Starting phenix.real_space_refine on Sun Sep 29 21:52:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw6_27751/09_2024/8dw6_27751.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw6_27751/09_2024/8dw6_27751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw6_27751/09_2024/8dw6_27751.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw6_27751/09_2024/8dw6_27751.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw6_27751/09_2024/8dw6_27751.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw6_27751/09_2024/8dw6_27751.cif" } resolution = 3.5 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 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 7 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23694 Number of models: 1 Model: "" Number of chains: 15 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} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 21079 SG CYS H 37 47.334 75.170 71.878 1.00334.75 S ATOM 21099 SG CYS H 40 46.656 75.858 68.175 1.00325.70 S ATOM 21298 SG CYS H 65 46.615 72.370 69.711 1.00349.75 S ATOM 21324 SG CYS H 68 49.914 74.147 69.241 1.00342.48 S Time building chain proxies: 14.57, per 1000 atoms: 0.61 Number of scatterers: 23694 At special positions: 0 Unit cell: (134.964, 130.824, 141.588, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 132 16.00 P 32 15.00 Mg 5 11.99 O 4586 8.00 N 3943 7.00 C 14995 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.45 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 401 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 65 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 37 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 68 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 40 " Number of angles added : 6 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5530 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 20 sheets defined 53.8% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 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: 3.727A pdb=" N ASP A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 269 removed outlier: 3.551A pdb=" N LYS A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 301 Processing helix chain 'A' and resid 328 through 347 Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 390 through 396 Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 12 through 20 Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 24 through 28 removed outlier: 3.542A pdb=" N TYR B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE B 28 " --> pdb=" O SER B 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 24 through 28' Processing helix chain 'B' and resid 31 through 48 Processing helix chain 'B' and resid 52 through 58 Processing helix chain 'B' and resid 66 through 80 Processing helix chain 'B' and resid 88 through 119 removed outlier: 3.530A 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: 3.511A 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: 3.569A pdb=" N ASP B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 Processing helix chain 'B' and resid 255 through 269 removed outlier: 3.842A pdb=" N LYS B 269 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 Processing helix chain 'B' and resid 327 through 347 removed outlier: 3.590A 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: 3.629A 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: 3.639A pdb=" N ILE C 315 " --> pdb=" O TYR C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 347 Processing helix chain 'C' and resid 357 through 361 removed outlier: 3.653A pdb=" N TRP C 361 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 375 through 381 removed outlier: 3.957A pdb=" N ALA C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 395 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 12 through 20 removed outlier: 3.607A pdb=" N LYS D 18 " --> pdb=" O ALA D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.503A 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: 3.594A pdb=" N LYS E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 28 removed outlier: 3.560A pdb=" N PHE E 28 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 47 Processing helix chain 'E' and resid 52 through 63 Processing helix chain 'E' and resid 66 through 79 Processing helix chain 'E' and resid 86 through 118 Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 133 through 141 removed outlier: 3.534A pdb=" N ALA E 141 " --> pdb=" O ILE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 166 Processing helix chain 'E' and resid 176 through 184 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 229 through 243 Processing helix chain 'E' and resid 246 through 251 removed outlier: 3.586A 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: 3.759A 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: 3.661A pdb=" N LEU F 142 " --> pdb=" O MET F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 167 Processing helix chain 'F' and resid 176 through 184 Processing helix chain 'F' and resid 202 through 216 Processing helix chain 'F' and resid 229 through 243 Processing helix chain 'F' and resid 245 through 252 Processing helix chain 'F' and resid 255 through 269 removed outlier: 3.706A pdb=" N LYS F 269 " --> pdb=" O LYS F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 302 Processing helix chain 'F' and resid 327 through 347 Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'H' and resid 4 through 17 Processing helix chain 'H' and resid 74 through 82 Processing helix chain 'H' and resid 82 through 97 removed outlier: 3.694A pdb=" N GLU H 88 " --> pdb=" O ASP H 84 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG H 94 " --> pdb=" O ILE H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 144 Processing helix chain 'H' and resid 147 through 152 Processing helix chain 'H' and resid 158 through 167 Processing helix chain 'H' and resid 221 through 225 Processing helix chain 'H' and resid 235 through 241 removed outlier: 3.805A pdb=" N PHE H 241 " --> pdb=" O ILE H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 274 through 287 Processing helix chain 'H' and resid 303 through 310 Processing helix chain 'H' and resid 314 through 324 Processing helix chain 'H' and resid 329 through 340 removed outlier: 3.549A pdb=" N LYS H 338 " --> pdb=" O MET H 334 " (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: 6.222A 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: 3.626A pdb=" N PHE B 383 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS B 405 " --> pdb=" O MET B 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 427 through 429 removed outlier: 6.512A pdb=" N MET A 384 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU A 192 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N LEU A 385 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 194 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL A 387 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N MET A 196 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR A 191 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 7.742A 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: 5.955A pdb=" N LEU A 195 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA A 353 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU A 222 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A 221 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LYS A 278 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.337A 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: 6.243A pdb=" N TYR C 223 " --> pdb=" O LYS C 278 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASN C 220 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE C 309 " --> pdb=" O ASN C 220 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU C 222 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.934A 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: 6.511A pdb=" N VAL D 221 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 7.747A 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: 7.490A pdb=" N ILE D 309 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU D 222 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 171 through 172 Processing sheet with id=AA9, first strand: chain 'C' and resid 398 through 399 Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 153 removed outlier: 3.876A pdb=" N ALA E 353 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA E 354 " --> pdb=" O LEU E 195 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU E 192 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU E 385 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 6.324A 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: 5.930A pdb=" N LEU D 195 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 6.391A 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: 7.511A pdb=" N VAL D 387 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N MET D 196 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N MET D 384 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 171 through 172 Processing sheet with id=AB5, first strand: chain 'F' and resid 349 through 352 removed outlier: 3.708A pdb=" N PHE F 383 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 275 through 279 removed outlier: 6.324A 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 32 through 35 Processing sheet with id=AB9, first strand: chain 'H' and resid 124 through 126 removed outlier: 5.826A pdb=" N LEU H 180 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY H 196 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE H 182 " --> pdb=" O PHE H 194 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE H 194 " --> pdb=" O ILE H 182 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE H 184 " --> pdb=" O GLU H 192 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 219 through 220 removed outlier: 4.026A pdb=" N ILE H 248 " --> pdb=" O LEU H 233 " (cutoff:3.500A) removed outlier: 6.062A 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 1155 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: 8.84 Time building geometry restraints manager: 6.45 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: 7554 1.35 - 1.50: 6439 1.50 - 1.65: 9975 1.65 - 1.80: 113 1.80 - 1.95: 116 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 1.360 -0.039 1.00e-02 1.00e+04 1.54e+01 bond pdb=" CE1 HIS B 152 " pdb=" NE2 HIS B 152 " ideal model delta sigma weight residual 1.321 1.357 -0.036 1.00e-02 1.00e+04 1.27e+01 bond pdb=" N VAL E 19 " pdb=" CA VAL E 19 " ideal model delta sigma weight residual 1.452 1.492 -0.039 1.18e-02 7.18e+03 1.12e+01 bond pdb=" N TRP E 20 " pdb=" CA TRP E 20 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.04e-02 9.25e+03 1.02e+01 bond pdb=" N TRP D 20 " pdb=" CA TRP D 20 " ideal model delta sigma weight residual 1.462 1.492 -0.030 9.50e-03 1.11e+04 1.00e+01 ... (remaining 24192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 32380 2.49 - 4.99: 402 4.99 - 7.48: 20 7.48 - 9.97: 4 9.97 - 12.46: 1 Bond angle restraints: 32807 Sorted by residual: angle pdb=" O SER B 63 " pdb=" C SER B 63 " pdb=" N SER B 64 " ideal model delta sigma weight residual 120.83 124.40 -3.57 7.40e-01 1.83e+00 2.32e+01 angle pdb=" PB AGS C 501 " pdb=" O3B AGS C 501 " pdb=" PG AGS C 501 " ideal model delta sigma weight residual 120.12 132.58 -12.46 3.00e+00 1.11e-01 1.73e+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 1.54e+01 angle pdb=" C GLY F 151 " pdb=" N HIS F 152 " pdb=" CA HIS F 152 " ideal model delta sigma weight residual 122.30 117.05 5.25 1.35e+00 5.49e-01 1.51e+01 angle pdb=" N ASP F 382 " pdb=" CA ASP F 382 " pdb=" C ASP F 382 " ideal model delta sigma weight residual 114.31 109.39 4.92 1.29e+00 6.01e-01 1.46e+01 ... (remaining 32802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 14426 35.65 - 71.31: 194 71.31 - 106.96: 6 106.96 - 142.62: 1 142.62 - 178.27: 4 Dihedral angle restraints: 14631 sinusoidal: 6069 harmonic: 8562 Sorted by residual: dihedral pdb=" O1B AGS E 501 " pdb=" O3B AGS E 501 " pdb=" PB AGS E 501 " pdb=" PG AGS E 501 " ideal model delta sinusoidal sigma weight residual 68.91 -112.82 -178.27 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A AGS F 501 " pdb=" O3A AGS F 501 " pdb=" PA AGS F 501 " pdb=" PB AGS F 501 " ideal model delta sinusoidal sigma weight residual -67.73 106.44 -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 -88.60 157.51 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 14628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2674 0.043 - 0.087: 647 0.087 - 0.130: 280 0.130 - 0.173: 32 0.173 - 0.217: 14 Chirality restraints: 3647 Sorted by residual: 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 1.17e+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 1.16e+00 chirality pdb=" CA VAL D 310 " pdb=" N VAL D 310 " pdb=" C VAL D 310 " pdb=" CB VAL D 310 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 3644 not shown) Planarity restraints: 4071 Sorted by residual: 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 2.26e-02 5.11e+00 pdb=" C SER B 145 " 0.039 2.00e-02 2.50e+03 pdb=" O SER B 145 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE B 146 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 402 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.39e+00 pdb=" C LYS A 402 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS A 402 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN A 403 " 0.012 2.00e-02 2.50e+03 ... (remaining 4068 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.46: 130 2.46 - 3.07: 16732 3.07 - 3.68: 36697 3.68 - 4.29: 55693 4.29 - 4.90: 91037 Nonbonded interactions: 200289 Sorted by model distance: nonbonded pdb=" O1B AGS C 501 " pdb="MG MG C 502 " model vdw 1.856 2.170 nonbonded pdb=" O3B AGS B 501 " pdb="MG MG B 502 " model vdw 1.972 2.170 nonbonded pdb=" OE2 GLU B 227 " pdb="MG MG B 502 " model vdw 1.979 2.170 nonbonded pdb=" O2G AGS E 501 " pdb="MG MG E 502 " model vdw 1.985 2.170 nonbonded pdb=" O2B AGS F 501 " pdb="MG MG F 502 " model vdw 1.993 2.170 ... (remaining 200284 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 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: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 57.500 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.140 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6040 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 0.049 24197 Z= 0.285 Angle : 0.647 12.463 32807 Z= 0.420 Chirality : 0.046 0.217 3647 Planarity : 0.004 0.075 4071 Dihedral : 12.246 178.273 9101 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.26 % Allowed : 6.70 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.45 (0.16), residues: 2898 helix: 1.44 (0.14), residues: 1431 sheet: -0.28 (0.28), residues: 391 loop : -1.00 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 351 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 0.003 0.000 ARG H 143 *********************** 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 859 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 802 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 PHE cc_start: 0.6112 (m-80) cc_final: 0.5694 (m-80) REVERT: A 12 ASP cc_start: 0.6533 (t0) cc_final: 0.5717 (m-30) REVERT: A 100 GLN cc_start: 0.7097 (mt0) cc_final: 0.6601 (tm-30) REVERT: A 121 PRO cc_start: 0.5631 (Cg_exo) cc_final: 0.5401 (Cg_endo) REVERT: A 196 MET cc_start: 0.6497 (mmt) cc_final: 0.5185 (ptm) REVERT: A 291 ARG cc_start: 0.5841 (mtm-85) cc_final: 0.5410 (mtt180) REVERT: A 337 GLU cc_start: 0.5584 (mt-10) cc_final: 0.5099 (mt-10) REVERT: A 418 LEU cc_start: 0.5957 (mp) cc_final: 0.5704 (mt) REVERT: B 7 SER cc_start: 0.8367 (m) cc_final: 0.8119 (p) REVERT: B 41 LYS cc_start: 0.7079 (ttpt) cc_final: 0.6744 (tttt) REVERT: B 188 GLU cc_start: 0.6146 (mt-10) cc_final: 0.5868 (mt-10) REVERT: B 196 MET cc_start: 0.4982 (mtm) cc_final: 0.4442 (mtp) REVERT: B 228 MET cc_start: 0.5909 (mtm) cc_final: 0.5290 (mtp) REVERT: B 288 ASN cc_start: 0.6941 (m-40) cc_final: 0.6733 (m110) REVERT: B 296 GLU cc_start: 0.5907 (tt0) cc_final: 0.5562 (tt0) REVERT: B 320 ARG cc_start: 0.5952 (mtm180) cc_final: 0.5727 (mtm-85) REVERT: B 384 MET cc_start: 0.7524 (mtt) cc_final: 0.7211 (mtp) REVERT: C 19 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.8205 (m) REVERT: C 39 LEU cc_start: 0.8084 (mt) cc_final: 0.7792 (mt) REVERT: C 47 TYR cc_start: 0.4941 (m-80) cc_final: 0.4543 (m-80) REVERT: C 168 LYS cc_start: 0.6696 (mptt) cc_final: 0.6374 (mmmt) REVERT: C 228 MET cc_start: 0.6258 (mtm) cc_final: 0.5887 (mtt) REVERT: C 295 ASN cc_start: 0.7874 (t0) cc_final: 0.7670 (t0) REVERT: D 1 MET cc_start: 0.6411 (ptm) cc_final: 0.5957 (ptm) REVERT: D 3 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6465 (tt0) REVERT: D 41 LYS cc_start: 0.6231 (ttpp) cc_final: 0.5667 (pttp) REVERT: D 128 MET cc_start: 0.6819 (tpp) cc_final: 0.6249 (ttm) REVERT: D 130 ASP cc_start: 0.5184 (t0) cc_final: 0.4954 (t0) REVERT: D 155 MET cc_start: 0.6181 (tpt) cc_final: 0.5947 (tpt) REVERT: D 166 MET cc_start: 0.3289 (pmm) cc_final: 0.3031 (mtp) REVERT: D 244 VAL cc_start: 0.7519 (p) cc_final: 0.7304 (t) REVERT: D 303 PHE cc_start: 0.6660 (t80) cc_final: 0.6222 (t80) REVERT: D 304 VAL cc_start: 0.6499 (t) cc_final: 0.6291 (p) REVERT: D 398 GLN cc_start: 0.5966 (mt0) cc_final: 0.5602 (pt0) REVERT: E 16 PHE cc_start: 0.6732 (t80) cc_final: 0.6511 (t80) REVERT: E 32 PRO cc_start: 0.5070 (Cg_endo) cc_final: 0.4827 (Cg_exo) REVERT: E 43 HIS cc_start: 0.4527 (t-90) cc_final: 0.4192 (t70) REVERT: E 115 THR cc_start: 0.7155 (m) cc_final: 0.6909 (t) REVERT: E 243 ASP cc_start: 0.6967 (t0) cc_final: 0.6743 (t0) REVERT: E 312 TYR cc_start: 0.1230 (t80) cc_final: 0.1013 (t80) REVERT: E 380 THR cc_start: 0.4910 (OUTLIER) cc_final: 0.4625 (m) REVERT: E 427 LYS cc_start: 0.6165 (ttpp) cc_final: 0.5784 (ptmt) REVERT: F 11 PHE cc_start: 0.7538 (m-80) cc_final: 0.6710 (m-80) REVERT: F 75 THR cc_start: 0.6246 (m) cc_final: 0.5801 (t) REVERT: F 139 ARG cc_start: 0.5517 (ttm-80) cc_final: 0.5098 (mtt-85) REVERT: F 274 ARG cc_start: 0.4448 (mtm-85) cc_final: 0.4054 (mtt90) REVERT: F 370 ASP cc_start: 0.4897 (m-30) cc_final: 0.4588 (m-30) REVERT: F 384 MET cc_start: 0.6003 (mtp) cc_final: 0.5550 (ttm) REVERT: F 423 LYS cc_start: 0.6348 (mttm) cc_final: 0.5189 (pttm) REVERT: H 18 HIS cc_start: 0.3467 (OUTLIER) cc_final: 0.3031 (p-80) REVERT: H 86 TYR cc_start: 0.4931 (t80) cc_final: 0.4646 (t80) REVERT: H 143 ARG cc_start: 0.4873 (mmt180) cc_final: 0.4628 (tpp80) REVERT: H 145 ILE cc_start: 0.5506 (mm) cc_final: 0.5248 (mm) REVERT: H 161 LYS cc_start: 0.4016 (tmmt) cc_final: 0.3695 (mmtt) REVERT: H 180 LEU cc_start: 0.6327 (mt) cc_final: 0.6053 (mt) REVERT: H 276 ASP cc_start: 0.6957 (OUTLIER) cc_final: 0.6607 (m-30) REVERT: H 279 LYS cc_start: 0.7912 (tttt) cc_final: 0.7682 (ttpp) REVERT: H 299 TRP cc_start: 0.7266 (m-90) cc_final: 0.6969 (m-90) outliers start: 57 outliers final: 7 residues processed: 839 average time/residue: 0.3946 time to fit residues: 488.0223 Evaluate side-chains 432 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 421 time to evaluate : 2.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 276 ASP Chi-restraints excluded: chain H residue 282 THR Chi-restraints excluded: chain H residue 295 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 7.9990 chunk 220 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 228 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 264 optimal weight: 20.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 HIS A 116 ASN A 167 ASN A 327 ASN A 425 ASN B 8 HIS B 100 GLN B 200 ASN B 403 GLN C 114 GLN C 140 GLN D 35 ASN D 99 GLN D 116 ASN D 422 GLN E 87 HIS E 403 GLN E 412 ASN ** E 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN F 302 ASN H 64 HIS H 317 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 24197 Z= 0.188 Angle : 0.588 8.688 32807 Z= 0.312 Chirality : 0.043 0.343 3647 Planarity : 0.004 0.047 4071 Dihedral : 10.578 172.394 3414 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.94 % Allowed : 11.97 % Favored : 86.09 % 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: 0.41 (0.16), residues: 2898 helix: 1.40 (0.14), residues: 1461 sheet: -0.35 (0.27), residues: 392 loop : -1.05 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 150 HIS 0.008 0.001 HIS A 87 PHE 0.023 0.002 PHE A 28 TYR 0.023 0.002 TYR E 256 ARG 0.008 0.001 ARG H 126 *********************** 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 526 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 477 time to evaluate : 2.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.6140 (mmtm) cc_final: 0.5002 (ttpt) REVERT: A 100 GLN cc_start: 0.7051 (mt0) cc_final: 0.6616 (tm-30) REVERT: A 121 PRO cc_start: 0.5508 (Cg_exo) cc_final: 0.5291 (Cg_endo) REVERT: A 196 MET cc_start: 0.6436 (mmt) cc_final: 0.6219 (mmt) REVERT: A 203 LYS cc_start: 0.6316 (mttm) cc_final: 0.6019 (ptpp) REVERT: A 337 GLU cc_start: 0.5793 (mt-10) cc_final: 0.5558 (mt-10) REVERT: A 385 LEU cc_start: 0.6336 (mt) cc_final: 0.6022 (tp) REVERT: A 425 ASN cc_start: 0.3862 (t160) cc_final: 0.3574 (t0) REVERT: B 26 GLU cc_start: 0.6161 (pt0) cc_final: 0.5941 (mt-10) REVERT: B 296 GLU cc_start: 0.5992 (tt0) cc_final: 0.5596 (tt0) REVERT: B 418 LEU cc_start: 0.6506 (tp) cc_final: 0.5839 (tt) REVERT: C 39 LEU cc_start: 0.8028 (mt) cc_final: 0.7735 (mt) REVERT: C 168 LYS cc_start: 0.6651 (mptt) cc_final: 0.6348 (mmmt) REVERT: D 1 MET cc_start: 0.6518 (ptm) cc_final: 0.6087 (ptm) REVERT: D 3 GLU cc_start: 0.6793 (mt-10) cc_final: 0.6475 (tt0) REVERT: D 41 LYS cc_start: 0.6323 (ttpp) cc_final: 0.5731 (pttp) REVERT: D 128 MET cc_start: 0.6833 (tpp) cc_final: 0.6221 (ttm) REVERT: D 241 MET cc_start: 0.7264 (mmt) cc_final: 0.7032 (mmt) REVERT: D 303 PHE cc_start: 0.6632 (t80) cc_final: 0.6152 (t80) REVERT: E 32 PRO cc_start: 0.5203 (Cg_endo) cc_final: 0.4921 (Cg_exo) REVERT: E 43 HIS cc_start: 0.4594 (t-90) cc_final: 0.4151 (t-170) REVERT: E 76 LEU cc_start: 0.5786 (OUTLIER) cc_final: 0.5366 (mm) REVERT: E 115 THR cc_start: 0.7046 (m) cc_final: 0.6834 (t) REVERT: E 243 ASP cc_start: 0.6743 (t0) cc_final: 0.6510 (t0) REVERT: E 260 LYS cc_start: 0.4966 (mmmm) cc_final: 0.4298 (tttp) REVERT: E 427 LYS cc_start: 0.6355 (ttpp) cc_final: 0.5870 (ptmt) REVERT: F 120 PRO cc_start: 0.3725 (Cg_endo) cc_final: 0.3489 (Cg_exo) REVERT: F 265 LYS cc_start: 0.7017 (mmtm) cc_final: 0.6755 (mtmm) REVERT: F 274 ARG cc_start: 0.4595 (mtm-85) cc_final: 0.4180 (mtt90) REVERT: F 298 LYS cc_start: 0.6486 (mtmt) cc_final: 0.6008 (mppt) REVERT: F 333 LYS cc_start: 0.3923 (ttpp) cc_final: 0.3574 (ttpt) REVERT: F 337 GLU cc_start: 0.6000 (mm-30) cc_final: 0.5703 (mm-30) REVERT: F 384 MET cc_start: 0.6249 (mtp) cc_final: 0.5510 (ttm) REVERT: F 423 LYS cc_start: 0.6281 (mttm) cc_final: 0.5150 (pttm) REVERT: H 92 GLU cc_start: 0.5039 (tp30) cc_final: 0.4703 (tp30) REVERT: H 154 TRP cc_start: 0.4521 (m-90) cc_final: 0.4072 (m-90) REVERT: H 194 PHE cc_start: 0.4727 (p90) cc_final: 0.4517 (p90) REVERT: H 219 ILE cc_start: 0.5086 (pt) cc_final: 0.4736 (tt) REVERT: H 222 VAL cc_start: 0.6410 (OUTLIER) cc_final: 0.6117 (p) REVERT: H 271 GLU cc_start: 0.6235 (OUTLIER) cc_final: 0.5752 (mt-10) REVERT: H 276 ASP cc_start: 0.7025 (m-30) cc_final: 0.6766 (t0) REVERT: H 303 ASP cc_start: 0.4781 (p0) cc_final: 0.3690 (p0) REVERT: H 305 ASN cc_start: 0.6644 (t0) cc_final: 0.6241 (p0) REVERT: H 306 ASP cc_start: 0.6082 (m-30) cc_final: 0.5778 (m-30) REVERT: H 307 MET cc_start: 0.6377 (mtm) cc_final: 0.6103 (mtt) REVERT: H 308 ILE cc_start: 0.7704 (mt) cc_final: 0.7450 (pt) outliers start: 49 outliers final: 22 residues processed: 514 average time/residue: 0.3582 time to fit residues: 282.1704 Evaluate side-chains 390 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 365 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain H residue 13 TYR Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 271 GLU Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 219 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 264 optimal weight: 5.9990 chunk 285 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 262 optimal weight: 0.0010 chunk 90 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 overall best weight: 3.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN B 100 GLN B 200 ASN C 57 ASN C 100 GLN C 422 GLN ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN E 87 HIS F 403 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6358 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24197 Z= 0.269 Angle : 0.653 9.726 32807 Z= 0.346 Chirality : 0.045 0.292 3647 Planarity : 0.005 0.046 4071 Dihedral : 10.656 173.930 3399 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.17 % Allowed : 13.24 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 2898 helix: 1.00 (0.14), residues: 1461 sheet: -0.37 (0.27), residues: 392 loop : -1.17 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP F 428 HIS 0.006 0.002 HIS D 8 PHE 0.021 0.002 PHE C 174 TYR 0.019 0.002 TYR B 312 ARG 0.007 0.001 ARG D 236 *********************** 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 499 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 419 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6714 (t0) cc_final: 0.5963 (m-30) REVERT: A 38 LYS cc_start: 0.7545 (mmmm) cc_final: 0.7330 (mmmm) REVERT: A 100 GLN cc_start: 0.7439 (mt0) cc_final: 0.6824 (tm-30) REVERT: A 121 PRO cc_start: 0.5893 (Cg_exo) cc_final: 0.5677 (Cg_endo) REVERT: A 385 LEU cc_start: 0.6589 (mt) cc_final: 0.6194 (tp) REVERT: A 425 ASN cc_start: 0.3627 (t160) cc_final: 0.3365 (t0) REVERT: B 418 LEU cc_start: 0.6641 (tp) cc_final: 0.6057 (tt) REVERT: C 39 LEU cc_start: 0.8038 (mt) cc_final: 0.7754 (mt) REVERT: C 155 MET cc_start: 0.7184 (tpp) cc_final: 0.6873 (tpp) REVERT: D 1 MET cc_start: 0.6554 (ptm) cc_final: 0.6045 (ptm) REVERT: D 3 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6605 (tt0) REVERT: D 24 ASP cc_start: 0.6740 (OUTLIER) cc_final: 0.6520 (m-30) REVERT: D 41 LYS cc_start: 0.6672 (ttpp) cc_final: 0.6017 (pttp) REVERT: D 128 MET cc_start: 0.7119 (tpp) cc_final: 0.6398 (ttm) REVERT: D 159 GLU cc_start: 0.4914 (mm-30) cc_final: 0.4335 (mp0) REVERT: D 241 MET cc_start: 0.7292 (mmt) cc_final: 0.7052 (mmt) REVERT: D 263 MET cc_start: 0.5988 (mmt) cc_final: 0.5561 (tpp) REVERT: D 303 PHE cc_start: 0.6738 (t80) cc_final: 0.6327 (t80) REVERT: D 363 SER cc_start: 0.4776 (p) cc_final: 0.4505 (t) REVERT: E 32 PRO cc_start: 0.5259 (Cg_endo) cc_final: 0.5000 (Cg_exo) REVERT: E 76 LEU cc_start: 0.5794 (OUTLIER) cc_final: 0.5435 (mm) REVERT: E 331 THR cc_start: 0.6325 (m) cc_final: 0.5949 (t) REVERT: E 427 LYS cc_start: 0.6406 (ttpp) cc_final: 0.6097 (ptmt) REVERT: F 9 LEU cc_start: 0.6152 (mt) cc_final: 0.5760 (mp) REVERT: F 79 LYS cc_start: 0.6540 (mttm) cc_final: 0.6139 (ttmm) REVERT: F 139 ARG cc_start: 0.6010 (mtp-110) cc_final: 0.5773 (mtt-85) REVERT: F 248 ASP cc_start: 0.5283 (m-30) cc_final: 0.4946 (m-30) REVERT: F 263 MET cc_start: 0.6457 (mmm) cc_final: 0.6061 (tmm) REVERT: F 265 LYS cc_start: 0.7051 (mmtm) cc_final: 0.6656 (mmtp) REVERT: F 274 ARG cc_start: 0.4774 (mtm-85) cc_final: 0.4293 (mtt90) REVERT: F 298 LYS cc_start: 0.6429 (mtmt) cc_final: 0.5962 (mppt) REVERT: F 384 MET cc_start: 0.6328 (mtp) cc_final: 0.5948 (ttp) REVERT: F 423 LYS cc_start: 0.6458 (mttm) cc_final: 0.4813 (ptmm) REVERT: H 154 TRP cc_start: 0.4591 (m-90) cc_final: 0.4113 (m-90) REVERT: H 193 SER cc_start: 0.5933 (m) cc_final: 0.5392 (m) REVERT: H 194 PHE cc_start: 0.4686 (p90) cc_final: 0.4402 (p90) REVERT: H 242 ILE cc_start: 0.5126 (mm) cc_final: 0.4889 (mm) REVERT: H 276 ASP cc_start: 0.6905 (m-30) cc_final: 0.6650 (t0) REVERT: H 279 LYS cc_start: 0.7790 (ptmt) cc_final: 0.7444 (ptpt) REVERT: H 281 MET cc_start: 0.6518 (mtt) cc_final: 0.5847 (mmt) REVERT: H 294 TRP cc_start: 0.6455 (m100) cc_final: 0.6144 (m100) REVERT: H 303 ASP cc_start: 0.4534 (p0) cc_final: 0.3990 (p0) REVERT: H 307 MET cc_start: 0.6515 (mtm) cc_final: 0.6298 (ttm) outliers start: 80 outliers final: 41 residues processed: 484 average time/residue: 0.3608 time to fit residues: 273.5217 Evaluate side-chains 376 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 333 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 271 GLU Chi-restraints excluded: chain H residue 299 TRP Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 265 optimal weight: 10.0000 chunk 281 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 251 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN A 399 GLN B 100 GLN B 200 ASN B 399 GLN C 253 HIS ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 HIS E 412 ASN F 399 GLN H 71 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24197 Z= 0.274 Angle : 0.640 8.883 32807 Z= 0.343 Chirality : 0.045 0.308 3647 Planarity : 0.005 0.045 4071 Dihedral : 10.769 177.112 3399 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.84 % Allowed : 14.35 % Favored : 81.81 % 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 (0.15), residues: 2898 helix: 0.86 (0.14), residues: 1456 sheet: -0.63 (0.26), residues: 401 loop : -1.31 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP F 428 HIS 0.010 0.002 HIS E 43 PHE 0.019 0.002 PHE E 28 TYR 0.025 0.002 TYR D 165 ARG 0.009 0.001 ARG D 161 *********************** 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 484 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 387 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6893 (t0) cc_final: 0.6159 (m-30) REVERT: A 100 GLN cc_start: 0.7366 (mt0) cc_final: 0.6963 (tm-30) REVERT: A 121 PRO cc_start: 0.5828 (Cg_exo) cc_final: 0.5622 (Cg_endo) REVERT: A 380 THR cc_start: 0.7702 (p) cc_final: 0.7440 (t) REVERT: A 385 LEU cc_start: 0.6512 (mt) cc_final: 0.6165 (tp) REVERT: A 417 PHE cc_start: 0.3549 (t80) cc_final: 0.2904 (t80) REVERT: B 112 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6730 (tt0) REVERT: B 296 GLU cc_start: 0.6384 (tt0) cc_final: 0.6049 (tt0) REVERT: B 418 LEU cc_start: 0.6716 (tp) cc_final: 0.6034 (tt) REVERT: C 39 LEU cc_start: 0.8026 (mt) cc_final: 0.7810 (mt) REVERT: C 155 MET cc_start: 0.7275 (tpp) cc_final: 0.7051 (tpp) REVERT: C 371 ILE cc_start: 0.8095 (tp) cc_final: 0.7893 (tp) REVERT: D 1 MET cc_start: 0.6648 (ptm) cc_final: 0.6089 (ptm) REVERT: D 3 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6600 (tt0) REVERT: D 41 LYS cc_start: 0.6935 (ttpp) cc_final: 0.6288 (pttp) REVERT: D 134 ILE cc_start: 0.7801 (mm) cc_final: 0.7502 (mt) REVERT: D 152 HIS cc_start: 0.5203 (t70) cc_final: 0.4562 (t-170) REVERT: D 241 MET cc_start: 0.7295 (mmt) cc_final: 0.7094 (mmt) REVERT: D 263 MET cc_start: 0.6150 (mmt) cc_final: 0.5642 (tpp) REVERT: D 303 PHE cc_start: 0.6774 (t80) cc_final: 0.6406 (t80) REVERT: E 43 HIS cc_start: 0.4207 (t70) cc_final: 0.3900 (t-170) REVERT: E 76 LEU cc_start: 0.5687 (OUTLIER) cc_final: 0.5253 (mt) REVERT: E 131 VAL cc_start: 0.7171 (m) cc_final: 0.6958 (p) REVERT: E 181 LYS cc_start: 0.7495 (mmmt) cc_final: 0.7283 (ptmm) REVERT: E 228 MET cc_start: 0.6739 (ptt) cc_final: 0.6448 (ptp) REVERT: E 331 THR cc_start: 0.6165 (m) cc_final: 0.5832 (t) REVERT: F 9 LEU cc_start: 0.6013 (mt) cc_final: 0.5531 (mt) REVERT: F 48 HIS cc_start: 0.5408 (m90) cc_final: 0.5196 (m170) REVERT: F 139 ARG cc_start: 0.5890 (mtp-110) cc_final: 0.5554 (mtt-85) REVERT: F 263 MET cc_start: 0.6300 (mmm) cc_final: 0.6051 (tmm) REVERT: F 265 LYS cc_start: 0.7146 (mmtm) cc_final: 0.6736 (mmtp) REVERT: F 274 ARG cc_start: 0.4547 (mtm-85) cc_final: 0.4090 (mtt90) REVERT: F 384 MET cc_start: 0.6453 (mtp) cc_final: 0.5894 (ttm) REVERT: F 423 LYS cc_start: 0.6273 (mttm) cc_final: 0.5766 (mmtt) REVERT: H 49 LYS cc_start: 0.1708 (mttt) cc_final: 0.1388 (tptp) REVERT: H 154 TRP cc_start: 0.4657 (m-90) cc_final: 0.4139 (m-90) REVERT: H 242 ILE cc_start: 0.5212 (mm) cc_final: 0.4968 (mm) REVERT: H 255 LEU cc_start: 0.6019 (OUTLIER) cc_final: 0.5790 (mp) REVERT: H 294 TRP cc_start: 0.6625 (m100) cc_final: 0.6312 (m100) outliers start: 97 outliers final: 69 residues processed: 464 average time/residue: 0.3434 time to fit residues: 250.5888 Evaluate side-chains 403 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 332 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 422 GLN Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 392 GLU Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 299 TRP Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 0.9990 chunk 159 optimal weight: 0.6980 chunk 4 optimal weight: 0.2980 chunk 209 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 240 optimal weight: 0.0470 chunk 194 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 252 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 HIS A 167 ASN ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 GLN B 100 GLN B 200 ASN C 57 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 ASN F 8 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24197 Z= 0.159 Angle : 0.547 9.040 32807 Z= 0.290 Chirality : 0.041 0.292 3647 Planarity : 0.003 0.038 4071 Dihedral : 10.427 168.603 3399 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.34 % Allowed : 16.41 % Favored : 81.25 % 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: 1.22 (0.14), residues: 1457 sheet: -0.46 (0.27), residues: 400 loop : -1.23 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 428 HIS 0.007 0.001 HIS E 43 PHE 0.022 0.001 PHE H 194 TYR 0.019 0.001 TYR F 15 ARG 0.006 0.000 ARG D 322 *********************** 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 434 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 375 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6919 (t0) cc_final: 0.6235 (m-30) REVERT: A 100 GLN cc_start: 0.7316 (mt0) cc_final: 0.6960 (tm-30) REVERT: A 291 ARG cc_start: 0.5452 (mtm-85) cc_final: 0.5068 (mmt90) REVERT: A 417 PHE cc_start: 0.3474 (t80) cc_final: 0.2843 (t80) REVERT: B 79 LYS cc_start: 0.7325 (mmmt) cc_final: 0.6721 (mmtp) REVERT: B 112 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6725 (tt0) REVERT: B 228 MET cc_start: 0.6863 (ttp) cc_final: 0.6660 (ttp) REVERT: B 296 GLU cc_start: 0.6449 (tt0) cc_final: 0.6129 (tt0) REVERT: B 418 LEU cc_start: 0.6746 (tp) cc_final: 0.6087 (tt) REVERT: C 1 MET cc_start: 0.7897 (ptm) cc_final: 0.7351 (ptt) REVERT: C 158 TYR cc_start: 0.6582 (p90) cc_final: 0.6368 (p90) REVERT: C 165 TYR cc_start: 0.7757 (m-10) cc_final: 0.7535 (m-10) REVERT: C 428 TRP cc_start: 0.7292 (m-10) cc_final: 0.6904 (m-10) REVERT: D 1 MET cc_start: 0.6626 (ptm) cc_final: 0.6144 (ptm) REVERT: D 3 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6556 (tt0) REVERT: D 41 LYS cc_start: 0.6984 (ttpp) cc_final: 0.6345 (pttp) REVERT: D 48 HIS cc_start: 0.5512 (m90) cc_final: 0.4982 (m-70) REVERT: D 128 MET cc_start: 0.7236 (tpp) cc_final: 0.6609 (ttm) REVERT: D 134 ILE cc_start: 0.7735 (mm) cc_final: 0.7400 (mt) REVERT: D 152 HIS cc_start: 0.5168 (t70) cc_final: 0.4398 (t-170) REVERT: D 263 MET cc_start: 0.6073 (mmt) cc_final: 0.5604 (tpp) REVERT: E 43 HIS cc_start: 0.4222 (t70) cc_final: 0.3803 (t70) REVERT: E 76 LEU cc_start: 0.5731 (OUTLIER) cc_final: 0.5393 (mm) REVERT: E 131 VAL cc_start: 0.7185 (m) cc_final: 0.6953 (p) REVERT: E 331 THR cc_start: 0.6160 (m) cc_final: 0.5848 (t) REVERT: F 9 LEU cc_start: 0.6001 (mt) cc_final: 0.5480 (mt) REVERT: F 79 LYS cc_start: 0.6746 (mttm) cc_final: 0.6434 (ttmm) REVERT: F 152 HIS cc_start: 0.6780 (t70) cc_final: 0.6515 (t-170) REVERT: F 228 MET cc_start: 0.4386 (mtm) cc_final: 0.2924 (mmp) REVERT: F 265 LYS cc_start: 0.7139 (mmtm) cc_final: 0.6728 (mmtp) REVERT: F 274 ARG cc_start: 0.4612 (mtm-85) cc_final: 0.4120 (mtt90) REVERT: F 337 GLU cc_start: 0.6204 (mm-30) cc_final: 0.5751 (mm-30) REVERT: F 384 MET cc_start: 0.6368 (mtp) cc_final: 0.5923 (ttm) REVERT: F 423 LYS cc_start: 0.6428 (mttm) cc_final: 0.4803 (ptmm) REVERT: H 49 LYS cc_start: 0.1768 (mttt) cc_final: 0.1483 (tptp) REVERT: H 149 LYS cc_start: 0.6214 (mmtt) cc_final: 0.6005 (mmmt) REVERT: H 154 TRP cc_start: 0.4596 (m-90) cc_final: 0.4098 (m-90) REVERT: H 242 ILE cc_start: 0.5104 (mm) cc_final: 0.4803 (mm) REVERT: H 279 LYS cc_start: 0.7828 (ptmt) cc_final: 0.7505 (ptpt) REVERT: H 294 TRP cc_start: 0.6525 (m100) cc_final: 0.6296 (m100) REVERT: H 311 GLU cc_start: 0.5439 (OUTLIER) cc_final: 0.5011 (mp0) outliers start: 59 outliers final: 35 residues processed: 421 average time/residue: 0.3464 time to fit residues: 228.8517 Evaluate side-chains 370 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 333 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 271 GLU Chi-restraints excluded: chain H residue 299 TRP Chi-restraints excluded: chain H residue 311 GLU Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 0.0770 chunk 253 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 165 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 281 optimal weight: 0.5980 chunk 233 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 overall best weight: 2.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 ASN A 167 ASN ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN B 200 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS D 422 GLN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24197 Z= 0.241 Angle : 0.606 10.804 32807 Z= 0.320 Chirality : 0.043 0.288 3647 Planarity : 0.004 0.053 4071 Dihedral : 10.580 166.556 3399 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.09 % Allowed : 16.41 % Favored : 80.50 % 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: 1.07 (0.14), residues: 1453 sheet: -0.53 (0.27), residues: 402 loop : -1.36 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP F 428 HIS 0.006 0.001 HIS F 8 PHE 0.016 0.002 PHE D 37 TYR 0.020 0.002 TYR A 312 ARG 0.005 0.001 ARG D 322 *********************** 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 432 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 354 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7020 (t0) cc_final: 0.6330 (m-30) REVERT: A 76 LEU cc_start: 0.5632 (OUTLIER) cc_final: 0.5332 (mm) REVERT: A 100 GLN cc_start: 0.7393 (mt0) cc_final: 0.7045 (tm-30) REVERT: A 417 PHE cc_start: 0.3635 (t80) cc_final: 0.3037 (t80) REVERT: B 79 LYS cc_start: 0.7462 (mmmt) cc_final: 0.7078 (mmtp) REVERT: B 93 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7235 (mm-30) REVERT: B 103 MET cc_start: 0.7321 (mmp) cc_final: 0.6937 (mmm) REVERT: B 228 MET cc_start: 0.6887 (ttp) cc_final: 0.6657 (ttp) REVERT: B 418 LEU cc_start: 0.6773 (tp) cc_final: 0.6124 (tt) REVERT: C 1 MET cc_start: 0.7866 (ptm) cc_final: 0.7329 (ptt) REVERT: C 165 TYR cc_start: 0.7780 (m-10) cc_final: 0.7567 (m-10) REVERT: C 428 TRP cc_start: 0.7555 (m-10) cc_final: 0.7115 (m-10) REVERT: D 1 MET cc_start: 0.6616 (ptm) cc_final: 0.6139 (ptm) REVERT: D 3 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6587 (tt0) REVERT: D 23 MET cc_start: 0.7427 (mmp) cc_final: 0.7103 (mmp) REVERT: D 41 LYS cc_start: 0.7019 (ttpp) cc_final: 0.6405 (pttp) REVERT: D 48 HIS cc_start: 0.5514 (m90) cc_final: 0.4978 (m-70) REVERT: D 93 GLU cc_start: 0.6956 (mm-30) cc_final: 0.5968 (tp30) REVERT: D 134 ILE cc_start: 0.7830 (mm) cc_final: 0.7455 (mt) REVERT: D 152 HIS cc_start: 0.5156 (t70) cc_final: 0.4471 (t-170) REVERT: D 200 ASN cc_start: 0.6469 (OUTLIER) cc_final: 0.6240 (t0) REVERT: D 263 MET cc_start: 0.6170 (mmt) cc_final: 0.5598 (tpp) REVERT: E 43 HIS cc_start: 0.4386 (t70) cc_final: 0.3973 (t70) REVERT: E 76 LEU cc_start: 0.5731 (OUTLIER) cc_final: 0.5383 (mm) REVERT: E 131 VAL cc_start: 0.7090 (m) cc_final: 0.6862 (p) REVERT: E 331 THR cc_start: 0.6076 (m) cc_final: 0.5765 (t) REVERT: E 429 VAL cc_start: 0.8065 (OUTLIER) cc_final: 0.7774 (p) REVERT: F 9 LEU cc_start: 0.6149 (mt) cc_final: 0.5821 (mp) REVERT: F 79 LYS cc_start: 0.6728 (mttm) cc_final: 0.6400 (ttmm) REVERT: F 175 LYS cc_start: 0.5256 (tttt) cc_final: 0.4741 (tptp) REVERT: F 265 LYS cc_start: 0.7111 (mmtm) cc_final: 0.6717 (mmtp) REVERT: F 274 ARG cc_start: 0.4519 (mtm-85) cc_final: 0.4106 (mtt90) REVERT: F 321 ILE cc_start: 0.4897 (mt) cc_final: 0.4635 (mm) REVERT: F 384 MET cc_start: 0.6406 (mtp) cc_final: 0.5939 (ttm) REVERT: H 18 HIS cc_start: 0.3071 (OUTLIER) cc_final: 0.2726 (p-80) REVERT: H 49 LYS cc_start: 0.1981 (mttt) cc_final: 0.1669 (tptp) REVERT: H 145 ILE cc_start: 0.4940 (mp) cc_final: 0.4441 (tt) REVERT: H 154 TRP cc_start: 0.4725 (m-90) cc_final: 0.4112 (m-90) REVERT: H 242 ILE cc_start: 0.5150 (mm) cc_final: 0.4775 (mm) REVERT: H 255 LEU cc_start: 0.6019 (OUTLIER) cc_final: 0.5805 (mp) REVERT: H 279 LYS cc_start: 0.7898 (ptmt) cc_final: 0.7512 (ptpt) REVERT: H 294 TRP cc_start: 0.6591 (m100) cc_final: 0.6333 (m100) outliers start: 78 outliers final: 57 residues processed: 415 average time/residue: 0.3519 time to fit residues: 231.0324 Evaluate side-chains 389 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 326 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 271 GLU Chi-restraints excluded: chain H residue 299 TRP Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 334 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 205 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 237 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 280 optimal weight: 9.9990 chunk 175 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 167 ASN ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN B 100 GLN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 ASN ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24197 Z= 0.309 Angle : 0.677 9.471 32807 Z= 0.358 Chirality : 0.046 0.287 3647 Planarity : 0.005 0.041 4071 Dihedral : 10.994 169.391 3399 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.61 % Allowed : 16.45 % Favored : 79.94 % 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: -0.46 (0.15), residues: 2898 helix: 0.73 (0.14), residues: 1457 sheet: -0.74 (0.27), residues: 400 loop : -1.56 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 428 HIS 0.008 0.002 HIS F 8 PHE 0.018 0.003 PHE E 28 TYR 0.025 0.002 TYR B 214 ARG 0.006 0.001 ARG E 101 *********************** 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 453 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 362 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7178 (t0) cc_final: 0.6490 (m-30) REVERT: A 76 LEU cc_start: 0.5773 (OUTLIER) cc_final: 0.5471 (mm) REVERT: A 100 GLN cc_start: 0.7462 (mt0) cc_final: 0.7177 (tm-30) REVERT: A 128 MET cc_start: 0.3725 (tpt) cc_final: 0.3383 (tpt) REVERT: B 103 MET cc_start: 0.7362 (mmp) cc_final: 0.6993 (mmm) REVERT: B 177 ARG cc_start: 0.6405 (mtm180) cc_final: 0.6121 (mtm-85) REVERT: B 188 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6908 (mt-10) REVERT: B 228 MET cc_start: 0.6859 (ttp) cc_final: 0.6628 (ttp) REVERT: B 267 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6379 (ttt-90) REVERT: C 1 MET cc_start: 0.7840 (ptm) cc_final: 0.7327 (ptt) REVERT: C 85 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6287 (mm-30) REVERT: C 155 MET cc_start: 0.7663 (tpp) cc_final: 0.7333 (tpp) REVERT: C 196 MET cc_start: 0.7857 (ttp) cc_final: 0.7627 (ttp) REVERT: C 428 TRP cc_start: 0.7598 (m-10) cc_final: 0.7190 (m100) REVERT: D 1 MET cc_start: 0.6467 (ptm) cc_final: 0.6053 (ptm) REVERT: D 3 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6667 (tt0) REVERT: D 23 MET cc_start: 0.7352 (mmp) cc_final: 0.7041 (mmp) REVERT: D 41 LYS cc_start: 0.7371 (ttpp) cc_final: 0.6447 (pttp) REVERT: D 48 HIS cc_start: 0.5637 (m90) cc_final: 0.5058 (m-70) REVERT: D 52 SER cc_start: 0.7416 (p) cc_final: 0.7159 (t) REVERT: D 93 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6022 (tp30) REVERT: D 103 MET cc_start: 0.7298 (mmp) cc_final: 0.7058 (mmm) REVERT: D 134 ILE cc_start: 0.7788 (mm) cc_final: 0.7352 (mt) REVERT: D 152 HIS cc_start: 0.5229 (t70) cc_final: 0.4518 (t-170) REVERT: D 200 ASN cc_start: 0.6368 (OUTLIER) cc_final: 0.6105 (t0) REVERT: D 263 MET cc_start: 0.6178 (mmt) cc_final: 0.5644 (tpp) REVERT: E 18 LYS cc_start: 0.6002 (mmtm) cc_final: 0.5300 (tptt) REVERT: E 43 HIS cc_start: 0.4515 (t70) cc_final: 0.4103 (t-90) REVERT: E 76 LEU cc_start: 0.5684 (OUTLIER) cc_final: 0.5289 (mm) REVERT: E 131 VAL cc_start: 0.7073 (m) cc_final: 0.6853 (p) REVERT: E 331 THR cc_start: 0.6138 (m) cc_final: 0.5927 (t) REVERT: E 391 GLU cc_start: 0.6099 (pt0) cc_final: 0.5890 (pt0) REVERT: F 9 LEU cc_start: 0.6385 (mt) cc_final: 0.6046 (mp) REVERT: F 152 HIS cc_start: 0.6607 (t-170) cc_final: 0.6386 (t-170) REVERT: F 175 LYS cc_start: 0.5141 (tttt) cc_final: 0.4721 (tptp) REVERT: F 265 LYS cc_start: 0.7053 (mmtm) cc_final: 0.6749 (mptt) REVERT: F 274 ARG cc_start: 0.4579 (mtm-85) cc_final: 0.4190 (mtt90) REVERT: F 321 ILE cc_start: 0.4775 (mt) cc_final: 0.4470 (mm) REVERT: F 384 MET cc_start: 0.6301 (mtp) cc_final: 0.5851 (ttm) REVERT: H 18 HIS cc_start: 0.3214 (OUTLIER) cc_final: 0.2901 (p-80) REVERT: H 49 LYS cc_start: 0.2214 (mttt) cc_final: 0.1881 (tptp) REVERT: H 242 ILE cc_start: 0.5083 (mm) cc_final: 0.4733 (mm) REVERT: H 294 TRP cc_start: 0.6704 (m100) cc_final: 0.6459 (m100) REVERT: H 307 MET cc_start: 0.6744 (ttm) cc_final: 0.6018 (mtt) outliers start: 91 outliers final: 70 residues processed: 434 average time/residue: 0.3281 time to fit residues: 225.3475 Evaluate side-chains 407 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 331 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 267 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 392 GLU Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 271 GLU Chi-restraints excluded: chain H residue 299 TRP Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 334 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 178 optimal weight: 10.0000 chunk 191 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 ASN ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.5764 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= 0.163 Angle : 0.570 10.265 32807 Z= 0.300 Chirality : 0.042 0.280 3647 Planarity : 0.004 0.039 4071 Dihedral : 10.643 169.095 3399 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.18 % Allowed : 17.76 % 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: 0.02 (0.16), residues: 2898 helix: 1.21 (0.14), residues: 1455 sheet: -0.49 (0.28), residues: 395 loop : -1.47 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 428 HIS 0.008 0.001 HIS A 43 PHE 0.019 0.001 PHE B 104 TYR 0.016 0.001 TYR B 324 ARG 0.005 0.000 ARG C 322 *********************** 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 427 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 372 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7028 (t0) cc_final: 0.6397 (m-30) REVERT: A 76 LEU cc_start: 0.5791 (OUTLIER) cc_final: 0.5521 (mm) REVERT: A 128 MET cc_start: 0.3716 (tpt) cc_final: 0.3451 (tpt) REVERT: A 291 ARG cc_start: 0.5224 (mtm-85) cc_final: 0.4933 (mtt90) REVERT: B 103 MET cc_start: 0.7274 (mmp) cc_final: 0.7029 (mmm) REVERT: B 163 LEU cc_start: 0.7644 (mm) cc_final: 0.6974 (tp) REVERT: B 228 MET cc_start: 0.6927 (ttp) cc_final: 0.6718 (ttp) REVERT: B 296 GLU cc_start: 0.6381 (tt0) cc_final: 0.6060 (tt0) REVERT: B 302 ASN cc_start: 0.6024 (OUTLIER) cc_final: 0.5744 (t0) REVERT: B 359 GLN cc_start: 0.5715 (pm20) cc_final: 0.5437 (pm20) REVERT: C 1 MET cc_start: 0.7915 (ptm) cc_final: 0.7434 (ptt) REVERT: C 196 MET cc_start: 0.7819 (ttp) cc_final: 0.7538 (ttp) REVERT: D 1 MET cc_start: 0.6270 (ptm) cc_final: 0.5882 (ptm) REVERT: D 3 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6593 (tt0) REVERT: D 23 MET cc_start: 0.7331 (mmp) cc_final: 0.7010 (mmp) REVERT: D 41 LYS cc_start: 0.7162 (ttpp) cc_final: 0.6435 (pttp) REVERT: D 48 HIS cc_start: 0.5655 (m90) cc_final: 0.5138 (m-70) REVERT: D 52 SER cc_start: 0.7420 (p) cc_final: 0.7179 (t) REVERT: D 93 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6041 (tp30) REVERT: D 103 MET cc_start: 0.7276 (mmp) cc_final: 0.7075 (mmm) REVERT: D 263 MET cc_start: 0.6105 (mmt) cc_final: 0.5765 (tpp) REVERT: D 419 MET cc_start: 0.7489 (tpp) cc_final: 0.7207 (tpt) REVERT: E 18 LYS cc_start: 0.5746 (mmtm) cc_final: 0.5127 (tptt) REVERT: E 43 HIS cc_start: 0.4514 (t70) cc_final: 0.4189 (t70) REVERT: E 76 LEU cc_start: 0.5818 (OUTLIER) cc_final: 0.5403 (mm) REVERT: E 131 VAL cc_start: 0.7051 (m) cc_final: 0.6810 (p) REVERT: E 299 LEU cc_start: 0.5902 (OUTLIER) cc_final: 0.5661 (tt) REVERT: E 331 THR cc_start: 0.6122 (m) cc_final: 0.5860 (t) REVERT: E 391 GLU cc_start: 0.6127 (pt0) cc_final: 0.5902 (pt0) REVERT: E 428 TRP cc_start: 0.7305 (m-10) cc_final: 0.6835 (m-10) REVERT: F 274 ARG cc_start: 0.4688 (mtm-85) cc_final: 0.4200 (mtt90) REVERT: F 321 ILE cc_start: 0.4789 (mt) cc_final: 0.4466 (mm) REVERT: F 337 GLU cc_start: 0.6201 (mm-30) cc_final: 0.5691 (mm-30) REVERT: F 384 MET cc_start: 0.6300 (mtp) cc_final: 0.5834 (ttm) REVERT: H 18 HIS cc_start: 0.3182 (OUTLIER) cc_final: 0.2863 (p-80) REVERT: H 49 LYS cc_start: 0.2279 (mttt) cc_final: 0.1917 (tptp) REVERT: H 92 GLU cc_start: 0.5287 (tp30) cc_final: 0.4781 (tp30) REVERT: H 159 TRP cc_start: 0.2733 (OUTLIER) cc_final: 0.2317 (t-100) REVERT: H 201 LYS cc_start: 0.1747 (tppt) cc_final: 0.1322 (mmtt) REVERT: H 213 TYR cc_start: 0.3016 (p90) cc_final: 0.2506 (t80) REVERT: H 242 ILE cc_start: 0.5019 (mm) cc_final: 0.4667 (mm) REVERT: H 279 LYS cc_start: 0.7899 (ptmt) cc_final: 0.7564 (ptpt) REVERT: H 294 TRP cc_start: 0.6676 (m100) cc_final: 0.6412 (m100) REVERT: H 307 MET cc_start: 0.6737 (ttm) cc_final: 0.6027 (mtt) outliers start: 55 outliers final: 41 residues processed: 411 average time/residue: 0.3391 time to fit residues: 220.1950 Evaluate side-chains 387 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 340 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 159 TRP Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 271 GLU Chi-restraints excluded: chain H residue 299 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 chunk 245 optimal weight: 9.9990 chunk 261 optimal weight: 0.3980 chunk 157 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 205 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 236 optimal weight: 8.9990 chunk 247 optimal weight: 3.9990 chunk 260 optimal weight: 3.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN B 100 GLN B 200 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 ASN F 302 ASN H 48 ASN H 325 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 24197 Z= 0.277 Angle : 0.651 11.245 32807 Z= 0.344 Chirality : 0.045 0.288 3647 Planarity : 0.004 0.040 4071 Dihedral : 10.899 168.942 3399 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.50 % Allowed : 17.80 % Favored : 79.71 % 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: -0.31 (0.16), residues: 2898 helix: 0.90 (0.14), residues: 1460 sheet: -0.62 (0.27), residues: 395 loop : -1.58 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 428 HIS 0.006 0.001 HIS B 87 PHE 0.022 0.002 PHE E 174 TYR 0.029 0.002 TYR D 15 ARG 0.005 0.001 ARG D 322 *********************** 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 404 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 341 time to evaluate : 2.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7178 (t0) cc_final: 0.6482 (m-30) REVERT: A 76 LEU cc_start: 0.5828 (OUTLIER) cc_final: 0.5548 (mm) REVERT: A 128 MET cc_start: 0.3555 (tpt) cc_final: 0.3351 (tpt) REVERT: A 291 ARG cc_start: 0.5257 (mtm-85) cc_final: 0.4867 (mmt90) REVERT: A 403 GLN cc_start: 0.6981 (tt0) cc_final: 0.6633 (tt0) REVERT: B 89 TRP cc_start: 0.6807 (t60) cc_final: 0.6574 (t60) REVERT: B 103 MET cc_start: 0.7385 (mmp) cc_final: 0.7062 (mmm) REVERT: B 163 LEU cc_start: 0.7708 (mm) cc_final: 0.6981 (tp) REVERT: B 177 ARG cc_start: 0.6417 (mtm180) cc_final: 0.6107 (mtm-85) REVERT: B 188 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6840 (mt-10) REVERT: B 228 MET cc_start: 0.6944 (ttp) cc_final: 0.6725 (ttp) REVERT: B 359 GLN cc_start: 0.5776 (pm20) cc_final: 0.5466 (pm20) REVERT: C 1 MET cc_start: 0.7757 (ptm) cc_final: 0.7357 (ptt) REVERT: C 85 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6316 (mm-30) REVERT: C 428 TRP cc_start: 0.7657 (m-10) cc_final: 0.7339 (m-10) REVERT: D 1 MET cc_start: 0.6279 (ptm) cc_final: 0.5892 (ptm) REVERT: D 3 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6682 (tt0) REVERT: D 23 MET cc_start: 0.7348 (mmp) cc_final: 0.7052 (mmp) REVERT: D 41 LYS cc_start: 0.7508 (ttpp) cc_final: 0.6548 (pttp) REVERT: D 48 HIS cc_start: 0.5738 (m90) cc_final: 0.5183 (m-70) REVERT: D 52 SER cc_start: 0.7369 (p) cc_final: 0.7162 (t) REVERT: D 93 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6067 (tp30) REVERT: D 103 MET cc_start: 0.7268 (mmp) cc_final: 0.7047 (mmm) REVERT: D 263 MET cc_start: 0.6205 (mmt) cc_final: 0.5588 (tpp) REVERT: E 18 LYS cc_start: 0.5869 (mmtm) cc_final: 0.5262 (tptt) REVERT: E 43 HIS cc_start: 0.4582 (t70) cc_final: 0.4319 (t-90) REVERT: E 76 LEU cc_start: 0.5761 (OUTLIER) cc_final: 0.5309 (mm) REVERT: E 131 VAL cc_start: 0.7058 (m) cc_final: 0.6828 (p) REVERT: E 299 LEU cc_start: 0.6198 (OUTLIER) cc_final: 0.5913 (tt) REVERT: E 331 THR cc_start: 0.5993 (m) cc_final: 0.5685 (t) REVERT: F 171 LYS cc_start: 0.2990 (OUTLIER) cc_final: 0.2730 (mmtt) REVERT: F 175 LYS cc_start: 0.5190 (tttt) cc_final: 0.4704 (tptp) REVERT: F 263 MET cc_start: 0.5880 (tmm) cc_final: 0.4769 (tmm) REVERT: F 274 ARG cc_start: 0.4626 (mtm-85) cc_final: 0.4121 (mtt90) REVERT: F 321 ILE cc_start: 0.4706 (mt) cc_final: 0.4394 (mm) REVERT: F 384 MET cc_start: 0.6252 (mtp) cc_final: 0.5867 (ttm) REVERT: H 18 HIS cc_start: 0.3119 (OUTLIER) cc_final: 0.2841 (p-80) REVERT: H 49 LYS cc_start: 0.2072 (mttt) cc_final: 0.1768 (tptp) REVERT: H 242 ILE cc_start: 0.5034 (mm) cc_final: 0.4687 (mm) REVERT: H 294 TRP cc_start: 0.6750 (m100) cc_final: 0.6435 (m100) REVERT: H 307 MET cc_start: 0.6710 (ttm) cc_final: 0.6042 (mtt) outliers start: 63 outliers final: 51 residues processed: 392 average time/residue: 0.3534 time to fit residues: 218.8626 Evaluate side-chains 386 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 329 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 271 GLU Chi-restraints excluded: chain H residue 297 SER Chi-restraints excluded: chain H residue 299 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 6.9990 chunk 276 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 192 optimal weight: 4.9990 chunk 289 optimal weight: 6.9990 chunk 266 optimal weight: 0.8980 chunk 230 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 141 optimal weight: 0.4980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 ASN F 87 HIS F 302 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24197 Z= 0.176 Angle : 0.585 12.072 32807 Z= 0.309 Chirality : 0.043 0.283 3647 Planarity : 0.004 0.038 4071 Dihedral : 10.754 168.380 3399 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.06 % Allowed : 18.35 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.16), residues: 2898 helix: 1.16 (0.14), residues: 1454 sheet: -0.45 (0.28), residues: 395 loop : -1.58 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 89 HIS 0.012 0.001 HIS F 87 PHE 0.020 0.002 PHE B 104 TYR 0.045 0.001 TYR D 15 ARG 0.006 0.000 ARG D 322 ********************** 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 394 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 342 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7049 (t0) cc_final: 0.6468 (m-30) REVERT: A 76 LEU cc_start: 0.5824 (OUTLIER) cc_final: 0.5558 (mm) REVERT: A 256 TYR cc_start: 0.6884 (t80) cc_final: 0.6333 (t80) REVERT: A 291 ARG cc_start: 0.5060 (mtm-85) cc_final: 0.4833 (mtt90) REVERT: B 89 TRP cc_start: 0.6843 (t60) cc_final: 0.6592 (t60) REVERT: B 103 MET cc_start: 0.7360 (mmp) cc_final: 0.7125 (mmm) REVERT: B 163 LEU cc_start: 0.7634 (mm) cc_final: 0.6970 (tp) REVERT: B 177 ARG cc_start: 0.6358 (mtm180) cc_final: 0.6060 (mtm-85) REVERT: B 228 MET cc_start: 0.6914 (ttp) cc_final: 0.6700 (ttp) REVERT: B 267 ARG cc_start: 0.6739 (OUTLIER) cc_final: 0.6355 (ttt-90) REVERT: B 296 GLU cc_start: 0.6352 (tt0) cc_final: 0.6023 (tt0) REVERT: B 359 GLN cc_start: 0.5855 (pm20) cc_final: 0.5617 (pm20) REVERT: C 1 MET cc_start: 0.7711 (ptm) cc_final: 0.7343 (ptt) REVERT: C 85 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.6146 (mm-30) REVERT: C 112 GLU cc_start: 0.7215 (tt0) cc_final: 0.6942 (tt0) REVERT: D 1 MET cc_start: 0.6148 (ptm) cc_final: 0.5830 (ptm) REVERT: D 3 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6637 (tt0) REVERT: D 41 LYS cc_start: 0.7432 (ttpp) cc_final: 0.6523 (pttp) REVERT: D 48 HIS cc_start: 0.5686 (m90) cc_final: 0.5202 (m-70) REVERT: D 52 SER cc_start: 0.7404 (p) cc_final: 0.7191 (t) REVERT: D 93 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6722 (mm-30) REVERT: D 103 MET cc_start: 0.7219 (mmp) cc_final: 0.6298 (mtt) REVERT: D 263 MET cc_start: 0.6206 (mmt) cc_final: 0.5794 (tpp) REVERT: D 419 MET cc_start: 0.7491 (tpp) cc_final: 0.7164 (tpt) REVERT: E 18 LYS cc_start: 0.5578 (mmtm) cc_final: 0.5055 (tptt) REVERT: E 43 HIS cc_start: 0.4604 (t70) cc_final: 0.4302 (t-90) REVERT: E 76 LEU cc_start: 0.5850 (OUTLIER) cc_final: 0.5387 (mm) REVERT: E 131 VAL cc_start: 0.7071 (m) cc_final: 0.6827 (p) REVERT: E 299 LEU cc_start: 0.5894 (OUTLIER) cc_final: 0.5667 (tt) REVERT: E 331 THR cc_start: 0.6126 (m) cc_final: 0.5826 (t) REVERT: F 175 LYS cc_start: 0.5252 (tttt) cc_final: 0.4774 (tptp) REVERT: F 263 MET cc_start: 0.5941 (tmm) cc_final: 0.4728 (tmm) REVERT: F 274 ARG cc_start: 0.4593 (mtm-85) cc_final: 0.4131 (mtt90) REVERT: F 321 ILE cc_start: 0.4765 (mt) cc_final: 0.4433 (mm) REVERT: F 337 GLU cc_start: 0.6278 (mm-30) cc_final: 0.6072 (mm-30) REVERT: F 384 MET cc_start: 0.6234 (mtp) cc_final: 0.5957 (ttm) REVERT: H 18 HIS cc_start: 0.3319 (OUTLIER) cc_final: 0.3055 (p-80) REVERT: H 49 LYS cc_start: 0.1989 (mttt) cc_final: 0.1656 (tptp) REVERT: H 92 GLU cc_start: 0.5357 (tp30) cc_final: 0.4826 (tp30) REVERT: H 242 ILE cc_start: 0.4985 (mm) cc_final: 0.4628 (mm) REVERT: H 294 TRP cc_start: 0.6722 (m100) cc_final: 0.6398 (m100) REVERT: H 307 MET cc_start: 0.6678 (ttm) cc_final: 0.6000 (mtt) outliers start: 52 outliers final: 42 residues processed: 382 average time/residue: 0.3368 time to fit residues: 204.0563 Evaluate side-chains 381 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 333 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 267 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 271 GLU Chi-restraints excluded: chain H residue 297 SER Chi-restraints excluded: chain H residue 299 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 5.9990 chunk 245 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 212 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 231 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 237 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 ASN F 302 ASN H 48 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.149800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.126720 restraints weight = 43167.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.126913 restraints weight = 30610.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.127530 restraints weight = 24567.688| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.6306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 24197 Z= 0.296 Angle : 0.670 11.989 32807 Z= 0.355 Chirality : 0.046 0.299 3647 Planarity : 0.005 0.057 4071 Dihedral : 11.077 175.850 3399 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.46 % Allowed : 18.27 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.16), residues: 2898 helix: 0.78 (0.14), residues: 1455 sheet: -0.59 (0.28), residues: 389 loop : -1.66 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 428 HIS 0.007 0.002 HIS F 8 PHE 0.024 0.003 PHE E 383 TYR 0.027 0.002 TYR B 214 ARG 0.006 0.001 ARG D 322 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5327.79 seconds wall clock time: 96 minutes 5.39 seconds (5765.39 seconds total)