Starting phenix.real_space_refine on Fri Jun 20 09:37:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dvf_27737/06_2025/8dvf_27737.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dvf_27737/06_2025/8dvf_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/cci-nas-00/data/ceres_data/8dvf_27737/06_2025/8dvf_27737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dvf_27737/06_2025/8dvf_27737.map" model { file = "/net/cci-nas-00/data/ceres_data/8dvf_27737/06_2025/8dvf_27737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dvf_27737/06_2025/8dvf_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 14.33, per 1000 atoms: 0.60 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: 6.22 Conformation dependent library (CDL) restraints added in 3.1 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: 2.58 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: 8.02 Time building geometry restraints manager: 7.21 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 54.060 Find NCS groups from input model: 1.470 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.310 ------------------------------------------------------------------------------- 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= 0.300 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 Details of bonding type rmsd hydrogen bonds : bond 0.15940 ( 1158) hydrogen bonds : angle 6.57971 ( 3303) covalent geometry : bond 0.00440 (24197) covalent geometry : angle 0.68184 (32807) *********************** 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 to be fit. rotamer outliers: 45 poor density : 764 time to evaluate : 2.875 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: 0.4004 time to fit residues: 471.8823 Evaluate side-chains 394 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 384 time to evaluate : 2.599 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.150424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.125800 restraints weight = 39460.715| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.16 r_work: 0.3453 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 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= 0.170 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 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 1158) hydrogen bonds : angle 5.13740 ( 3303) covalent geometry : bond 0.00383 (24197) covalent geometry : angle 0.60223 (32807) *********************** 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 to be fit. rotamer outliers: 69 poor density : 404 time to evaluate : 2.606 Fit side-chains REVERT: A 19 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8146 (t) REVERT: A 38 LYS cc_start: 0.7585 (mttm) cc_final: 0.6771 (mmtm) REVERT: A 178 ILE cc_start: 0.7801 (tp) cc_final: 0.7505 (tp) REVERT: C 85 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6635 (mm-30) REVERT: C 157 ASP cc_start: 0.7808 (m-30) cc_final: 0.7510 (m-30) REVERT: D 103 MET cc_start: 0.7153 (mmm) cc_final: 0.6934 (mtp) REVERT: D 264 GLU cc_start: 0.6619 (mm-30) cc_final: 0.6408 (mm-30) REVERT: E 389 GLU cc_start: 0.6545 (tt0) cc_final: 0.6187 (tp30) REVERT: E 392 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6367 (mm-30) REVERT: E 414 TRP cc_start: 0.7284 (m-90) cc_final: 0.6673 (m-90) REVERT: F 418 LEU cc_start: 0.6045 (OUTLIER) cc_final: 0.5664 (tt) REVERT: H 36 ARG cc_start: 0.3685 (ttm170) cc_final: 0.3278 (ttp80) REVERT: H 51 ARG cc_start: 0.5917 (mtt180) cc_final: 0.5193 (mtp85) REVERT: H 80 GLU cc_start: 0.7737 (mm-30) cc_final: 0.5921 (pt0) REVERT: H 244 ASN cc_start: 0.6633 (m-40) cc_final: 0.6348 (t0) REVERT: H 264 ARG cc_start: 0.6858 (ptt180) cc_final: 0.6222 (ptt180) REVERT: H 278 ILE cc_start: 0.8388 (pp) cc_final: 0.7920 (mm) REVERT: H 281 MET cc_start: 0.7687 (mmt) cc_final: 0.7134 (mmm) REVERT: H 307 MET cc_start: 0.6663 (mtm) cc_final: 0.6146 (mtp) outliers start: 69 outliers final: 42 residues processed: 455 average time/residue: 0.3573 time to fit residues: 253.4740 Evaluate side-chains 360 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 316 time to evaluate : 2.959 ------------------------------------------------------------------------------- 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 197 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 199 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 280 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 127 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 279 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN B 200 ASN B 355 GLN C 35 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 GLN D 114 GLN D 167 ASN F 116 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.143489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.117678 restraints weight = 39819.232| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.09 r_work: 0.3334 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 24197 Z= 0.283 Angle : 0.741 10.267 32807 Z= 0.390 Chirality : 0.049 0.244 3647 Planarity : 0.005 0.051 4071 Dihedral : 11.127 157.635 3411 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.80 % Allowed : 14.07 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 2898 helix: 0.73 (0.13), residues: 1445 sheet: -0.56 (0.26), residues: 405 loop : -1.45 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 266 HIS 0.007 0.002 HIS H 274 PHE 0.024 0.003 PHE H 81 TYR 0.020 0.002 TYR F 15 ARG 0.006 0.001 ARG F 322 Details of bonding type rmsd hydrogen bonds : bond 0.04939 ( 1158) hydrogen bonds : angle 5.27930 ( 3303) covalent geometry : bond 0.00659 (24197) covalent geometry : angle 0.74148 (32807) *********************** 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 446 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 350 time to evaluate : 2.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7707 (mttm) cc_final: 0.7284 (ttmm) REVERT: A 74 LYS cc_start: 0.6935 (tptp) cc_final: 0.6364 (ttpp) REVERT: A 291 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.6910 (ttm-80) REVERT: A 345 GLU cc_start: 0.7785 (tp30) cc_final: 0.7517 (tp30) REVERT: B 1 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7915 (ptp) REVERT: C 13 GLN cc_start: 0.7718 (tp40) cc_final: 0.7483 (mm-40) REVERT: C 113 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8293 (mp) REVERT: C 175 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8037 (tptt) REVERT: C 431 ILE cc_start: 0.7122 (mm) cc_final: 0.6872 (mt) REVERT: D 103 MET cc_start: 0.7257 (mmm) cc_final: 0.7032 (mtp) REVERT: D 167 ASN cc_start: 0.6203 (OUTLIER) cc_final: 0.5926 (t0) REVERT: D 264 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6318 (mm-30) REVERT: E 389 GLU cc_start: 0.6902 (tt0) cc_final: 0.6424 (tp30) REVERT: E 392 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6829 (mm-30) REVERT: E 414 TRP cc_start: 0.7340 (m-90) cc_final: 0.6714 (m-90) REVERT: F 181 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7115 (ttmm) REVERT: F 243 ASP cc_start: 0.7394 (m-30) cc_final: 0.6993 (t0) REVERT: F 399 GLN cc_start: 0.6987 (OUTLIER) cc_final: 0.6722 (tp40) REVERT: H 36 ARG cc_start: 0.4297 (ttm170) cc_final: 0.3466 (ttp80) REVERT: H 94 ARG cc_start: 0.7197 (tpp-160) cc_final: 0.6714 (mmm160) REVERT: H 158 GLU cc_start: 0.3196 (OUTLIER) cc_final: 0.2815 (pm20) REVERT: H 244 ASN cc_start: 0.6627 (m-40) cc_final: 0.6327 (t0) REVERT: H 264 ARG cc_start: 0.6619 (ptt180) cc_final: 0.6086 (ptt180) REVERT: H 278 ILE cc_start: 0.8369 (pp) cc_final: 0.8145 (mm) REVERT: H 281 MET cc_start: 0.7826 (mmt) cc_final: 0.7349 (mmm) REVERT: H 295 ASP cc_start: 0.6628 (p0) cc_final: 0.6307 (p0) REVERT: H 307 MET cc_start: 0.6596 (mtm) cc_final: 0.6341 (mtp) outliers start: 96 outliers final: 62 residues processed: 422 average time/residue: 0.4131 time to fit residues: 269.0173 Evaluate side-chains 371 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 301 time to evaluate : 2.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 1 MET 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 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 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 113 ILE 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 366 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 167 ASN 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 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 50 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 145 SER 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 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 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 131 VAL Chi-restraints excluded: chain F residue 156 ASP 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 328 SER Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain H residue 158 GLU 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 304 VAL Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain H residue 328 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 207 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 275 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 GLN D 114 GLN ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN F 398 GLN H 325 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.146140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.120678 restraints weight = 39649.296| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.16 r_work: 0.3388 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24197 Z= 0.124 Angle : 0.550 7.121 32807 Z= 0.294 Chirality : 0.042 0.247 3647 Planarity : 0.004 0.068 4071 Dihedral : 10.662 158.274 3409 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.97 % Allowed : 15.46 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.16), residues: 2898 helix: 1.13 (0.14), residues: 1452 sheet: -0.42 (0.27), residues: 401 loop : -1.41 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 162 HIS 0.011 0.001 HIS D 152 PHE 0.015 0.002 PHE A 104 TYR 0.017 0.001 TYR F 15 ARG 0.006 0.000 ARG H 94 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 1158) hydrogen bonds : angle 4.87930 ( 3303) covalent geometry : bond 0.00273 (24197) covalent geometry : angle 0.55041 (32807) *********************** 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 417 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 342 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7532 (mttm) cc_final: 0.7188 (ttmm) REVERT: A 74 LYS cc_start: 0.6921 (tptp) cc_final: 0.6442 (ttpp) REVERT: A 417 PHE cc_start: 0.4744 (t80) cc_final: 0.4479 (t80) REVERT: C 13 GLN cc_start: 0.7620 (tp40) cc_final: 0.7393 (mm-40) REVERT: C 113 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8262 (mp) REVERT: D 103 MET cc_start: 0.7263 (mmm) cc_final: 0.6938 (mtp) REVERT: D 112 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7101 (tm-30) REVERT: D 128 MET cc_start: 0.5749 (ttt) cc_final: 0.5548 (ttt) REVERT: D 406 SER cc_start: 0.8072 (t) cc_final: 0.7671 (p) REVERT: E 389 GLU cc_start: 0.6819 (tt0) cc_final: 0.6462 (tp30) REVERT: E 392 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6763 (mm-30) REVERT: E 414 TRP cc_start: 0.7306 (m-90) cc_final: 0.6648 (m-90) REVERT: F 181 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7065 (ttmm) REVERT: F 243 ASP cc_start: 0.7370 (m-30) cc_final: 0.6989 (t0) REVERT: F 399 GLN cc_start: 0.6927 (OUTLIER) cc_final: 0.6584 (tp40) REVERT: F 418 LEU cc_start: 0.6129 (OUTLIER) cc_final: 0.5778 (tp) REVERT: H 36 ARG cc_start: 0.4231 (ttm170) cc_final: 0.3247 (ttp80) REVERT: H 80 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7069 (mp0) REVERT: H 244 ASN cc_start: 0.6727 (m-40) cc_final: 0.6331 (t0) REVERT: H 264 ARG cc_start: 0.6329 (ptt180) cc_final: 0.5915 (ptt180) REVERT: H 281 MET cc_start: 0.7672 (mmt) cc_final: 0.7213 (mmm) REVERT: H 295 ASP cc_start: 0.6434 (p0) cc_final: 0.5855 (p0) REVERT: H 322 MET cc_start: 0.8142 (mtp) cc_final: 0.7938 (mtp) outliers start: 75 outliers final: 45 residues processed: 395 average time/residue: 0.4297 time to fit residues: 264.3348 Evaluate side-chains 345 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 295 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL 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 201 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 25 SER Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 131 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 167 ASN 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 318 SER Chi-restraints excluded: chain E residue 22 TYR 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 325 SER 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 90 LEU 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 254 ILE Chi-restraints excluded: chain F residue 282 THR 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 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 Chi-restraints excluded: chain H residue 331 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 199 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 202 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 164 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN C 398 GLN D 114 GLN D 167 ASN ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN F 216 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.144283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.118736 restraints weight = 39842.697| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.14 r_work: 0.3354 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24197 Z= 0.182 Angle : 0.595 8.342 32807 Z= 0.314 Chirality : 0.043 0.252 3647 Planarity : 0.004 0.038 4071 Dihedral : 10.705 159.351 3407 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.57 % Allowed : 15.46 % Favored : 80.98 % 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: -0.12 (0.15), residues: 2898 helix: 1.06 (0.14), residues: 1449 sheet: -0.56 (0.26), residues: 401 loop : -1.48 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 162 HIS 0.005 0.001 HIS E 8 PHE 0.020 0.002 PHE H 81 TYR 0.017 0.002 TYR F 15 ARG 0.006 0.001 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 1158) hydrogen bonds : angle 4.92004 ( 3303) covalent geometry : bond 0.00424 (24197) covalent geometry : angle 0.59457 (32807) *********************** 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 400 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 310 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7584 (mttm) cc_final: 0.7257 (ttmm) REVERT: A 74 LYS cc_start: 0.7010 (tptp) cc_final: 0.6474 (ttpp) REVERT: A 355 GLN cc_start: 0.7424 (tp40) cc_final: 0.6435 (mm-40) REVERT: A 417 PHE cc_start: 0.4956 (t80) cc_final: 0.4336 (t80) REVERT: B 431 ILE cc_start: 0.7098 (mm) cc_final: 0.6793 (mt) REVERT: C 47 TYR cc_start: 0.5691 (OUTLIER) cc_final: 0.5089 (m-10) REVERT: C 113 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8298 (mp) REVERT: C 139 ARG cc_start: 0.7067 (mtm-85) cc_final: 0.6780 (mtm-85) REVERT: C 175 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7942 (tptt) REVERT: D 103 MET cc_start: 0.7335 (mmm) cc_final: 0.7010 (mtp) REVERT: D 112 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7068 (tm-30) REVERT: D 134 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7593 (mt) REVERT: E 23 MET cc_start: 0.8116 (mmp) cc_final: 0.7851 (mmt) REVERT: E 389 GLU cc_start: 0.6838 (tt0) cc_final: 0.6454 (tp30) REVERT: E 392 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6791 (mm-30) REVERT: E 414 TRP cc_start: 0.7291 (m-90) cc_final: 0.6680 (m-90) REVERT: F 181 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7195 (ttmm) REVERT: F 243 ASP cc_start: 0.7376 (m-30) cc_final: 0.7008 (t0) REVERT: F 326 GLU cc_start: 0.6154 (mp0) cc_final: 0.5525 (mp0) REVERT: F 399 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.6728 (tp40) REVERT: F 418 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5752 (tp) REVERT: H 36 ARG cc_start: 0.4226 (ttm170) cc_final: 0.3211 (ttp80) REVERT: H 158 GLU cc_start: 0.3060 (OUTLIER) cc_final: 0.2700 (pm20) REVERT: H 194 PHE cc_start: 0.3601 (p90) cc_final: 0.3143 (p90) REVERT: H 244 ASN cc_start: 0.6779 (m-40) cc_final: 0.6358 (t0) REVERT: H 252 GLN cc_start: 0.4584 (OUTLIER) cc_final: 0.3875 (tm-30) REVERT: H 264 ARG cc_start: 0.6399 (ptt180) cc_final: 0.5939 (ptt90) REVERT: H 281 MET cc_start: 0.7725 (mmt) cc_final: 0.7311 (mmm) REVERT: H 292 MET cc_start: 0.8384 (tpt) cc_final: 0.8178 (tpt) REVERT: H 295 ASP cc_start: 0.6483 (p0) cc_final: 0.5864 (p0) outliers start: 90 outliers final: 53 residues processed: 378 average time/residue: 0.3531 time to fit residues: 208.8449 Evaluate side-chains 356 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 293 time to evaluate : 2.954 ------------------------------------------------------------------------------- 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 76 LEU 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 144 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 200 ASN 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 113 ILE Chi-restraints excluded: chain C residue 131 VAL 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 366 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 56 LEU 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 318 SER 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 50 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 244 VAL 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 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 254 ILE Chi-restraints excluded: chain F residue 282 THR 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 158 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 252 GLN 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 116 optimal weight: 0.0470 chunk 278 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 192 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 265 optimal weight: 0.0870 chunk 201 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 57 optimal weight: 0.1980 chunk 147 optimal weight: 0.9980 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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** E 425 ASN F 200 ASN H 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.147268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.122301 restraints weight = 39414.577| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.09 r_work: 0.3415 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 24197 Z= 0.109 Angle : 0.524 8.015 32807 Z= 0.278 Chirality : 0.041 0.199 3647 Planarity : 0.003 0.040 4071 Dihedral : 10.408 159.371 3407 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.73 % Allowed : 16.17 % 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: 0.21 (0.16), residues: 2898 helix: 1.37 (0.14), residues: 1458 sheet: -0.41 (0.27), residues: 405 loop : -1.41 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 159 HIS 0.006 0.001 HIS H 274 PHE 0.017 0.001 PHE H 194 TYR 0.026 0.001 TYR H 86 ARG 0.008 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.03236 ( 1158) hydrogen bonds : angle 4.66813 ( 3303) covalent geometry : bond 0.00236 (24197) covalent geometry : angle 0.52361 (32807) *********************** 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 399 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 330 time to evaluate : 2.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7479 (mttm) cc_final: 0.7114 (ttmm) REVERT: A 355 GLN cc_start: 0.7486 (tp40) cc_final: 0.6437 (mm-40) REVERT: B 312 TYR cc_start: 0.4615 (t80) cc_final: 0.4304 (t80) REVERT: C 113 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8332 (mp) REVERT: D 103 MET cc_start: 0.7303 (mmm) cc_final: 0.6937 (mtp) REVERT: D 112 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7137 (tm-30) REVERT: D 406 SER cc_start: 0.8081 (t) cc_final: 0.7721 (p) REVERT: E 389 GLU cc_start: 0.6871 (tt0) cc_final: 0.6525 (tp30) REVERT: E 392 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6656 (mm-30) REVERT: E 414 TRP cc_start: 0.7307 (m-90) cc_final: 0.6221 (m-90) REVERT: F 243 ASP cc_start: 0.7239 (m-30) cc_final: 0.6928 (t0) REVERT: F 399 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.6572 (tp40) REVERT: F 401 ILE cc_start: 0.6394 (mm) cc_final: 0.5888 (mm) REVERT: F 418 LEU cc_start: 0.6315 (OUTLIER) cc_final: 0.5935 (tp) REVERT: H 36 ARG cc_start: 0.4225 (ttm170) cc_final: 0.3182 (ttp80) REVERT: H 80 GLU cc_start: 0.7852 (mm-30) cc_final: 0.6587 (mp0) REVERT: H 158 GLU cc_start: 0.3273 (OUTLIER) cc_final: 0.2999 (pm20) REVERT: H 159 TRP cc_start: 0.3703 (t-100) cc_final: 0.3244 (t-100) REVERT: H 190 LYS cc_start: 0.6761 (pttt) cc_final: 0.6485 (pptt) REVERT: H 244 ASN cc_start: 0.6781 (m-40) cc_final: 0.6164 (t0) REVERT: H 281 MET cc_start: 0.7645 (mmt) cc_final: 0.7238 (mmm) REVERT: H 292 MET cc_start: 0.8302 (tpt) cc_final: 0.8076 (tpt) REVERT: H 295 ASP cc_start: 0.6357 (p0) cc_final: 0.5714 (p0) outliers start: 69 outliers final: 41 residues processed: 378 average time/residue: 0.3578 time to fit residues: 210.8632 Evaluate side-chains 343 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 297 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP 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 201 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 113 ILE 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 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 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 310 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 GLU 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 46 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 200 ASN 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 418 LEU Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 260 PHE 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 45 optimal weight: 8.9990 chunk 246 optimal weight: 0.9980 chunk 229 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 273 optimal weight: 6.9990 chunk 253 optimal weight: 4.9990 chunk 218 optimal weight: 8.9990 chunk 191 optimal weight: 0.8980 chunk 206 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.145867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.120949 restraints weight = 39919.159| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.19 r_work: 0.3386 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24197 Z= 0.146 Angle : 0.558 9.092 32807 Z= 0.294 Chirality : 0.042 0.212 3647 Planarity : 0.003 0.038 4071 Dihedral : 10.471 159.653 3406 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.54 % Allowed : 16.73 % Favored : 80.74 % 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: 0.13 (0.16), residues: 2898 helix: 1.30 (0.14), residues: 1459 sheet: -0.44 (0.26), residues: 403 loop : -1.44 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 428 HIS 0.006 0.001 HIS H 274 PHE 0.017 0.002 PHE H 81 TYR 0.030 0.001 TYR H 86 ARG 0.004 0.000 ARG F 340 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 1158) hydrogen bonds : angle 4.70160 ( 3303) covalent geometry : bond 0.00338 (24197) covalent geometry : angle 0.55820 (32807) *********************** 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 371 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 307 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7542 (mttm) cc_final: 0.7253 (ttmm) REVERT: A 74 LYS cc_start: 0.6999 (mmmm) cc_final: 0.6383 (mtpt) REVERT: A 76 LEU cc_start: 0.7877 (tp) cc_final: 0.7612 (mt) REVERT: B 306 THR cc_start: 0.8374 (p) cc_final: 0.7988 (m) REVERT: C 113 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8347 (mp) REVERT: D 95 GLU cc_start: 0.8304 (tp30) cc_final: 0.8007 (mm-30) REVERT: D 103 MET cc_start: 0.7233 (mmm) cc_final: 0.6941 (mtp) REVERT: D 112 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7158 (tm-30) REVERT: D 406 SER cc_start: 0.8166 (t) cc_final: 0.7728 (p) REVERT: E 371 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7287 (tp) REVERT: E 389 GLU cc_start: 0.6901 (tt0) cc_final: 0.6527 (tp30) REVERT: E 392 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6727 (mm-30) REVERT: E 414 TRP cc_start: 0.7361 (m-90) cc_final: 0.6244 (m-90) REVERT: F 181 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7204 (ttmm) REVERT: F 243 ASP cc_start: 0.7215 (m-30) cc_final: 0.6911 (t0) REVERT: F 247 ASP cc_start: 0.6562 (m-30) cc_final: 0.6332 (m-30) REVERT: F 399 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6664 (tp40) REVERT: F 418 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.6013 (tp) REVERT: H 36 ARG cc_start: 0.4357 (ttm170) cc_final: 0.3287 (ttp80) REVERT: H 80 GLU cc_start: 0.7867 (mm-30) cc_final: 0.6636 (mp0) REVERT: H 158 GLU cc_start: 0.3248 (OUTLIER) cc_final: 0.2954 (pm20) REVERT: H 159 TRP cc_start: 0.3380 (t-100) cc_final: 0.3009 (t-100) REVERT: H 244 ASN cc_start: 0.6769 (m-40) cc_final: 0.6092 (t0) REVERT: H 252 GLN cc_start: 0.4429 (OUTLIER) cc_final: 0.3781 (tm-30) REVERT: H 281 MET cc_start: 0.7712 (mmt) cc_final: 0.7327 (mmm) REVERT: H 292 MET cc_start: 0.8368 (tpt) cc_final: 0.8098 (tpt) REVERT: H 295 ASP cc_start: 0.6499 (p0) cc_final: 0.5917 (p0) REVERT: H 322 MET cc_start: 0.8271 (mtp) cc_final: 0.8067 (mtp) outliers start: 64 outliers final: 42 residues processed: 355 average time/residue: 0.3626 time to fit residues: 201.1813 Evaluate side-chains 337 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 287 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP 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 200 ASN Chi-restraints excluded: chain B residue 201 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 113 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 142 LEU 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 56 LEU 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 310 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 201 VAL 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 418 LEU Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 285 VAL 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 100 optimal weight: 0.9990 chunk 189 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 9 optimal weight: 0.4980 chunk 106 optimal weight: 7.9990 chunk 282 optimal weight: 0.0020 chunk 271 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 145 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 overall best weight: 2.8994 ------------------------------------------------------------------------------- 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** F 200 ASN F 219 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.145094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.120237 restraints weight = 39693.727| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.16 r_work: 0.3377 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24197 Z= 0.164 Angle : 0.577 9.472 32807 Z= 0.304 Chirality : 0.043 0.218 3647 Planarity : 0.004 0.036 4071 Dihedral : 10.573 160.290 3406 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.89 % Allowed : 16.69 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2898 helix: 1.23 (0.14), residues: 1456 sheet: -0.49 (0.26), residues: 400 loop : -1.45 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 162 HIS 0.004 0.001 HIS E 8 PHE 0.018 0.002 PHE H 81 TYR 0.027 0.001 TYR H 86 ARG 0.005 0.000 ARG F 340 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 1158) hydrogen bonds : angle 4.74401 ( 3303) covalent geometry : bond 0.00383 (24197) covalent geometry : angle 0.57672 (32807) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 291 time to evaluate : 4.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8086 (mp0) cc_final: 0.7826 (mp0) REVERT: A 38 LYS cc_start: 0.7584 (mttm) cc_final: 0.7289 (ttmm) REVERT: A 291 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.6960 (ttm-80) REVERT: A 355 GLN cc_start: 0.7426 (tp40) cc_final: 0.6349 (mm-40) REVERT: B 306 THR cc_start: 0.8493 (p) cc_final: 0.8100 (m) REVERT: C 113 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8297 (mp) REVERT: C 175 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8013 (tttm) REVERT: D 95 GLU cc_start: 0.8383 (tp30) cc_final: 0.8130 (mm-30) REVERT: D 103 MET cc_start: 0.7431 (mmm) cc_final: 0.7123 (mtp) REVERT: D 112 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7421 (tm-30) REVERT: E 23 MET cc_start: 0.8181 (mmp) cc_final: 0.7919 (mmt) REVERT: E 389 GLU cc_start: 0.7072 (tt0) cc_final: 0.6505 (tp30) REVERT: E 392 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6862 (mm-30) REVERT: E 414 TRP cc_start: 0.7473 (m-90) cc_final: 0.6309 (m-90) REVERT: F 23 MET cc_start: 0.8324 (mmt) cc_final: 0.8101 (mmt) REVERT: F 181 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7299 (ttmm) REVERT: F 243 ASP cc_start: 0.7432 (m-30) cc_final: 0.7085 (t0) REVERT: F 247 ASP cc_start: 0.6752 (m-30) cc_final: 0.6534 (m-30) REVERT: F 399 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.6716 (tp40) REVERT: F 418 LEU cc_start: 0.6427 (OUTLIER) cc_final: 0.5945 (tp) REVERT: H 36 ARG cc_start: 0.4367 (ttm170) cc_final: 0.3278 (ttp80) REVERT: H 80 GLU cc_start: 0.7784 (mm-30) cc_final: 0.6610 (mp0) REVERT: H 158 GLU cc_start: 0.3407 (OUTLIER) cc_final: 0.3062 (pm20) REVERT: H 244 ASN cc_start: 0.6848 (m-40) cc_final: 0.6173 (t0) REVERT: H 281 MET cc_start: 0.7844 (mmt) cc_final: 0.7440 (mmm) REVERT: H 295 ASP cc_start: 0.6632 (p0) cc_final: 0.6074 (p0) outliers start: 73 outliers final: 53 residues processed: 348 average time/residue: 0.4141 time to fit residues: 226.7950 Evaluate side-chains 343 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 282 time to evaluate : 2.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 200 ASN 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 113 ILE 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 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 56 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 50 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 GLU 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 8 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 200 ASN 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 418 LEU Chi-restraints excluded: chain H residue 158 GLU 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 191 optimal weight: 0.7980 chunk 268 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 243 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 ASN ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 355 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.144981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.120182 restraints weight = 39521.372| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.15 r_work: 0.3371 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24197 Z= 0.159 Angle : 0.577 10.510 32807 Z= 0.303 Chirality : 0.043 0.243 3647 Planarity : 0.004 0.036 4071 Dihedral : 10.619 160.880 3406 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.85 % Allowed : 16.77 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.16), residues: 2898 helix: 1.20 (0.14), residues: 1456 sheet: -0.52 (0.26), residues: 406 loop : -1.45 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 162 HIS 0.005 0.001 HIS H 274 PHE 0.016 0.002 PHE H 81 TYR 0.025 0.001 TYR H 86 ARG 0.005 0.000 ARG F 340 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 1158) hydrogen bonds : angle 4.75103 ( 3303) covalent geometry : bond 0.00372 (24197) covalent geometry : angle 0.57664 (32807) *********************** 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 365 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 293 time to evaluate : 2.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7722 (mp0) cc_final: 0.7513 (mp0) REVERT: A 38 LYS cc_start: 0.7578 (mttm) cc_final: 0.7200 (ttmm) REVERT: A 243 ASP cc_start: 0.8093 (m-30) cc_final: 0.7685 (m-30) REVERT: A 291 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.6851 (ttm-80) REVERT: B 306 THR cc_start: 0.8405 (p) cc_final: 0.8006 (m) REVERT: C 113 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8280 (mp) REVERT: C 175 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7892 (tptt) REVERT: D 95 GLU cc_start: 0.8176 (tp30) cc_final: 0.7946 (mm-30) REVERT: D 103 MET cc_start: 0.7253 (mmm) cc_final: 0.6980 (mtp) REVERT: D 112 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7138 (tm-30) REVERT: D 134 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7492 (mt) REVERT: E 23 MET cc_start: 0.8062 (mmp) cc_final: 0.7789 (mmt) REVERT: E 320 ARG cc_start: 0.5960 (ptt180) cc_final: 0.5552 (ttp80) REVERT: E 392 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6801 (mm-30) REVERT: E 414 TRP cc_start: 0.7380 (m-90) cc_final: 0.6257 (m-90) REVERT: F 23 MET cc_start: 0.8267 (mmt) cc_final: 0.8044 (mmt) REVERT: F 181 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7293 (ttmm) REVERT: F 243 ASP cc_start: 0.7198 (m-30) cc_final: 0.6956 (t0) REVERT: F 399 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6687 (tp40) REVERT: F 418 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.5904 (tp) REVERT: H 36 ARG cc_start: 0.4333 (ttm170) cc_final: 0.3273 (ttp80) REVERT: H 80 GLU cc_start: 0.7822 (mm-30) cc_final: 0.6649 (mp0) REVERT: H 158 GLU cc_start: 0.3440 (OUTLIER) cc_final: 0.3164 (pm20) REVERT: H 244 ASN cc_start: 0.6794 (m-40) cc_final: 0.6140 (t0) REVERT: H 281 MET cc_start: 0.7748 (mmt) cc_final: 0.7389 (mmm) REVERT: H 295 ASP cc_start: 0.6454 (p0) cc_final: 0.5863 (p0) outliers start: 72 outliers final: 55 residues processed: 349 average time/residue: 0.3405 time to fit residues: 187.1914 Evaluate side-chains 347 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 283 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 113 ILE 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 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 56 LEU 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 50 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 163 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 8 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 90 LEU 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 418 LEU Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 158 GLU 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 314 THR 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 146 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 221 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 chunk 251 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS B 62 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.146576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.121952 restraints weight = 39705.945| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.12 r_work: 0.3404 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24197 Z= 0.115 Angle : 0.547 12.852 32807 Z= 0.287 Chirality : 0.042 0.264 3647 Planarity : 0.003 0.037 4071 Dihedral : 10.454 161.009 3406 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.90 % Allowed : 17.84 % 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: 0.22 (0.16), residues: 2898 helix: 1.39 (0.14), residues: 1459 sheet: -0.46 (0.27), residues: 407 loop : -1.41 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 154 HIS 0.006 0.001 HIS H 274 PHE 0.011 0.001 PHE B 417 TYR 0.024 0.001 TYR H 86 ARG 0.006 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.03215 ( 1158) hydrogen bonds : angle 4.62008 ( 3303) covalent geometry : bond 0.00256 (24197) covalent geometry : angle 0.54745 (32807) ********************** 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 343 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 295 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7725 (mp0) cc_final: 0.7472 (mp0) REVERT: A 38 LYS cc_start: 0.7570 (mttm) cc_final: 0.7224 (ttmm) REVERT: A 76 LEU cc_start: 0.7832 (tp) cc_final: 0.7520 (mt) REVERT: A 243 ASP cc_start: 0.7942 (m-30) cc_final: 0.7617 (m-30) REVERT: B 306 THR cc_start: 0.8313 (p) cc_final: 0.7905 (m) REVERT: C 113 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8252 (mp) REVERT: C 142 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7160 (mt) REVERT: D 95 GLU cc_start: 0.8140 (tp30) cc_final: 0.7933 (mm-30) REVERT: D 103 MET cc_start: 0.7278 (mmm) cc_final: 0.6991 (mtp) REVERT: D 112 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: D 134 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7421 (mt) REVERT: E 23 MET cc_start: 0.8064 (mmp) cc_final: 0.7801 (mmt) REVERT: E 320 ARG cc_start: 0.5909 (ptt180) cc_final: 0.5483 (ttp80) REVERT: E 392 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6750 (mm-30) REVERT: E 413 LYS cc_start: 0.7619 (tppt) cc_final: 0.6948 (tptp) REVERT: E 414 TRP cc_start: 0.7386 (m-90) cc_final: 0.6277 (m-90) REVERT: F 243 ASP cc_start: 0.7177 (m-30) cc_final: 0.6934 (t0) REVERT: F 399 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.6755 (tp40) REVERT: F 418 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.5957 (tp) REVERT: H 36 ARG cc_start: 0.4229 (ttm170) cc_final: 0.3204 (ttp80) REVERT: H 80 GLU cc_start: 0.7734 (mm-30) cc_final: 0.6571 (mp0) REVERT: H 158 GLU cc_start: 0.3628 (OUTLIER) cc_final: 0.3164 (pm20) REVERT: H 244 ASN cc_start: 0.6763 (m-40) cc_final: 0.6153 (t0) REVERT: H 274 HIS cc_start: 0.6959 (t-170) cc_final: 0.6601 (t-170) REVERT: H 281 MET cc_start: 0.7664 (mmt) cc_final: 0.7290 (mmm) REVERT: H 292 MET cc_start: 0.8332 (tpt) cc_final: 0.8041 (tpt) REVERT: H 295 ASP cc_start: 0.6466 (p0) cc_final: 0.5830 (p0) outliers start: 48 outliers final: 39 residues processed: 331 average time/residue: 0.3464 time to fit residues: 179.6273 Evaluate side-chains 330 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 284 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 227 GLU 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 200 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 142 LEU 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 404 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 56 LEU 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 50 VAL Chi-restraints excluded: chain E residue 163 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 46 GLU Chi-restraints excluded: chain F residue 90 LEU 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 418 LEU Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 314 THR 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 9 optimal weight: 0.9980 chunk 213 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 274 optimal weight: 0.0040 chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 HIS ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 ASN B 399 GLN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 200 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.145108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.120356 restraints weight = 39601.993| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.13 r_work: 0.3380 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24197 Z= 0.154 Angle : 0.574 12.172 32807 Z= 0.301 Chirality : 0.043 0.206 3647 Planarity : 0.004 0.036 4071 Dihedral : 10.561 161.515 3406 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.46 % Allowed : 17.48 % Favored : 80.06 % 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: 0.15 (0.16), residues: 2898 helix: 1.32 (0.14), residues: 1450 sheet: -0.46 (0.27), residues: 393 loop : -1.38 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 162 HIS 0.010 0.001 HIS B 87 PHE 0.015 0.002 PHE D 37 TYR 0.024 0.001 TYR H 86 ARG 0.007 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 1158) hydrogen bonds : angle 4.67940 ( 3303) covalent geometry : bond 0.00361 (24197) covalent geometry : angle 0.57447 (32807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12202.66 seconds wall clock time: 215 minutes 24.18 seconds (12924.18 seconds total)