A 352 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASN A 193 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ALA A 354 " --> pdb=" O ASN A 193 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU A 195 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA A 353 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU A 222 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A 221 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LYS A 278 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TYR A 223 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 152 through 153 removed outlier: 6.614A pdb=" N VAL C 221 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LYS C 278 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR C 223 " --> pdb=" O LYS C 278 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASN C 220 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE C 309 " --> pdb=" O ASN C 220 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU C 222 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA C 353 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 383 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N MET C 384 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 172 Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 422 Processing sheet with id=AA7, first strand: chain 'C' and resid 152 through 153 removed outlier: 6.510A pdb=" N VAL D 221 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LYS D 278 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR D 223 " --> pdb=" O LYS D 278 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE D 309 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU D 222 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 171 through 172 Processing sheet with id=AA9, first strand: chain 'C' and resid 398 through 399 Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 153 removed outlier: 3.876A pdb=" N ALA E 353 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA E 354 " --> pdb=" O LEU E 195 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU E 192 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU E 385 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL E 194 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL E 387 " --> pdb=" O VAL E 194 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N MET E 196 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N MET E 384 " --> pdb=" O ILE E 404 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 171 through 172 Processing sheet with id=AB3, first strand: chain 'D' and resid 349 through 354 removed outlier: 6.037A pdb=" N THR D 191 " --> pdb=" O LEU D 350 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR D 352 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASN D 193 " --> pdb=" O THR D 352 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ALA D 354 " --> pdb=" O ASN D 193 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEU D 195 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU D 192 " --> pdb=" O PHE D 383 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N LEU D 385 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL D 194 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL D 387 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N MET D 196 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N MET D 384 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 171 through 172 Processing sheet with id=AB5, first strand: chain 'F' and resid 349 through 352 removed outlier: 3.708A pdb=" N PHE F 383 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 275 through 279 removed outlier: 6.325A pdb=" N LEU F 222 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 419 through 422 Processing sheet with id=AB8, first strand: chain 'H' and resid 23 through 26 Processing sheet with id=AB9, first strand: chain 'H' and resid 124 through 126 removed outlier: 3.753A pdb=" N SER H 193 " --> pdb=" O ILE H 184 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 219 through 220 removed outlier: 3.536A pdb=" N ILE H 248 " --> pdb=" O LEU H 233 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL H 230 " --> pdb=" O VAL H 265 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 290 through 292 removed outlier: 3.508A pdb=" N ALA H 327 " --> pdb=" O VAL H 291 " (cutoff:3.500A) 1158 hydrogen bonds defined for protein. 3303 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: 7.13 Time building geometry restraints manager: 6.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 7549 1.35 - 1.50: 6411 1.50 - 1.65: 10008 1.65 - 1.80: 105 1.80 - 1.95: 124 Bond restraints: 24197 Sorted by residual: bond pdb=" CE1 HIS D 87 " pdb=" NE2 HIS D 87 " ideal model delta sigma weight residual 1.321 1.359 -0.038 1.00e-02 1.00e+04 1.48e+01 bond pdb=" CE1 HIS B 152 " pdb=" NE2 HIS B 152 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.24e+01 bond pdb=" N VAL E 19 " pdb=" CA VAL E 19 " ideal model delta sigma weight residual 1.452 1.492 -0.039 1.18e-02 7.18e+03 1.12e+01 bond pdb=" N TRP D 20 " pdb=" CA TRP D 20 " ideal model delta sigma weight residual 1.462 1.492 -0.030 9.50e-03 1.11e+04 9.92e+00 bond pdb=" N TRP E 20 " pdb=" CA TRP E 20 " ideal model delta sigma weight residual 1.459 1.492 -0.032 1.04e-02 9.25e+03 9.69e+00 ... (remaining 24192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 32329 2.49 - 4.98: 442 4.98 - 7.48: 28 7.48 - 9.97: 7 9.97 - 12.46: 1 Bond angle restraints: 32807 Sorted by residual: angle pdb=" PB AGS C 501 " pdb=" O3B AGS C 501 " pdb=" PG AGS C 501 " ideal model delta sigma weight residual 120.12 132.58 -12.46 3.00e+00 1.11e-01 1.73e+01 angle pdb=" N ASP A 82 " pdb=" CA ASP A 82 " pdb=" C ASP A 82 " ideal model delta sigma weight residual 112.57 108.05 4.52 1.13e+00 7.83e-01 1.60e+01 angle pdb=" N GLU H 92 " pdb=" CA GLU H 92 " pdb=" C GLU H 92 " ideal model delta sigma weight residual 111.71 107.18 4.53 1.15e+00 7.56e-01 1.55e+01 angle pdb=" CA PHE D 383 " pdb=" CB PHE D 383 " pdb=" CG PHE D 383 " ideal model delta sigma weight residual 113.80 117.73 -3.93 1.00e+00 1.00e+00 1.55e+01 angle pdb=" C GLY F 151 " pdb=" N HIS F 152 " pdb=" CA HIS F 152 " ideal model delta sigma weight residual 122.30 117.07 5.23 1.35e+00 5.49e-01 1.50e+01 ... (remaining 32802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 14414 35.65 - 71.31: 202 71.31 - 106.96: 10 106.96 - 142.62: 1 142.62 - 178.27: 4 Dihedral angle restraints: 14631 sinusoidal: 6069 harmonic: 8562 Sorted by residual: dihedral pdb=" O1B AGS E 501 " pdb=" O3B AGS E 501 " pdb=" PB AGS E 501 " pdb=" PG AGS E 501 " ideal model delta sinusoidal sigma weight residual 68.91 -112.82 -178.27 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A AGS F 501 " pdb=" O3A AGS F 501 " pdb=" PA AGS F 501 " pdb=" PB AGS F 501 " ideal model delta sinusoidal sigma weight residual -67.73 106.43 -174.16 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1B AGS B 501 " pdb=" O3B AGS B 501 " pdb=" PB AGS B 501 " pdb=" PG AGS B 501 " ideal model delta sinusoidal sigma weight residual 68.91 -88.62 157.53 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 14628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2650 0.044 - 0.088: 645 0.088 - 0.132: 288 0.132 - 0.176: 48 0.176 - 0.220: 16 Chirality restraints: 3647 Sorted by residual: chirality pdb=" CA ILE H 93 " pdb=" N ILE H 93 " pdb=" C ILE H 93 " pdb=" CB ILE H 93 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA VAL A 150 " pdb=" N VAL A 150 " pdb=" C VAL A 150 " pdb=" CB VAL A 150 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ARG A 124 " pdb=" N ARG A 124 " pdb=" C ARG A 124 " pdb=" CB ARG A 124 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 3644 not shown) Planarity restraints: 4071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 266 " 0.018 2.00e-02 2.50e+03 2.32e-02 1.35e+01 pdb=" CG TRP H 266 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP H 266 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP H 266 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 266 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP H 266 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP H 266 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 266 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 266 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP H 266 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 373 " -0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLU A 373 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU A 373 " -0.021 2.00e-02 2.50e+03 pdb=" N SER A 374 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 145 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C SER B 145 " 0.039 2.00e-02 2.50e+03 pdb=" O SER B 145 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE B 146 " -0.013 2.00e-02 2.50e+03 ... (remaining 4068 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 113 2.47 - 3.07: 16357 3.07 - 3.68: 36394 3.68 - 4.29: 55354 4.29 - 4.90: 90583 Nonbonded interactions: 198801 Sorted by model distance: nonbonded pdb=" O1B AGS C 501 " pdb="MG MG C 502 " model vdw 1.856 2.170 nonbonded pdb=" O3B AGS B 501 " pdb="MG MG B 502 " model vdw 1.972 2.170 nonbonded pdb=" OE2 GLU B 227 " pdb="MG MG B 502 " model vdw 1.979 2.170 nonbonded pdb=" O2G AGS E 501 " pdb="MG MG E 502 " model vdw 1.985 2.170 nonbonded pdb=" O2B AGS F 501 " pdb="MG MG F 502 " model vdw 1.993 2.170 ... (remaining 198796 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: 1.660 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: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 48.580 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 : 0.004 0.051 24197 Z= 0.295 Angle : 0.682 12.461 32807 Z= 0.446 Chirality : 0.049 0.220 3647 Planarity : 0.004 0.075 4071 Dihedral : 12.486 178.275 9101 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.78 % Allowed : 7.25 % Favored : 90.96 % 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: 0.23 (0.16), residues: 2898 helix: 1.29 (0.14), residues: 1435 sheet: -0.35 (0.27), residues: 407 loop : -1.20 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP H 266 HIS 0.008 0.001 HIS B 152 PHE 0.022 0.002 PHE D 383 TYR 0.014 0.001 TYR E 329 ARG 0.004 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 722 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7054 (m) cc_final: 0.6730 (t) REVERT: A 327 ASN cc_start: 0.3766 (OUTLIER) cc_final: 0.3367 (p0) REVERT: A 347 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7665 (mm-30) REVERT: A 368 MET cc_start: 0.6148 (OUTLIER) cc_final: 0.5816 (ttm) REVERT: A 369 SER cc_start: 0.5907 (m) cc_final: 0.5494 (p) REVERT: B 48 HIS cc_start: 0.7610 (m90) cc_final: 0.7105 (m90) REVERT: B 96 LYS cc_start: 0.8324 (mtpp) cc_final: 0.8100 (mtpp) REVERT: B 267 ARG cc_start: 0.7854 (ttp-170) cc_final: 0.7587 (ttp-170) REVERT: B 422 GLN cc_start: 0.6749 (mt0) cc_final: 0.6413 (mm-40) REVERT: C 128 MET cc_start: 0.5747 (tpp) cc_final: 0.5430 (mmt) REVERT: C 323 VAL cc_start: 0.7577 (t) cc_final: 0.7043 (t) REVERT: D 26 GLU cc_start: 0.7746 (mp0) cc_final: 0.7447 (mm-30) REVERT: D 265 LYS cc_start: 0.7855 (ttmm) cc_final: 0.7465 (tmmt) REVERT: E 109 LYS cc_start: 0.7506 (tptt) cc_final: 0.7221 (ttmt) REVERT: E 338 GLU cc_start: 0.6474 (mt-10) cc_final: 0.6216 (mp0) REVERT: E 380 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.7935 (p) REVERT: F 128 MET cc_start: 0.6055 (ttt) cc_final: 0.5835 (ttm) REVERT: F 156 ASP cc_start: 0.7667 (t0) cc_final: 0.7429 (t0) REVERT: F 167 ASN cc_start: 0.6020 (OUTLIER) cc_final: 0.4854 (m-40) REVERT: F 213 ASP cc_start: 0.7586 (m-30) cc_final: 0.7311 (m-30) REVERT: F 276 ILE cc_start: 0.8836 (mt) cc_final: 0.8628 (tt) REVERT: F 345 GLU cc_start: 0.7727 (tt0) cc_final: 0.7486 (tt0) REVERT: F 355 GLN cc_start: 0.6770 (tt0) cc_final: 0.6483 (pm20) REVERT: F 399 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.6921 (tp40) REVERT: F 423 LYS cc_start: 0.8029 (mttm) cc_final: 0.7779 (mttp) REVERT: H 161 LYS cc_start: 0.4172 (tmmt) cc_final: 0.3865 (mttt) REVERT: H 283 LYS cc_start: 0.7693 (tttt) cc_final: 0.7449 (mtmt) REVERT: H 294 TRP cc_start: 0.7286 (m100) cc_final: 0.7085 (m100) REVERT: H 305 ASN cc_start: 0.6222 (t0) cc_final: 0.5935 (t0) REVERT: H 307 MET cc_start: 0.6672 (mtt) cc_final: 0.6405 (mtt) outliers start: 45 outliers final: 4 residues processed: 750 average time/residue: 0.4100 time to fit residues: 448.8129 Evaluate side-chains 381 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 372 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 138 optimal weight: 0.9990 chunk 169 optimal weight: 0.0970 chunk 264 optimal weight: 20.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN A 140 GLN A 167 ASN A 288 ASN A 327 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS C 114 GLN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN C 288 ASN C 295 ASN D 48 HIS D 116 ASN D 200 ASN E 114 GLN F 8 HIS F 62 ASN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN H 325 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24197 Z= 0.184 Angle : 0.553 8.028 32807 Z= 0.301 Chirality : 0.042 0.240 3647 Planarity : 0.004 0.050 4071 Dihedral : 10.802 174.222 3415 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.78 % Allowed : 11.06 % Favored : 87.16 % 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 (0.16), residues: 2898 helix: 1.48 (0.14), residues: 1456 sheet: -0.30 (0.27), residues: 406 loop : -1.15 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 266 HIS 0.014 0.001 HIS B 253 PHE 0.014 0.002 PHE A 417 TYR 0.019 0.001 TYR H 213 ARG 0.007 0.001 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 401 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.6200 (pp20) cc_final: 0.5999 (pp20) REVERT: A 263 MET cc_start: 0.7120 (mmm) cc_final: 0.6853 (mmm) REVERT: A 302 ASN cc_start: 0.7399 (p0) cc_final: 0.6692 (m-40) REVERT: A 345 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7236 (mt-10) REVERT: A 369 SER cc_start: 0.6098 (m) cc_final: 0.5731 (p) REVERT: B 48 HIS cc_start: 0.7637 (m90) cc_final: 0.7323 (m90) REVERT: B 317 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7327 (pttm) REVERT: B 333 LYS cc_start: 0.7701 (ttpp) cc_final: 0.7358 (ttmt) REVERT: B 422 GLN cc_start: 0.6876 (mt0) cc_final: 0.6324 (mm-40) REVERT: C 13 GLN cc_start: 0.7765 (tp40) cc_final: 0.7275 (tp-100) REVERT: C 69 GLU cc_start: 0.7022 (pt0) cc_final: 0.6455 (mm-30) REVERT: C 128 MET cc_start: 0.5914 (tpp) cc_final: 0.5501 (mmt) REVERT: C 158 TYR cc_start: 0.6823 (p90) cc_final: 0.6490 (p90) REVERT: D 247 ASP cc_start: 0.7712 (m-30) cc_final: 0.7193 (t70) REVERT: E 306 THR cc_start: 0.8265 (m) cc_final: 0.7871 (t) REVERT: E 338 GLU cc_start: 0.6597 (mt-10) cc_final: 0.6210 (mp0) REVERT: E 419 MET cc_start: 0.8569 (tpt) cc_final: 0.8322 (tpt) REVERT: F 167 ASN cc_start: 0.6033 (OUTLIER) cc_final: 0.5091 (m-40) REVERT: F 213 ASP cc_start: 0.7526 (m-30) cc_final: 0.7232 (m-30) REVERT: F 226 MET cc_start: 0.8311 (mmm) cc_final: 0.7549 (mmt) REVERT: F 227 GLU cc_start: 0.6920 (pt0) cc_final: 0.6588 (tt0) REVERT: F 276 ILE cc_start: 0.8834 (mt) cc_final: 0.8633 (tt) REVERT: F 355 GLN cc_start: 0.7051 (tt0) cc_final: 0.6728 (pm20) REVERT: F 399 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7024 (tp40) REVERT: H 161 LYS cc_start: 0.3945 (tmmt) cc_final: 0.3623 (mmtt) REVERT: H 260 PHE cc_start: 0.6804 (m-80) cc_final: 0.5800 (m-10) REVERT: H 263 ARG cc_start: 0.5579 (ptt180) cc_final: 0.5198 (mtm110) REVERT: H 292 MET cc_start: 0.6030 (tpp) cc_final: 0.5121 (tpt) REVERT: H 328 GLN cc_start: 0.6832 (pt0) cc_final: 0.6565 (pt0) outliers start: 45 outliers final: 19 residues processed: 434 average time/residue: 0.3769 time to fit residues: 247.4554 Evaluate side-chains 332 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 310 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 219 optimal weight: 0.8980 chunk 179 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 264 optimal weight: 0.0170 chunk 285 optimal weight: 9.9990 chunk 235 optimal weight: 7.9990 chunk 262 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 overall best weight: 3.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 125 ASN A 140 GLN A 403 GLN A 422 GLN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN D 13 GLN D 48 HIS ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 24197 Z= 0.298 Angle : 0.618 12.059 32807 Z= 0.329 Chirality : 0.045 0.279 3647 Planarity : 0.004 0.054 4071 Dihedral : 10.987 178.465 3407 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.13 % Allowed : 12.41 % Favored : 84.46 % 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: 0.37 (0.16), residues: 2898 helix: 1.38 (0.14), residues: 1451 sheet: -0.19 (0.27), residues: 399 loop : -1.17 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 162 HIS 0.007 0.001 HIS B 8 PHE 0.017 0.002 PHE H 81 TYR 0.016 0.002 TYR H 86 ARG 0.006 0.001 ARG E 274 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 347 time to evaluate : 2.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.6056 (pp20) cc_final: 0.5733 (pp20) REVERT: A 275 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8562 (tp) REVERT: A 279 GLN cc_start: 0.7532 (tm-30) cc_final: 0.7297 (tp40) REVERT: A 330 THR cc_start: 0.7633 (m) cc_final: 0.7408 (t) REVERT: A 368 MET cc_start: 0.5931 (OUTLIER) cc_final: 0.5685 (ttp) REVERT: B 48 HIS cc_start: 0.7707 (m90) cc_final: 0.7360 (m90) REVERT: B 248 ASP cc_start: 0.7593 (m-30) cc_final: 0.7384 (m-30) REVERT: B 333 LYS cc_start: 0.7847 (ttpp) cc_final: 0.7341 (ttpt) REVERT: B 422 GLN cc_start: 0.7096 (mt0) cc_final: 0.6658 (mm-40) REVERT: C 69 GLU cc_start: 0.7160 (pt0) cc_final: 0.6446 (mm-30) REVERT: C 128 MET cc_start: 0.5670 (tpp) cc_final: 0.5288 (mmt) REVERT: D 247 ASP cc_start: 0.7710 (m-30) cc_final: 0.7199 (t70) REVERT: E 24 ASP cc_start: 0.6520 (m-30) cc_final: 0.6304 (m-30) REVERT: E 100 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7934 (tm-30) REVERT: E 338 GLU cc_start: 0.6677 (mt-10) cc_final: 0.6087 (mp0) REVERT: F 131 VAL cc_start: 0.8275 (OUTLIER) cc_final: 0.8006 (p) REVERT: F 226 MET cc_start: 0.8361 (mmm) cc_final: 0.7601 (mmt) REVERT: H 34 ARG cc_start: 0.3437 (ttt180) cc_final: 0.3040 (ttm170) REVERT: H 88 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.6101 (mm-30) REVERT: H 271 GLU cc_start: 0.7291 (mt-10) cc_final: 0.7085 (mt-10) REVERT: H 273 ARG cc_start: 0.7011 (mtp85) cc_final: 0.6762 (mtt-85) REVERT: H 292 MET cc_start: 0.6781 (tpp) cc_final: 0.6243 (tpt) outliers start: 79 outliers final: 53 residues processed: 408 average time/residue: 0.3648 time to fit residues: 228.7732 Evaluate side-chains 360 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 303 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 359 GLN Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 0.8980 chunk 199 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 126 optimal weight: 0.9990 chunk 177 optimal weight: 20.0000 chunk 265 optimal weight: 3.9990 chunk 281 optimal weight: 20.0000 chunk 138 optimal weight: 1.9990 chunk 251 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 GLN C 35 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN D 48 HIS D 200 ASN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24197 Z= 0.258 Angle : 0.576 9.820 32807 Z= 0.308 Chirality : 0.044 0.290 3647 Planarity : 0.004 0.036 4071 Dihedral : 10.949 175.996 3407 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.66 % Allowed : 14.39 % Favored : 82.96 % 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: 0.41 (0.16), residues: 2898 helix: 1.44 (0.14), residues: 1449 sheet: -0.22 (0.27), residues: 390 loop : -1.17 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 162 HIS 0.006 0.001 HIS B 8 PHE 0.022 0.002 PHE C 104 TYR 0.027 0.002 TYR D 329 ARG 0.008 0.001 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 330 time to evaluate : 2.857 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.6120 (pp20) cc_final: 0.5777 (pp20) REVERT: A 263 MET cc_start: 0.7248 (mmm) cc_final: 0.6957 (mmm) REVERT: A 368 MET cc_start: 0.5957 (OUTLIER) cc_final: 0.5700 (ttp) REVERT: B 48 HIS cc_start: 0.7747 (m90) cc_final: 0.7428 (m90) REVERT: B 312 TYR cc_start: 0.6928 (t80) cc_final: 0.6603 (t80) REVERT: B 333 LYS cc_start: 0.7917 (ttpp) cc_final: 0.7320 (ttpt) REVERT: B 422 GLN cc_start: 0.7084 (mt0) cc_final: 0.6726 (mm-40) REVERT: C 69 GLU cc_start: 0.7144 (pt0) cc_final: 0.6493 (mm-30) REVERT: C 128 MET cc_start: 0.5708 (tpp) cc_final: 0.5415 (mmt) REVERT: C 188 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8067 (mt-10) REVERT: D 247 ASP cc_start: 0.7745 (m-30) cc_final: 0.7254 (t70) REVERT: E 23 MET cc_start: 0.8370 (mmt) cc_final: 0.8159 (mmt) REVERT: E 48 HIS cc_start: 0.5694 (m90) cc_final: 0.5217 (m170) REVERT: E 338 GLU cc_start: 0.6650 (mt-10) cc_final: 0.5976 (mp0) REVERT: E 377 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8023 (mp) REVERT: F 226 MET cc_start: 0.8440 (mmm) cc_final: 0.7774 (mmt) REVERT: F 367 ASN cc_start: 0.6676 (p0) cc_final: 0.6102 (m-40) REVERT: H 34 ARG cc_start: 0.3398 (ttt180) cc_final: 0.3011 (ttm170) REVERT: H 88 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.6089 (mm-30) REVERT: H 271 GLU cc_start: 0.7214 (mt-10) cc_final: 0.7007 (mt-10) REVERT: H 292 MET cc_start: 0.6925 (tpp) cc_final: 0.6430 (tpt) outliers start: 67 outliers final: 49 residues processed: 380 average time/residue: 0.3594 time to fit residues: 210.8989 Evaluate side-chains 350 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 298 time to evaluate : 3.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 240 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 0.0000 chunk 252 optimal weight: 0.0370 chunk 70 optimal weight: 1.9990 overall best weight: 1.6068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN D 200 ASN F 125 ASN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24197 Z= 0.182 Angle : 0.530 9.639 32807 Z= 0.284 Chirality : 0.042 0.244 3647 Planarity : 0.003 0.037 4071 Dihedral : 10.814 176.165 3405 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.81 % Allowed : 14.35 % Favored : 82.84 % 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: 0.54 (0.16), residues: 2898 helix: 1.57 (0.14), residues: 1450 sheet: -0.12 (0.27), residues: 379 loop : -1.15 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 20 HIS 0.005 0.001 HIS B 8 PHE 0.018 0.001 PHE C 104 TYR 0.022 0.001 TYR D 329 ARG 0.003 0.000 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 318 time to evaluate : 2.763 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.6163 (pp20) cc_final: 0.5844 (pp20) REVERT: A 163 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8184 (tp) REVERT: A 263 MET cc_start: 0.7354 (mmm) cc_final: 0.6997 (mmm) REVERT: A 368 MET cc_start: 0.5970 (OUTLIER) cc_final: 0.5715 (ttp) REVERT: B 48 HIS cc_start: 0.7792 (m90) cc_final: 0.7522 (m90) REVERT: B 312 TYR cc_start: 0.6995 (t80) cc_final: 0.6623 (t80) REVERT: B 333 LYS cc_start: 0.7889 (ttpp) cc_final: 0.7298 (ttpt) REVERT: B 422 GLN cc_start: 0.7025 (mt0) cc_final: 0.6811 (mm-40) REVERT: C 69 GLU cc_start: 0.7099 (pt0) cc_final: 0.6495 (mm-30) REVERT: C 128 MET cc_start: 0.5672 (tpp) cc_final: 0.5245 (mmt) REVERT: C 188 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8053 (mt-10) REVERT: D 247 ASP cc_start: 0.7765 (m-30) cc_final: 0.7304 (t70) REVERT: E 77 ILE cc_start: 0.7814 (pt) cc_final: 0.7066 (mt) REVERT: E 269 LYS cc_start: 0.8280 (mttm) cc_final: 0.7928 (mtpt) REVERT: E 306 THR cc_start: 0.8335 (m) cc_final: 0.7889 (t) REVERT: E 338 GLU cc_start: 0.6632 (mt-10) cc_final: 0.5927 (mp0) REVERT: E 377 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7980 (mp) REVERT: F 367 ASN cc_start: 0.6703 (p0) cc_final: 0.6191 (m-40) REVERT: H 34 ARG cc_start: 0.3367 (ttt180) cc_final: 0.2995 (ttm170) REVERT: H 88 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.6080 (mm-30) REVERT: H 271 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6734 (mt-10) REVERT: H 292 MET cc_start: 0.6907 (tpp) cc_final: 0.6435 (tpt) outliers start: 71 outliers final: 52 residues processed: 372 average time/residue: 0.3626 time to fit residues: 207.8973 Evaluate side-chains 357 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 301 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 359 GLN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 9.9990 chunk 253 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 69 optimal weight: 0.0010 chunk 281 optimal weight: 10.0000 chunk 233 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN ** D 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24197 Z= 0.224 Angle : 0.548 9.987 32807 Z= 0.293 Chirality : 0.042 0.256 3647 Planarity : 0.004 0.039 4071 Dihedral : 10.868 176.026 3405 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.09 % Allowed : 14.51 % Favored : 82.40 % 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: 0.51 (0.16), residues: 2898 helix: 1.56 (0.14), residues: 1449 sheet: -0.12 (0.28), residues: 377 loop : -1.18 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 162 HIS 0.005 0.001 HIS B 8 PHE 0.020 0.002 PHE C 104 TYR 0.029 0.001 TYR D 312 ARG 0.004 0.000 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 319 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 TYR cc_start: 0.7486 (t80) cc_final: 0.7199 (t80) REVERT: A 263 MET cc_start: 0.7341 (mmm) cc_final: 0.6977 (mmm) REVERT: A 368 MET cc_start: 0.5975 (OUTLIER) cc_final: 0.5645 (ttp) REVERT: B 29 GLU cc_start: 0.5447 (mm-30) cc_final: 0.5222 (mm-30) REVERT: B 48 HIS cc_start: 0.7783 (m90) cc_final: 0.7515 (m90) REVERT: B 248 ASP cc_start: 0.7891 (m-30) cc_final: 0.7646 (m-30) REVERT: B 312 TYR cc_start: 0.7004 (t80) cc_final: 0.6547 (t80) REVERT: B 333 LYS cc_start: 0.7905 (ttpp) cc_final: 0.7305 (ttpt) REVERT: B 422 GLN cc_start: 0.7050 (mt0) cc_final: 0.6826 (mm-40) REVERT: C 69 GLU cc_start: 0.7081 (pt0) cc_final: 0.6477 (mm-30) REVERT: C 128 MET cc_start: 0.5648 (tpp) cc_final: 0.5210 (mmt) REVERT: C 188 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8071 (mt-10) REVERT: D 247 ASP cc_start: 0.7778 (m-30) cc_final: 0.7312 (t70) REVERT: E 77 ILE cc_start: 0.7851 (pt) cc_final: 0.7174 (mt) REVERT: E 124 ARG cc_start: 0.4824 (ptp-170) cc_final: 0.4509 (mtm110) REVERT: E 269 LYS cc_start: 0.8313 (mttm) cc_final: 0.7963 (mtpt) REVERT: E 338 GLU cc_start: 0.6642 (mt-10) cc_final: 0.5920 (mp0) REVERT: E 377 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7992 (mp) REVERT: F 367 ASN cc_start: 0.6633 (p0) cc_final: 0.6185 (m-40) REVERT: H 34 ARG cc_start: 0.3338 (ttt180) cc_final: 0.2958 (ttm170) REVERT: H 88 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.6089 (mm-30) REVERT: H 292 MET cc_start: 0.7029 (tpp) cc_final: 0.6529 (tpt) outliers start: 78 outliers final: 65 residues processed: 380 average time/residue: 0.3621 time to fit residues: 211.9750 Evaluate side-chains 362 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 294 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 359 GLN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 237 optimal weight: 10.0000 chunk 157 optimal weight: 0.6980 chunk 280 optimal weight: 8.9990 chunk 175 optimal weight: 9.9990 chunk 170 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 125 ASN B 87 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN D 200 ASN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24197 Z= 0.228 Angle : 0.552 9.444 32807 Z= 0.295 Chirality : 0.042 0.208 3647 Planarity : 0.004 0.041 4071 Dihedral : 10.910 176.247 3405 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.97 % Allowed : 14.70 % Favored : 82.32 % 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: 0.50 (0.16), residues: 2898 helix: 1.54 (0.14), residues: 1450 sheet: -0.14 (0.27), residues: 383 loop : -1.18 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 162 HIS 0.005 0.001 HIS B 8 PHE 0.022 0.002 PHE C 104 TYR 0.033 0.001 TYR D 312 ARG 0.007 0.000 ARG H 263 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 315 time to evaluate : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.7421 (mmm) cc_final: 0.7055 (mmm) REVERT: A 368 MET cc_start: 0.5944 (OUTLIER) cc_final: 0.5667 (ttp) REVERT: B 48 HIS cc_start: 0.7772 (m90) cc_final: 0.7504 (m90) REVERT: B 248 ASP cc_start: 0.7955 (m-30) cc_final: 0.7659 (m-30) REVERT: B 312 TYR cc_start: 0.7031 (t80) cc_final: 0.6548 (t80) REVERT: B 333 LYS cc_start: 0.7900 (ttpp) cc_final: 0.7277 (ttpt) REVERT: B 422 GLN cc_start: 0.7140 (mt0) cc_final: 0.6827 (mm110) REVERT: C 69 GLU cc_start: 0.7124 (pt0) cc_final: 0.6508 (mm-30) REVERT: C 128 MET cc_start: 0.5641 (tpp) cc_final: 0.5200 (mmt) REVERT: C 188 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8046 (mt-10) REVERT: D 247 ASP cc_start: 0.7722 (m-30) cc_final: 0.7225 (t70) REVERT: E 77 ILE cc_start: 0.7878 (pt) cc_final: 0.7185 (mt) REVERT: E 124 ARG cc_start: 0.4942 (ptp-170) cc_final: 0.4629 (mtm110) REVERT: E 128 MET cc_start: 0.7292 (mmm) cc_final: 0.7057 (mtp) REVERT: E 138 MET cc_start: 0.8451 (mmm) cc_final: 0.8243 (mmm) REVERT: E 269 LYS cc_start: 0.8326 (mttm) cc_final: 0.7881 (mmtm) REVERT: E 338 GLU cc_start: 0.6654 (mt-10) cc_final: 0.5864 (mp0) REVERT: E 377 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7985 (mp) REVERT: F 274 ARG cc_start: 0.7830 (mtp85) cc_final: 0.7606 (mtp-110) REVERT: F 367 ASN cc_start: 0.6678 (p0) cc_final: 0.6261 (m-40) REVERT: H 34 ARG cc_start: 0.3285 (ttt180) cc_final: 0.2947 (ttm170) REVERT: H 49 LYS cc_start: 0.1008 (mttt) cc_final: 0.0753 (ptpt) REVERT: H 88 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.6026 (mm-30) REVERT: H 292 MET cc_start: 0.7104 (tpp) cc_final: 0.6645 (tpp) outliers start: 75 outliers final: 60 residues processed: 375 average time/residue: 0.3663 time to fit residues: 209.5512 Evaluate side-chains 350 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 287 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 359 GLN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 7.9990 chunk 112 optimal weight: 0.0770 chunk 167 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 55 optimal weight: 0.0050 chunk 54 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 191 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 220 optimal weight: 0.6980 overall best weight: 1.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24197 Z= 0.170 Angle : 0.526 9.225 32807 Z= 0.281 Chirality : 0.041 0.209 3647 Planarity : 0.003 0.041 4071 Dihedral : 10.805 175.791 3405 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.22 % Allowed : 15.10 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.62 (0.16), residues: 2898 helix: 1.67 (0.14), residues: 1453 sheet: -0.12 (0.27), residues: 390 loop : -1.17 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 89 HIS 0.005 0.001 HIS B 8 PHE 0.023 0.001 PHE C 104 TYR 0.025 0.001 TYR D 329 ARG 0.003 0.000 ARG F 274 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 308 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8137 (tp) REVERT: A 259 TYR cc_start: 0.7470 (t80) cc_final: 0.6924 (t80) REVERT: A 263 MET cc_start: 0.7407 (mmm) cc_final: 0.7047 (mmm) REVERT: A 368 MET cc_start: 0.5933 (OUTLIER) cc_final: 0.5655 (ttp) REVERT: B 48 HIS cc_start: 0.7757 (m90) cc_final: 0.7515 (m90) REVERT: B 158 TYR cc_start: 0.7903 (p90) cc_final: 0.7370 (p90) REVERT: B 248 ASP cc_start: 0.7941 (m-30) cc_final: 0.7559 (m-30) REVERT: B 312 TYR cc_start: 0.7026 (t80) cc_final: 0.6604 (t80) REVERT: B 333 LYS cc_start: 0.7885 (ttpp) cc_final: 0.7259 (ttpt) REVERT: B 422 GLN cc_start: 0.7076 (mt0) cc_final: 0.6799 (mm110) REVERT: C 38 LYS cc_start: 0.7624 (mtmt) cc_final: 0.7312 (ptpt) REVERT: C 69 GLU cc_start: 0.7096 (pt0) cc_final: 0.6517 (mm-30) REVERT: C 128 MET cc_start: 0.5492 (tpp) cc_final: 0.5194 (mmt) REVERT: C 188 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8041 (mt-10) REVERT: D 247 ASP cc_start: 0.7671 (m-30) cc_final: 0.7223 (t70) REVERT: D 298 LYS cc_start: 0.7334 (ttpt) cc_final: 0.6548 (ptmt) REVERT: E 77 ILE cc_start: 0.7873 (pt) cc_final: 0.7163 (mt) REVERT: E 124 ARG cc_start: 0.4937 (ptp-170) cc_final: 0.4637 (mtm110) REVERT: E 128 MET cc_start: 0.7158 (mmm) cc_final: 0.6939 (mtp) REVERT: E 269 LYS cc_start: 0.8282 (mttm) cc_final: 0.7856 (mmtm) REVERT: E 338 GLU cc_start: 0.6701 (mt-10) cc_final: 0.5896 (mp0) REVERT: F 367 ASN cc_start: 0.6671 (p0) cc_final: 0.6255 (m-40) REVERT: H 34 ARG cc_start: 0.3586 (ttt180) cc_final: 0.3235 (ttm170) REVERT: H 49 LYS cc_start: 0.1129 (mttt) cc_final: 0.0786 (ptmt) REVERT: H 197 ARG cc_start: 0.3459 (tpt170) cc_final: 0.2983 (tpt90) REVERT: H 292 MET cc_start: 0.7100 (tpp) cc_final: 0.6613 (tpt) outliers start: 56 outliers final: 41 residues processed: 351 average time/residue: 0.3749 time to fit residues: 202.7331 Evaluate side-chains 326 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 283 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 9.9990 chunk 268 optimal weight: 9.9990 chunk 245 optimal weight: 5.9990 chunk 261 optimal weight: 0.8980 chunk 157 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 chunk 205 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 236 optimal weight: 7.9990 chunk 247 optimal weight: 2.9990 chunk 260 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS B 200 ASN B 253 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24197 Z= 0.285 Angle : 0.604 9.025 32807 Z= 0.320 Chirality : 0.043 0.172 3647 Planarity : 0.004 0.042 4071 Dihedral : 11.017 175.926 3405 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.58 % Allowed : 14.86 % Favored : 82.56 % 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: 0.38 (0.16), residues: 2898 helix: 1.45 (0.14), residues: 1448 sheet: -0.28 (0.27), residues: 391 loop : -1.21 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 162 HIS 0.008 0.001 HIS B 253 PHE 0.024 0.002 PHE C 104 TYR 0.037 0.002 TYR D 312 ARG 0.004 0.001 ARG H 263 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 289 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 TYR cc_start: 0.7538 (t80) cc_final: 0.6960 (t80) REVERT: A 263 MET cc_start: 0.7429 (mmm) cc_final: 0.7060 (mmm) REVERT: A 368 MET cc_start: 0.5968 (OUTLIER) cc_final: 0.5701 (ttp) REVERT: B 158 TYR cc_start: 0.7990 (p90) cc_final: 0.7316 (p90) REVERT: B 312 TYR cc_start: 0.7054 (t80) cc_final: 0.6597 (t80) REVERT: B 422 GLN cc_start: 0.7133 (mt0) cc_final: 0.6869 (mm-40) REVERT: C 38 LYS cc_start: 0.7650 (mtmt) cc_final: 0.7251 (ptpt) REVERT: C 69 GLU cc_start: 0.7059 (pt0) cc_final: 0.6460 (mm-30) REVERT: C 128 MET cc_start: 0.5628 (tpp) cc_final: 0.5157 (mmt) REVERT: C 188 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7970 (mt-10) REVERT: D 247 ASP cc_start: 0.7617 (m-30) cc_final: 0.7125 (t70) REVERT: D 293 LEU cc_start: 0.7636 (tp) cc_final: 0.7418 (tp) REVERT: D 298 LYS cc_start: 0.7341 (ttpt) cc_final: 0.6552 (ptmt) REVERT: E 77 ILE cc_start: 0.7886 (pt) cc_final: 0.7209 (mt) REVERT: E 269 LYS cc_start: 0.8312 (mttm) cc_final: 0.7853 (mmtm) REVERT: F 367 ASN cc_start: 0.6606 (p0) cc_final: 0.6391 (m-40) REVERT: H 49 LYS cc_start: 0.1322 (mttt) cc_final: 0.0990 (ptpt) REVERT: H 88 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.6093 (mm-30) REVERT: H 197 ARG cc_start: 0.3475 (tpt170) cc_final: 0.3024 (tpt90) REVERT: H 292 MET cc_start: 0.7204 (tpp) cc_final: 0.6742 (tpp) outliers start: 65 outliers final: 57 residues processed: 340 average time/residue: 0.3462 time to fit residues: 182.5374 Evaluate side-chains 334 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 275 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 359 GLN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 2.9990 chunk 276 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 289 optimal weight: 9.9990 chunk 266 optimal weight: 3.9990 chunk 230 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 178 optimal weight: 8.9990 chunk 141 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS B 253 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 324 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24197 Z= 0.273 Angle : 0.603 10.230 32807 Z= 0.318 Chirality : 0.043 0.184 3647 Planarity : 0.004 0.042 4071 Dihedral : 11.034 175.964 3405 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.62 % Allowed : 15.10 % Favored : 82.28 % 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: 0.33 (0.16), residues: 2898 helix: 1.42 (0.14), residues: 1447 sheet: -0.29 (0.27), residues: 390 loop : -1.26 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 162 HIS 0.022 0.001 HIS B 253 PHE 0.024 0.002 PHE C 104 TYR 0.037 0.002 TYR D 312 ARG 0.003 0.001 ARG H 263 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 280 time to evaluate : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 TYR cc_start: 0.7542 (t80) cc_final: 0.6988 (t80) REVERT: A 263 MET cc_start: 0.7430 (mmm) cc_final: 0.7052 (mmm) REVERT: A 368 MET cc_start: 0.5966 (OUTLIER) cc_final: 0.5701 (ttp) REVERT: B 158 TYR cc_start: 0.7984 (p90) cc_final: 0.7370 (p90) REVERT: B 248 ASP cc_start: 0.8119 (m-30) cc_final: 0.7782 (m-30) REVERT: B 312 TYR cc_start: 0.7017 (t80) cc_final: 0.6618 (t80) REVERT: B 333 LYS cc_start: 0.7905 (ttpp) cc_final: 0.7297 (ttpt) REVERT: B 422 GLN cc_start: 0.7142 (mt0) cc_final: 0.6925 (mm-40) REVERT: C 38 LYS cc_start: 0.7656 (mtmt) cc_final: 0.7256 (ptpt) REVERT: C 69 GLU cc_start: 0.7068 (pt0) cc_final: 0.6480 (mm-30) REVERT: C 128 MET cc_start: 0.5606 (tpp) cc_final: 0.5279 (mmt) REVERT: C 188 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7983 (mt-10) REVERT: D 247 ASP cc_start: 0.7618 (m-30) cc_final: 0.7129 (t70) REVERT: D 293 LEU cc_start: 0.7502 (tp) cc_final: 0.7300 (tp) REVERT: D 298 LYS cc_start: 0.7328 (ttpt) cc_final: 0.6563 (ptmt) REVERT: E 77 ILE cc_start: 0.7931 (pt) cc_final: 0.7252 (mt) REVERT: E 269 LYS cc_start: 0.8287 (mttm) cc_final: 0.7837 (mmtm) REVERT: F 337 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6719 (mt-10) REVERT: H 49 LYS cc_start: 0.1514 (mttt) cc_final: 0.1152 (ptpt) REVERT: H 88 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.6087 (mm-30) REVERT: H 197 ARG cc_start: 0.3535 (tpt170) cc_final: 0.3079 (tpt90) REVERT: H 292 MET cc_start: 0.7219 (tpp) cc_final: 0.6768 (tpp) outliers start: 66 outliers final: 58 residues processed: 332 average time/residue: 0.3559 time to fit residues: 183.5753 Evaluate side-chains 337 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 276 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 9.9990 chunk 245 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 212 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 231 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 237 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN D 412 ASN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.137723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.108495 restraints weight = 38486.573| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.20 r_work: 0.3187 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24197 Z= 0.206 Angle : 0.565 9.359 32807 Z= 0.300 Chirality : 0.042 0.162 3647 Planarity : 0.004 0.043 4071 Dihedral : 10.951 175.825 3405 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.46 % Allowed : 15.30 % Favored : 82.24 % 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: 0.43 (0.16), residues: 2898 helix: 1.52 (0.14), residues: 1449 sheet: -0.19 (0.27), residues: 390 loop : -1.26 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 162 HIS 0.005 0.001 HIS B 8 PHE 0.024 0.002 PHE C 104 TYR 0.030 0.001 TYR D 312 ARG 0.003 0.000 ARG A 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5294.78 seconds wall clock time: 95 minutes 26.03 seconds (5726.03 seconds total)