Starting phenix.real_space_refine on Sun Sep 29 21:44:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvf_27737/09_2024/8dvf_27737.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvf_27737/09_2024/8dvf_27737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvf_27737/09_2024/8dvf_27737.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvf_27737/09_2024/8dvf_27737.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvf_27737/09_2024/8dvf_27737.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvf_27737/09_2024/8dvf_27737.cif" } resolution = 3.3 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 23 residue(s): 0.07s 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: 14.54, per 1000 atoms: 0.61 Number of scatterers: 23693 At special positions: 0 Unit cell: (131.652, 130.824, 141.588, 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: 6.00 Conformation dependent library (CDL) restraints added in 2.9 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 53.9% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 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: 3.708A 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: 3.728A 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: 3.543A 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: 3.843A 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: 3.608A 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: 4.152A 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 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: 3.593A 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: 3.588A 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: 3.843A 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: 3.705A 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: 3.661A pdb=" N ARG H 14 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.644A 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 97 removed outlier: 3.858A pdb=" N GLU H 88 " --> pdb=" O ASP H 84 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG H 94 " --> pdb=" O ILE H 90 " (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: 3.607A 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: 3.605A 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: 3.853A 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 removed outlier: 3.513A pdb=" N ARG H 335 " --> pdb=" O MET H 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153 removed outlier: 6.564A pdb=" N VAL B 221 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 7.801A 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: 6.442A 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: 3.936A 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: 6.512A pdb=" N MET A 384 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.772A 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: 7.765A pdb=" N VAL A 387 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.401A 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: 7.742A 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: 7.760A pdb=" N ALA A 354 " --> pdb=" O ASN A 193 " (cutoff:3.500A) removed outlier: 5.954A 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: 6.470A 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: 7.739A 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: 6.615A pdb=" N VAL C 221 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LYS C 278 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.242A 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: 7.639A 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: 3.526A 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: 6.113A 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: 3.522A 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: 8.044A pdb=" N LEU E 385 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 6.324A 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: 6.346A pdb=" N ASN D 193 " --> pdb=" O THR D 352 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ALA D 354 " --> pdb=" O ASN D 193 " (cutoff:3.500A) removed outlier: 5.929A 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: 6.540A 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: 6.324A 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: 6.438A 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: 3.509A 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: 7.78 Time building geometry restraints manager: 6.96 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: 7550 1.35 - 1.50: 6427 1.50 - 1.65: 9991 1.65 - 1.80: 110 1.80 - 1.95: 119 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 1.47e+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 1.25e+01 bond pdb=" N ILE A 321 " pdb=" CA ILE A 321 " ideal model delta sigma weight residual 1.452 1.494 -0.042 1.18e-02 7.18e+03 1.25e+01 bond pdb=" N VAL E 19 " pdb=" CA VAL E 19 " ideal model delta sigma weight residual 1.452 1.492 -0.040 1.18e-02 7.18e+03 1.14e+01 bond pdb=" N VAL A 323 " pdb=" CA VAL A 323 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.08e-02 8.57e+03 1.11e+01 ... (remaining 24192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 32336 2.51 - 5.01: 435 5.01 - 7.52: 27 7.52 - 10.03: 8 10.03 - 12.53: 1 Bond angle restraints: 32807 Sorted by residual: angle pdb=" N ILE A 321 " pdb=" CA ILE A 321 " pdb=" C ILE A 321 " ideal model delta sigma weight residual 112.96 108.30 4.66 1.00e+00 1.00e+00 2.17e+01 angle pdb=" PB AGS C 501 " pdb=" O3B AGS C 501 " pdb=" PG AGS C 501 " ideal model delta sigma weight residual 120.12 132.65 -12.53 3.00e+00 1.11e-01 1.75e+01 angle pdb=" N ASP A 82 " pdb=" CA ASP A 82 " pdb=" C ASP A 82 " ideal model delta sigma weight residual 112.57 108.09 4.48 1.13e+00 7.83e-01 1.57e+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 122.30 117.08 5.22 1.35e+00 5.49e-01 1.49e+01 ... (remaining 32802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 14414 35.65 - 71.31: 203 71.31 - 106.96: 9 106.96 - 142.61: 1 142.61 - 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 -67.73 106.44 -174.17 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 - 0.047: 2726 0.047 - 0.093: 622 0.093 - 0.140: 242 0.140 - 0.186: 46 0.186 - 0.233: 11 Chirality restraints: 3647 Sorted by residual: chirality pdb=" CA ILE B 111 " pdb=" N ILE B 111 " pdb=" C ILE B 111 " pdb=" CB ILE B 111 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.35e+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 1.21e+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 1.20e+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 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 266 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 266 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP H 266 " -0.005 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 3.33e-02 1.11e+01 pdb=" C GLU A 373 " 0.058 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 2.29e-02 5.23e+00 pdb=" C SER B 145 " 0.040 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: 114 2.47 - 3.08: 16485 3.08 - 3.68: 36383 3.68 - 4.29: 55317 4.29 - 4.90: 90427 Nonbonded interactions: 198726 Sorted by model distance: nonbonded pdb=" O1B AGS C 501 " pdb="MG MG C 502 " model vdw 1.862 2.170 nonbonded pdb=" O3B AGS B 501 " pdb="MG MG B 502 " model vdw 1.973 2.170 nonbonded pdb=" OE2 GLU B 227 " pdb="MG MG B 502 " model vdw 1.980 2.170 nonbonded pdb=" O2G AGS E 501 " pdb="MG MG E 502 " model vdw 1.984 2.170 nonbonded pdb=" O2B AGS F 501 " pdb="MG MG F 502 " model vdw 1.993 2.170 ... (remaining 198721 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 1.000 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 51.580 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.100 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 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= 0.288 Angle : 0.682 12.535 32807 Z= 0.443 Chirality : 0.049 0.233 3647 Planarity : 0.004 0.075 4071 Dihedral : 12.507 178.268 9101 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.78 % Allowed : 7.13 % Favored : 91.08 % 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: 0.22 (0.16), residues: 2898 helix: 1.28 (0.14), residues: 1436 sheet: -0.35 (0.27), residues: 407 loop : -1.21 (0.18), residues: 1055 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 809 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 764 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 TYR cc_start: 0.7889 (m-80) cc_final: 0.7364 (m-80) REVERT: A 47 TYR cc_start: 0.6915 (m-10) cc_final: 0.6704 (m-10) REVERT: A 104 PHE cc_start: 0.7783 (t80) cc_final: 0.7430 (t80) REVERT: A 150 VAL cc_start: 0.8809 (t) cc_final: 0.8597 (m) REVERT: A 164 SER cc_start: 0.8518 (m) cc_final: 0.8224 (t) REVERT: A 228 MET cc_start: 0.6399 (mtp) cc_final: 0.5939 (mtp) REVERT: A 292 SER cc_start: 0.7262 (p) cc_final: 0.7025 (t) REVERT: A 333 LYS cc_start: 0.5793 (OUTLIER) cc_final: 0.5550 (tttp) REVERT: B 66 THR cc_start: 0.6091 (p) cc_final: 0.5695 (m) REVERT: B 150 VAL cc_start: 0.8593 (t) cc_final: 0.8333 (p) REVERT: B 299 LEU cc_start: 0.8502 (mt) cc_final: 0.8068 (mt) REVERT: B 312 TYR cc_start: 0.5027 (t80) cc_final: 0.4788 (t80) REVERT: C 85 GLU cc_start: 0.5980 (mm-30) cc_final: 0.5748 (mm-30) REVERT: C 150 VAL cc_start: 0.7503 (p) cc_final: 0.7095 (p) REVERT: C 157 ASP cc_start: 0.7634 (m-30) cc_final: 0.7303 (m-30) REVERT: C 263 MET cc_start: 0.8289 (mmm) cc_final: 0.8037 (mmp) REVERT: C 312 TYR cc_start: 0.4659 (t80) cc_final: 0.4421 (t80) REVERT: C 324 TYR cc_start: 0.7816 (m-80) cc_final: 0.7608 (m-80) REVERT: D 103 MET cc_start: 0.7495 (mmm) cc_final: 0.7255 (mtp) REVERT: D 293 LEU cc_start: 0.8466 (tp) cc_final: 0.8196 (tt) REVERT: D 384 MET cc_start: 0.8386 (mtm) cc_final: 0.8126 (mtm) REVERT: E 344 VAL cc_start: 0.7064 (p) cc_final: 0.6842 (m) REVERT: E 392 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6214 (mm-30) REVERT: E 414 TRP cc_start: 0.7134 (m-90) cc_final: 0.6528 (m-90) REVERT: F 233 CYS cc_start: 0.7658 (m) cc_final: 0.7428 (m) REVERT: F 279 GLN cc_start: 0.7377 (tt0) cc_final: 0.7074 (tt0) REVERT: F 303 PHE cc_start: 0.8055 (t80) cc_final: 0.7852 (t80) REVERT: F 311 ASP cc_start: 0.7476 (t0) cc_final: 0.6692 (p0) REVERT: F 399 GLN cc_start: 0.6490 (OUTLIER) cc_final: 0.5592 (mt0) REVERT: F 418 LEU cc_start: 0.6114 (OUTLIER) cc_final: 0.5881 (tt) REVERT: F 430 GLU cc_start: 0.5715 (mt-10) cc_final: 0.5410 (tt0) REVERT: H 35 PHE cc_start: 0.4147 (p90) cc_final: 0.3926 (p90) REVERT: H 51 ARG cc_start: 0.4962 (mtt180) cc_final: 0.4574 (mtp85) REVERT: H 80 GLU cc_start: 0.5633 (mm-30) cc_final: 0.4520 (pt0) REVERT: H 88 GLU cc_start: 0.6975 (pt0) cc_final: 0.6515 (pt0) REVERT: H 89 TYR cc_start: 0.6084 (t80) cc_final: 0.5859 (t80) REVERT: H 213 TYR cc_start: 0.4202 (p90) cc_final: 0.3856 (p90) REVERT: H 225 VAL cc_start: 0.5885 (t) cc_final: 0.5642 (t) REVERT: H 234 GLU cc_start: 0.5461 (mt-10) cc_final: 0.4972 (mt-10) REVERT: H 244 ASN cc_start: 0.5804 (m-40) cc_final: 0.5277 (t0) REVERT: H 254 ASP cc_start: 0.4001 (t0) cc_final: 0.3721 (t70) REVERT: H 264 ARG cc_start: 0.5244 (ptt180) cc_final: 0.4732 (ptt180) REVERT: H 270 ASN cc_start: 0.6320 (t0) cc_final: 0.6114 (t0) REVERT: H 276 ASP cc_start: 0.6781 (m-30) cc_final: 0.6504 (m-30) REVERT: H 278 ILE cc_start: 0.6903 (pp) cc_final: 0.6483 (mm) REVERT: H 281 MET cc_start: 0.6844 (mmt) cc_final: 0.6400 (mmm) REVERT: H 289 GLU cc_start: 0.6628 (mm-30) cc_final: 0.5600 (mm-30) REVERT: H 293 PHE cc_start: 0.6403 (m-80) cc_final: 0.5797 (m-80) REVERT: H 322 MET cc_start: 0.6755 (mtm) cc_final: 0.6541 (mtm) outliers start: 45 outliers final: 7 residues processed: 794 average time/residue: 0.3876 time to fit residues: 456.9324 Evaluate side-chains 394 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 384 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain H residue 334 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 9.9990 chunk 220 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 228 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 138 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 264 optimal weight: 0.3980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 116 ASN A 327 ASN A 403 GLN B 200 ASN B 355 GLN B 399 GLN C 8 HIS D 116 ASN D 167 ASN E 57 ASN E 114 GLN F 57 ASN F 398 GLN H 195 GLN H 328 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24197 Z= 0.248 Angle : 0.602 7.218 32807 Z= 0.325 Chirality : 0.044 0.184 3647 Planarity : 0.004 0.055 4071 Dihedral : 10.787 168.342 3418 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.73 % Allowed : 12.01 % Favored : 85.26 % 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: 0.25 (0.16), residues: 2898 helix: 1.26 (0.14), residues: 1455 sheet: -0.36 (0.27), residues: 415 loop : -1.15 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 266 HIS 0.008 0.001 HIS C 43 PHE 0.013 0.002 PHE D 65 TYR 0.020 0.002 TYR F 15 ARG 0.010 0.001 ARG C 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 473 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 404 time to evaluate : 2.689 Fit side-chains REVERT: A 19 VAL cc_start: 0.8470 (OUTLIER) cc_final: 0.8259 (t) REVERT: A 38 LYS cc_start: 0.7608 (mttm) cc_final: 0.6832 (mmtm) REVERT: A 178 ILE cc_start: 0.7703 (tp) cc_final: 0.7385 (tp) REVERT: C 85 GLU cc_start: 0.6723 (mm-30) cc_final: 0.6456 (mm-30) REVERT: C 157 ASP cc_start: 0.7810 (m-30) cc_final: 0.7453 (m-30) REVERT: D 103 MET cc_start: 0.7516 (mmm) cc_final: 0.7262 (mtp) REVERT: D 231 GLU cc_start: 0.7455 (mp0) cc_final: 0.6997 (tm-30) REVERT: E 389 GLU cc_start: 0.6668 (tt0) cc_final: 0.6341 (tp30) REVERT: E 392 GLU cc_start: 0.6581 (mt-10) cc_final: 0.6211 (mm-30) REVERT: E 414 TRP cc_start: 0.7225 (m-90) cc_final: 0.6563 (m-90) REVERT: F 1 MET cc_start: 0.8022 (ptm) cc_final: 0.7780 (ptt) REVERT: F 418 LEU cc_start: 0.6106 (OUTLIER) cc_final: 0.5749 (tt) REVERT: H 51 ARG cc_start: 0.4987 (mtt180) cc_final: 0.4666 (mtp85) REVERT: H 80 GLU cc_start: 0.5673 (mm-30) cc_final: 0.4608 (pt0) REVERT: H 244 ASN cc_start: 0.6148 (m-40) cc_final: 0.5334 (t0) REVERT: H 254 ASP cc_start: 0.3911 (t0) cc_final: 0.3651 (t70) REVERT: H 264 ARG cc_start: 0.5517 (ptt180) cc_final: 0.4853 (ptt180) REVERT: H 274 HIS cc_start: 0.4511 (t-170) cc_final: 0.4277 (t-170) REVERT: H 278 ILE cc_start: 0.6609 (pp) cc_final: 0.6354 (mm) REVERT: H 281 MET cc_start: 0.6864 (mmt) cc_final: 0.6429 (mmm) REVERT: H 289 GLU cc_start: 0.6699 (mm-30) cc_final: 0.5869 (mm-30) REVERT: H 307 MET cc_start: 0.6214 (mtm) cc_final: 0.5821 (mtp) outliers start: 69 outliers final: 42 residues processed: 455 average time/residue: 0.3433 time to fit residues: 242.5710 Evaluate side-chains 362 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 318 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 308 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 219 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 264 optimal weight: 5.9990 chunk 285 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 chunk 262 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN B 355 GLN C 35 ASN C 125 ASN D 114 GLN D 167 ASN H 195 GLN H 325 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24197 Z= 0.279 Angle : 0.605 8.498 32807 Z= 0.321 Chirality : 0.044 0.287 3647 Planarity : 0.004 0.071 4071 Dihedral : 10.702 160.038 3411 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.97 % Allowed : 13.79 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.14 (0.16), residues: 2898 helix: 1.21 (0.14), residues: 1446 sheet: -0.31 (0.27), residues: 405 loop : -1.29 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 361 HIS 0.005 0.001 HIS B 8 PHE 0.014 0.002 PHE D 37 TYR 0.020 0.002 TYR F 15 ARG 0.011 0.001 ARG H 94 *********************** 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 423 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 348 time to evaluate : 2.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7635 (mttm) cc_final: 0.7260 (ttmm) REVERT: C 85 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6810 (mm-30) REVERT: C 157 ASP cc_start: 0.7989 (m-30) cc_final: 0.7699 (m-30) REVERT: D 103 MET cc_start: 0.7519 (mmm) cc_final: 0.7318 (mtp) REVERT: D 231 GLU cc_start: 0.7597 (mp0) cc_final: 0.7110 (tm-30) REVERT: D 406 SER cc_start: 0.8069 (t) cc_final: 0.7790 (p) REVERT: E 392 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6371 (mm-30) REVERT: E 414 TRP cc_start: 0.7268 (m-90) cc_final: 0.6542 (m-90) REVERT: F 1 MET cc_start: 0.8254 (ptm) cc_final: 0.7966 (ptt) REVERT: F 79 LYS cc_start: 0.7855 (mmtt) cc_final: 0.7627 (tptt) REVERT: F 181 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7180 (ttmm) REVERT: F 321 ILE cc_start: 0.6911 (mt) cc_final: 0.5938 (mt) REVERT: F 399 GLN cc_start: 0.6756 (OUTLIER) cc_final: 0.6360 (tp40) REVERT: F 418 LEU cc_start: 0.6084 (OUTLIER) cc_final: 0.5641 (tt) REVERT: H 80 GLU cc_start: 0.5982 (mm-30) cc_final: 0.5538 (mp0) REVERT: H 213 TYR cc_start: 0.4207 (p90) cc_final: 0.3929 (p90) REVERT: H 244 ASN cc_start: 0.6171 (m-40) cc_final: 0.5262 (t0) REVERT: H 254 ASP cc_start: 0.3739 (t0) cc_final: 0.3525 (t70) REVERT: H 281 MET cc_start: 0.6994 (mmt) cc_final: 0.6580 (mmm) REVERT: H 289 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6477 (mp0) REVERT: H 295 ASP cc_start: 0.5852 (p0) cc_final: 0.5619 (p0) outliers start: 75 outliers final: 46 residues processed: 401 average time/residue: 0.3537 time to fit residues: 220.2148 Evaluate side-chains 355 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 306 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 419 MET Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 308 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 265 optimal weight: 6.9990 chunk 281 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 251 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN D 114 GLN D 167 ASN ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN H 188 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24197 Z= 0.253 Angle : 0.571 7.617 32807 Z= 0.305 Chirality : 0.043 0.262 3647 Planarity : 0.004 0.039 4071 Dihedral : 10.630 157.068 3408 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.65 % Allowed : 13.99 % Favored : 82.36 % 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: 0.09 (0.16), residues: 2898 helix: 1.20 (0.14), residues: 1449 sheet: -0.41 (0.26), residues: 405 loop : -1.34 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 162 HIS 0.005 0.001 HIS B 8 PHE 0.015 0.002 PHE D 37 TYR 0.016 0.001 TYR F 15 ARG 0.005 0.000 ARG C 139 *********************** 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 431 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 339 time to evaluate : 2.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7645 (mttm) cc_final: 0.7282 (ttmm) REVERT: A 345 GLU cc_start: 0.7773 (tp30) cc_final: 0.7530 (tp30) REVERT: C 85 GLU cc_start: 0.6926 (mm-30) cc_final: 0.6690 (mm-30) REVERT: C 118 GLU cc_start: 0.6019 (tm-30) cc_final: 0.5141 (tt0) REVERT: C 157 ASP cc_start: 0.7995 (m-30) cc_final: 0.7738 (m-30) REVERT: C 175 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8026 (tttm) REVERT: C 431 ILE cc_start: 0.6901 (mm) cc_final: 0.6652 (mt) REVERT: D 103 MET cc_start: 0.7510 (mmm) cc_final: 0.7278 (mtp) REVERT: D 134 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7638 (mt) REVERT: D 155 MET cc_start: 0.8053 (tpp) cc_final: 0.7831 (tpp) REVERT: D 231 GLU cc_start: 0.7676 (mp0) cc_final: 0.7167 (tm-30) REVERT: D 406 SER cc_start: 0.8249 (t) cc_final: 0.7819 (p) REVERT: E 389 GLU cc_start: 0.6886 (tt0) cc_final: 0.6476 (tp30) REVERT: E 392 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6479 (mm-30) REVERT: E 414 TRP cc_start: 0.7281 (m-90) cc_final: 0.6529 (m-90) REVERT: F 1 MET cc_start: 0.8224 (ptm) cc_final: 0.8008 (ptt) REVERT: F 181 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7202 (ttmm) REVERT: F 243 ASP cc_start: 0.7242 (m-30) cc_final: 0.6904 (t0) REVERT: F 399 GLN cc_start: 0.6744 (OUTLIER) cc_final: 0.6358 (tp40) REVERT: F 418 LEU cc_start: 0.6131 (OUTLIER) cc_final: 0.5683 (tt) REVERT: H 80 GLU cc_start: 0.5970 (mm-30) cc_final: 0.5525 (mp0) REVERT: H 244 ASN cc_start: 0.6335 (m-40) cc_final: 0.5361 (t0) REVERT: H 254 ASP cc_start: 0.3674 (t0) cc_final: 0.3434 (t70) REVERT: H 281 MET cc_start: 0.6964 (mmt) cc_final: 0.6647 (mmm) REVERT: H 289 GLU cc_start: 0.6754 (mm-30) cc_final: 0.6478 (mp0) REVERT: H 295 ASP cc_start: 0.5822 (p0) cc_final: 0.5599 (p0) REVERT: H 322 MET cc_start: 0.7760 (mtp) cc_final: 0.7524 (mtp) outliers start: 92 outliers final: 60 residues processed: 407 average time/residue: 0.3564 time to fit residues: 227.1997 Evaluate side-chains 369 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 304 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 308 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 0.7980 chunk 159 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 209 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 240 optimal weight: 0.4980 chunk 194 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 252 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN C 114 GLN C 125 ASN D 114 GLN ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 GLN H 252 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24197 Z= 0.285 Angle : 0.599 8.027 32807 Z= 0.317 Chirality : 0.044 0.276 3647 Planarity : 0.004 0.043 4071 Dihedral : 10.680 158.241 3408 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.65 % Allowed : 14.90 % Favored : 81.45 % 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: -0.05 (0.16), residues: 2898 helix: 1.11 (0.14), residues: 1448 sheet: -0.51 (0.26), residues: 400 loop : -1.42 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 162 HIS 0.005 0.001 HIS E 8 PHE 0.020 0.002 PHE D 146 TYR 0.021 0.002 TYR D 329 ARG 0.008 0.001 ARG C 139 *********************** 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 413 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 321 time to evaluate : 2.705 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7618 (mttm) cc_final: 0.7297 (ttmm) REVERT: A 74 LYS cc_start: 0.6779 (tptp) cc_final: 0.6345 (ttpp) REVERT: A 291 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7043 (ttm-80) REVERT: A 345 GLU cc_start: 0.7744 (tp30) cc_final: 0.7529 (tp30) REVERT: A 355 GLN cc_start: 0.7438 (tp40) cc_final: 0.6546 (mm-40) REVERT: C 47 TYR cc_start: 0.5648 (OUTLIER) cc_final: 0.5056 (m-10) REVERT: C 118 GLU cc_start: 0.6084 (tm-30) cc_final: 0.5237 (tt0) REVERT: C 175 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8131 (tttm) REVERT: C 431 ILE cc_start: 0.7000 (mm) cc_final: 0.6748 (mt) REVERT: D 103 MET cc_start: 0.7555 (mmm) cc_final: 0.7311 (mtp) REVERT: D 112 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6734 (tm-30) REVERT: D 231 GLU cc_start: 0.7697 (mp0) cc_final: 0.7168 (tm-30) REVERT: D 406 SER cc_start: 0.8400 (t) cc_final: 0.7885 (p) REVERT: E 100 GLN cc_start: 0.8325 (mm-40) cc_final: 0.8084 (mm-40) REVERT: E 389 GLU cc_start: 0.6927 (tt0) cc_final: 0.6553 (tp30) REVERT: E 392 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6680 (mm-30) REVERT: E 414 TRP cc_start: 0.7291 (m-90) cc_final: 0.6529 (m-90) REVERT: F 181 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7261 (ttmm) REVERT: F 243 ASP cc_start: 0.7231 (m-30) cc_final: 0.6887 (t0) REVERT: F 399 GLN cc_start: 0.6778 (OUTLIER) cc_final: 0.6535 (tp40) REVERT: F 418 LEU cc_start: 0.6228 (OUTLIER) cc_final: 0.5961 (tp) REVERT: H 190 LYS cc_start: 0.5862 (pptt) cc_final: 0.5173 (ttmt) REVERT: H 244 ASN cc_start: 0.6355 (m-40) cc_final: 0.5059 (t0) REVERT: H 254 ASP cc_start: 0.4026 (t0) cc_final: 0.3743 (t70) REVERT: H 274 HIS cc_start: 0.5067 (t-170) cc_final: 0.4659 (t-170) REVERT: H 281 MET cc_start: 0.7049 (mmt) cc_final: 0.6824 (mmm) REVERT: H 289 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6426 (mm-30) REVERT: H 295 ASP cc_start: 0.5800 (p0) cc_final: 0.5543 (p0) outliers start: 92 outliers final: 63 residues processed: 388 average time/residue: 0.3550 time to fit residues: 217.0038 Evaluate side-chains 360 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 290 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain H residue 331 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 10.0000 chunk 253 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 281 optimal weight: 20.0000 chunk 233 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 93 optimal weight: 0.4980 chunk 147 optimal weight: 0.6980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN F 398 GLN H 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24197 Z= 0.170 Angle : 0.535 8.028 32807 Z= 0.284 Chirality : 0.041 0.213 3647 Planarity : 0.003 0.040 4071 Dihedral : 10.485 158.142 3408 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.01 % Allowed : 15.93 % Favored : 81.05 % 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: 0.16 (0.16), residues: 2898 helix: 1.31 (0.14), residues: 1456 sheet: -0.38 (0.27), residues: 399 loop : -1.42 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 150 HIS 0.004 0.001 HIS B 8 PHE 0.012 0.001 PHE H 81 TYR 0.022 0.001 TYR D 329 ARG 0.005 0.000 ARG C 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 395 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 319 time to evaluate : 2.624 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7572 (mttm) cc_final: 0.7303 (ttmm) REVERT: A 69 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6235 (mp0) REVERT: A 74 LYS cc_start: 0.6726 (tptp) cc_final: 0.6278 (ttpp) REVERT: A 291 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7106 (ttm-80) REVERT: B 312 TYR cc_start: 0.4704 (t80) cc_final: 0.4161 (t80) REVERT: B 391 GLU cc_start: 0.7525 (tp30) cc_final: 0.7239 (tp30) REVERT: C 431 ILE cc_start: 0.6959 (mm) cc_final: 0.6711 (mt) REVERT: D 103 MET cc_start: 0.7526 (mmm) cc_final: 0.7218 (mtp) REVERT: D 112 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6863 (tm-30) REVERT: D 128 MET cc_start: 0.5594 (ttt) cc_final: 0.5368 (ttt) REVERT: D 406 SER cc_start: 0.8341 (t) cc_final: 0.7858 (p) REVERT: E 392 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6548 (mm-30) REVERT: E 414 TRP cc_start: 0.7245 (m-90) cc_final: 0.5964 (m-90) REVERT: F 181 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7272 (ttmm) REVERT: F 243 ASP cc_start: 0.7192 (m-30) cc_final: 0.6879 (t0) REVERT: H 80 GLU cc_start: 0.6049 (mm-30) cc_final: 0.5289 (mp0) REVERT: H 194 PHE cc_start: 0.3879 (p90) cc_final: 0.3532 (p90) REVERT: H 244 ASN cc_start: 0.6205 (m-40) cc_final: 0.4955 (t0) REVERT: H 254 ASP cc_start: 0.4105 (t0) cc_final: 0.3823 (t70) REVERT: H 281 MET cc_start: 0.6996 (mmt) cc_final: 0.6782 (mmm) REVERT: H 289 GLU cc_start: 0.6654 (mm-30) cc_final: 0.6311 (mm-30) REVERT: H 295 ASP cc_start: 0.5803 (p0) cc_final: 0.5519 (p0) outliers start: 76 outliers final: 48 residues processed: 376 average time/residue: 0.3506 time to fit residues: 204.0080 Evaluate side-chains 350 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 298 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain H residue 331 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 159 optimal weight: 0.0030 chunk 237 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 280 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN E 425 ASN H 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24197 Z= 0.190 Angle : 0.547 10.164 32807 Z= 0.288 Chirality : 0.042 0.218 3647 Planarity : 0.003 0.039 4071 Dihedral : 10.346 158.167 3403 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.93 % Allowed : 15.97 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.16), residues: 2898 helix: 1.37 (0.14), residues: 1453 sheet: -0.42 (0.26), residues: 403 loop : -1.41 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP H 150 HIS 0.004 0.001 HIS C 8 PHE 0.016 0.002 PHE H 81 TYR 0.033 0.001 TYR H 86 ARG 0.008 0.000 ARG A 124 *********************** 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 395 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 321 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7564 (mttm) cc_final: 0.7299 (ttmm) REVERT: A 69 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.6173 (mp0) REVERT: A 74 LYS cc_start: 0.6731 (tptp) cc_final: 0.6260 (ttpp) REVERT: A 291 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7151 (ttm-80) REVERT: B 391 GLU cc_start: 0.7581 (tp30) cc_final: 0.7284 (tp30) REVERT: C 13 GLN cc_start: 0.7396 (tp-100) cc_final: 0.7047 (mm-40) REVERT: C 124 ARG cc_start: 0.6846 (ptp-110) cc_final: 0.6619 (mtt90) REVERT: C 142 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7245 (mt) REVERT: C 175 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8109 (tttm) REVERT: D 103 MET cc_start: 0.7574 (mmm) cc_final: 0.7311 (mtp) REVERT: D 112 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6840 (tm-30) REVERT: D 406 SER cc_start: 0.8376 (t) cc_final: 0.7873 (p) REVERT: E 23 MET cc_start: 0.8265 (mmp) cc_final: 0.7999 (mmt) REVERT: E 389 GLU cc_start: 0.6877 (tt0) cc_final: 0.6544 (tp30) REVERT: E 392 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6610 (mm-30) REVERT: E 414 TRP cc_start: 0.7299 (m-90) cc_final: 0.6144 (m-90) REVERT: F 181 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7295 (ttmm) REVERT: F 243 ASP cc_start: 0.7150 (m-30) cc_final: 0.6853 (t0) REVERT: F 247 ASP cc_start: 0.6583 (m-30) cc_final: 0.6373 (m-30) REVERT: F 418 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.6065 (tp) REVERT: H 80 GLU cc_start: 0.6170 (mm-30) cc_final: 0.5498 (mp0) REVERT: H 190 LYS cc_start: 0.5932 (pptt) cc_final: 0.5246 (ttmt) REVERT: H 244 ASN cc_start: 0.6230 (m-40) cc_final: 0.4970 (t0) REVERT: H 254 ASP cc_start: 0.4221 (t0) cc_final: 0.3919 (t70) REVERT: H 274 HIS cc_start: 0.5109 (t-170) cc_final: 0.4743 (t-170) REVERT: H 289 GLU cc_start: 0.6589 (mm-30) cc_final: 0.6258 (mm-30) REVERT: H 295 ASP cc_start: 0.5776 (p0) cc_final: 0.5508 (p0) outliers start: 74 outliers final: 50 residues processed: 374 average time/residue: 0.3630 time to fit residues: 208.7092 Evaluate side-chains 355 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 298 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain H residue 331 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 84 optimal weight: 0.0870 chunk 55 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 220 optimal weight: 0.2980 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24197 Z= 0.164 Angle : 0.535 9.978 32807 Z= 0.282 Chirality : 0.041 0.187 3647 Planarity : 0.003 0.039 4071 Dihedral : 10.243 158.048 3402 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.58 % Allowed : 16.33 % Favored : 81.09 % 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: 0.34 (0.16), residues: 2898 helix: 1.51 (0.14), residues: 1455 sheet: -0.33 (0.27), residues: 395 loop : -1.38 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.001 TRP H 150 HIS 0.004 0.001 HIS C 8 PHE 0.013 0.001 PHE C 104 TYR 0.030 0.001 TYR D 329 ARG 0.008 0.000 ARG A 124 *********************** 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 371 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 306 time to evaluate : 2.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7556 (mttm) cc_final: 0.7204 (ttmm) REVERT: A 69 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.6114 (mp0) REVERT: A 243 ASP cc_start: 0.7919 (m-30) cc_final: 0.7515 (m-30) REVERT: A 291 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7074 (ttm-80) REVERT: B 267 ARG cc_start: 0.7654 (ttm-80) cc_final: 0.7336 (ttm170) REVERT: B 391 GLU cc_start: 0.7561 (tp30) cc_final: 0.7264 (tp30) REVERT: C 13 GLN cc_start: 0.7359 (tp-100) cc_final: 0.7110 (mm-40) REVERT: C 69 GLU cc_start: 0.6507 (mm-30) cc_final: 0.6304 (mm-30) REVERT: C 142 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7206 (mt) REVERT: C 175 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8100 (tttm) REVERT: D 103 MET cc_start: 0.7671 (mmm) cc_final: 0.7276 (mtp) REVERT: D 112 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6865 (tm-30) REVERT: D 134 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7546 (mt) REVERT: D 406 SER cc_start: 0.8365 (t) cc_final: 0.7889 (p) REVERT: E 23 MET cc_start: 0.8258 (mmp) cc_final: 0.7988 (mmt) REVERT: E 392 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6565 (mm-30) REVERT: E 413 LYS cc_start: 0.7552 (tppt) cc_final: 0.6881 (tptp) REVERT: E 414 TRP cc_start: 0.7312 (m-90) cc_final: 0.6146 (m-90) REVERT: F 181 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7299 (ttmm) REVERT: F 418 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6106 (tp) REVERT: H 80 GLU cc_start: 0.6126 (mm-30) cc_final: 0.5440 (mp0) REVERT: H 219 ILE cc_start: 0.6365 (OUTLIER) cc_final: 0.5938 (tp) REVERT: H 244 ASN cc_start: 0.6276 (m-40) cc_final: 0.4951 (t0) REVERT: H 254 ASP cc_start: 0.4295 (t0) cc_final: 0.4026 (t70) REVERT: H 274 HIS cc_start: 0.5109 (t-170) cc_final: 0.4769 (t-170) REVERT: H 289 GLU cc_start: 0.6556 (mm-30) cc_final: 0.6225 (mm-30) REVERT: H 295 ASP cc_start: 0.5721 (p0) cc_final: 0.5453 (p0) outliers start: 65 outliers final: 43 residues processed: 354 average time/residue: 0.3678 time to fit residues: 203.0896 Evaluate side-chains 339 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 287 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain H residue 331 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 10.0000 chunk 268 optimal weight: 10.0000 chunk 245 optimal weight: 0.7980 chunk 261 optimal weight: 0.0670 chunk 157 optimal weight: 0.4980 chunk 113 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 236 optimal weight: 10.0000 chunk 247 optimal weight: 20.0000 chunk 260 optimal weight: 9.9990 overall best weight: 4.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 HIS B 200 ASN B 399 GLN C 114 GLN C 398 GLN ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 24197 Z= 0.322 Angle : 0.630 9.567 32807 Z= 0.331 Chirality : 0.045 0.240 3647 Planarity : 0.004 0.037 4071 Dihedral : 10.684 159.255 3402 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.77 % Allowed : 16.57 % Favored : 80.66 % 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: -0.02 (0.16), residues: 2898 helix: 1.16 (0.14), residues: 1451 sheet: -0.52 (0.26), residues: 402 loop : -1.45 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP H 150 HIS 0.011 0.001 HIS B 87 PHE 0.021 0.002 PHE H 81 TYR 0.026 0.002 TYR D 329 ARG 0.004 0.001 ARG C 407 *********************** 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 383 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 313 time to evaluate : 2.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8135 (mp0) cc_final: 0.7748 (mp0) REVERT: A 38 LYS cc_start: 0.7686 (mttm) cc_final: 0.7399 (ttmm) REVERT: A 243 ASP cc_start: 0.7960 (m-30) cc_final: 0.7548 (m-30) REVERT: A 291 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7128 (ttm-80) REVERT: B 306 THR cc_start: 0.8761 (p) cc_final: 0.8455 (m) REVERT: B 370 ASP cc_start: 0.7058 (m-30) cc_final: 0.6836 (m-30) REVERT: B 391 GLU cc_start: 0.7599 (tp30) cc_final: 0.7303 (tp30) REVERT: C 13 GLN cc_start: 0.7364 (tp-100) cc_final: 0.7003 (mm-40) REVERT: C 47 TYR cc_start: 0.5805 (OUTLIER) cc_final: 0.5164 (m-10) REVERT: C 142 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7369 (mt) REVERT: C 175 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8173 (tptt) REVERT: D 103 MET cc_start: 0.7632 (mmm) cc_final: 0.7324 (mtp) REVERT: D 112 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6848 (tm-30) REVERT: D 134 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7658 (mt) REVERT: E 389 GLU cc_start: 0.7024 (tt0) cc_final: 0.6635 (tp30) REVERT: E 392 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6721 (mm-30) REVERT: E 414 TRP cc_start: 0.7328 (m-90) cc_final: 0.6645 (m-90) REVERT: F 181 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7316 (ttmm) REVERT: F 243 ASP cc_start: 0.7181 (m-30) cc_final: 0.6897 (t0) REVERT: F 274 ARG cc_start: 0.6478 (mtp180) cc_final: 0.6119 (ttp80) REVERT: F 418 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.5951 (tp) REVERT: H 80 GLU cc_start: 0.6143 (mm-30) cc_final: 0.5463 (mp0) REVERT: H 190 LYS cc_start: 0.5987 (pptt) cc_final: 0.5326 (mttt) REVERT: H 219 ILE cc_start: 0.6484 (OUTLIER) cc_final: 0.6095 (tp) REVERT: H 244 ASN cc_start: 0.6219 (m-40) cc_final: 0.4963 (t0) REVERT: H 254 ASP cc_start: 0.4159 (t0) cc_final: 0.3871 (t70) outliers start: 70 outliers final: 48 residues processed: 365 average time/residue: 0.3477 time to fit residues: 196.8474 Evaluate side-chains 347 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 290 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain H residue 331 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 6.9990 chunk 276 optimal weight: 30.0000 chunk 168 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 289 optimal weight: 8.9990 chunk 266 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN B 62 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 ASN ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 24197 Z= 0.342 Angle : 0.652 11.169 32807 Z= 0.342 Chirality : 0.045 0.246 3647 Planarity : 0.004 0.043 4071 Dihedral : 10.777 160.295 3402 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.54 % Allowed : 17.28 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.21 (0.15), residues: 2898 helix: 0.97 (0.14), residues: 1458 sheet: -0.65 (0.26), residues: 399 loop : -1.49 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.113 0.002 TRP H 150 HIS 0.032 0.002 HIS B 87 PHE 0.020 0.002 PHE H 81 TYR 0.029 0.002 TYR D 329 ARG 0.005 0.001 ARG C 139 ********************** 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 360 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 296 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8109 (mp0) cc_final: 0.7779 (mp0) REVERT: A 38 LYS cc_start: 0.7744 (mttm) cc_final: 0.7417 (ttmm) REVERT: A 243 ASP cc_start: 0.7948 (m-30) cc_final: 0.7595 (m-30) REVERT: A 291 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7150 (ttm-80) REVERT: B 370 ASP cc_start: 0.7087 (m-30) cc_final: 0.6867 (m-30) REVERT: B 391 GLU cc_start: 0.7571 (tp30) cc_final: 0.7281 (tp30) REVERT: B 431 ILE cc_start: 0.6997 (mm) cc_final: 0.6729 (mt) REVERT: C 13 GLN cc_start: 0.7370 (tp-100) cc_final: 0.6998 (mm-40) REVERT: C 124 ARG cc_start: 0.6697 (ptp-110) cc_final: 0.6410 (mtm-85) REVERT: C 142 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7383 (mt) REVERT: C 175 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8164 (tptt) REVERT: D 103 MET cc_start: 0.7622 (mmm) cc_final: 0.7324 (mtp) REVERT: D 112 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6767 (tm-30) REVERT: D 134 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7651 (mt) REVERT: D 264 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6678 (mm-30) REVERT: E 389 GLU cc_start: 0.7000 (tt0) cc_final: 0.6616 (tp30) REVERT: E 392 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6720 (mm-30) REVERT: E 414 TRP cc_start: 0.7314 (m-90) cc_final: 0.6625 (m-90) REVERT: F 181 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7342 (ttmm) REVERT: F 243 ASP cc_start: 0.7191 (m-30) cc_final: 0.6908 (t0) REVERT: F 418 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.5990 (tp) REVERT: H 80 GLU cc_start: 0.6118 (mm-30) cc_final: 0.5480 (mp0) REVERT: H 190 LYS cc_start: 0.6001 (pptt) cc_final: 0.5349 (mttt) REVERT: H 219 ILE cc_start: 0.6453 (OUTLIER) cc_final: 0.6136 (tp) REVERT: H 244 ASN cc_start: 0.6212 (m-40) cc_final: 0.4923 (t0) REVERT: H 254 ASP cc_start: 0.4178 (t0) cc_final: 0.3885 (t70) outliers start: 64 outliers final: 49 residues processed: 345 average time/residue: 0.3528 time to fit residues: 189.8150 Evaluate side-chains 349 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 292 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain H residue 331 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 0.7980 chunk 245 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 212 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 chunk 231 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 237 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 ASN ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 355 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.146677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.122147 restraints weight = 39381.306| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.02 r_work: 0.3413 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 24197 Z= 0.160 Angle : 0.562 11.158 32807 Z= 0.295 Chirality : 0.041 0.201 3647 Planarity : 0.003 0.041 4071 Dihedral : 10.463 160.191 3402 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.66 % Allowed : 18.07 % Favored : 80.26 % 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: 0.16 (0.16), residues: 2898 helix: 1.35 (0.14), residues: 1456 sheet: -0.42 (0.27), residues: 395 loop : -1.46 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.110 0.002 TRP H 150 HIS 0.008 0.001 HIS B 87 PHE 0.014 0.001 PHE C 104 TYR 0.027 0.001 TYR D 329 ARG 0.006 0.000 ARG A 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5549.88 seconds wall clock time: 99 minutes 48.22 seconds (5988.22 seconds total)