Starting phenix.real_space_refine on Fri Jun 20 09:43:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dw6_27751/06_2025/8dw6_27751.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dw6_27751/06_2025/8dw6_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/cci-nas-00/data/ceres_data/8dw6_27751/06_2025/8dw6_27751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dw6_27751/06_2025/8dw6_27751.map" model { file = "/net/cci-nas-00/data/ceres_data/8dw6_27751/06_2025/8dw6_27751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dw6_27751/06_2025/8dw6_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-5710/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: 15.07, per 1000 atoms: 0.64 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: 6.09 Conformation dependent library (CDL) restraints added in 2.9 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: 2.65 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: 8.38 Time building geometry restraints manager: 7.23 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: 2.700 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: 1.050 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 60.060 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.120 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.600 ------------------------------------------------------------------------------- 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 24201 Z= 0.292 Angle : 0.649 12.463 32813 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 Details of bonding type rmsd hydrogen bonds : bond 0.15726 ( 1155) hydrogen bonds : angle 6.43487 ( 3303) metal coordination : bond 0.01309 ( 4) metal coordination : angle 3.14693 ( 6) covalent geometry : bond 0.00433 (24197) covalent geometry : angle 0.64748 (32807) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 802 time to evaluate : 2.427 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: 0.5718 (m-30) REVERT: A 100 GLN cc_start: 0.7097 (mt0) cc_final: 0.6600 (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: 0.5186 (ptm) REVERT: A 291 ARG cc_start: 0.5841 (mtm-85) cc_final: 0.5411 (mtt180) REVERT: A 337 GLU cc_start: 0.5584 (mt-10) cc_final: 0.5097 (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: 0.5867 (mt-10) REVERT: B 196 MET cc_start: 0.4982 (mtm) cc_final: 0.4439 (mtp) REVERT: B 228 MET cc_start: 0.5909 (mtm) cc_final: 0.5291 (mtp) REVERT: B 288 ASN cc_start: 0.6941 (m-40) cc_final: 0.6732 (m110) REVERT: B 296 GLU cc_start: 0.5907 (tt0) cc_final: 0.5563 (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: 0.7209 (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: 0.6373 (mmmt) REVERT: C 228 MET cc_start: 0.6258 (mtm) cc_final: 0.5884 (mtt) REVERT: C 295 ASN cc_start: 0.7874 (t0) cc_final: 0.7669 (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: 0.3030 (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: 0.4191 (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: 0.1012 (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: 0.5097 (mtt-85) REVERT: F 274 ARG cc_start: 0.4448 (mtm-85) cc_final: 0.4055 (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: 0.5551 (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: 0.5247 (mm) REVERT: H 161 LYS cc_start: 0.4016 (tmmt) cc_final: 0.3696 (mmtt) REVERT: H 180 LEU cc_start: 0.6327 (mt) cc_final: 0.6054 (mt) REVERT: H 276 ASP cc_start: 0.6957 (OUTLIER) cc_final: 0.6608 (m-30) REVERT: H 279 LYS cc_start: 0.7912 (tttt) cc_final: 0.7683 (ttpp) REVERT: H 299 TRP cc_start: 0.7266 (m-90) cc_final: 0.6968 (m-90) outliers start: 57 outliers final: 7 residues processed: 839 average time/residue: 0.3997 time to fit residues: 496.0334 Evaluate side-chains 432 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 421 time to evaluate : 3.294 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.161061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.139680 restraints weight = 43117.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.139491 restraints weight = 31198.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.140690 restraints weight = 24112.313| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24201 Z= 0.136 Angle : 0.590 8.573 32813 Z= 0.313 Chirality : 0.043 0.355 3647 Planarity : 0.004 0.047 4071 Dihedral : 10.581 172.496 3414 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.98 % Allowed : 12.13 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.16), residues: 2898 helix: 1.43 (0.14), residues: 1460 sheet: -0.33 (0.28), residues: 392 loop : -1.06 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 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 0.009 0.001 ARG F 161 Details of bonding type rmsd hydrogen bonds : bond 0.04149 ( 1155) hydrogen bonds : angle 5.02457 ( 3303) metal coordination : bond 0.00747 ( 4) metal coordination : angle 4.32591 ( 6) covalent geometry : bond 0.00294 (24197) covalent geometry : angle 0.58761 (32807) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 478 time to evaluate : 2.677 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: 0.6251 (mmtm) cc_final: 0.5058 (ttpt) REVERT: A 121 PRO cc_start: 0.5476 (Cg_exo) cc_final: 0.5272 (Cg_endo) REVERT: A 196 MET cc_start: 0.6221 (mmt) cc_final: 0.6013 (mmt) REVERT: A 203 LYS cc_start: 0.6094 (mttm) cc_final: 0.5826 (ptpp) REVERT: A 337 GLU cc_start: 0.5669 (mt-10) cc_final: 0.5460 (mt-10) REVERT: A 385 LEU cc_start: 0.6336 (mt) cc_final: 0.5999 (tp) REVERT: A 425 ASN cc_start: 0.3849 (t160) cc_final: 0.3552 (t0) REVERT: B 296 GLU cc_start: 0.5599 (tt0) cc_final: 0.5198 (tt0) REVERT: B 418 LEU cc_start: 0.6400 (tp) cc_final: 0.5821 (tt) REVERT: C 39 LEU cc_start: 0.7834 (mt) cc_final: 0.7569 (mt) REVERT: D 1 MET cc_start: 0.6314 (ptm) cc_final: 0.5887 (ptm) REVERT: D 3 GLU cc_start: 0.6584 (mt-10) cc_final: 0.6302 (tt0) REVERT: D 41 LYS cc_start: 0.6183 (ttpp) cc_final: 0.5619 (pttp) REVERT: D 128 MET cc_start: 0.6664 (tpp) cc_final: 0.6119 (ttm) REVERT: D 303 PHE cc_start: 0.6496 (t80) cc_final: 0.6119 (t80) REVERT: E 32 PRO cc_start: 0.5156 (Cg_endo) cc_final: 0.4865 (Cg_exo) REVERT: E 43 HIS cc_start: 0.4393 (t-90) cc_final: 0.3964 (t-170) REVERT: E 76 LEU cc_start: 0.5852 (OUTLIER) cc_final: 0.5349 (mm) REVERT: E 115 THR cc_start: 0.6958 (m) cc_final: 0.6737 (t) REVERT: E 243 ASP cc_start: 0.6518 (t0) cc_final: 0.6299 (t0) REVERT: E 427 LYS cc_start: 0.6124 (ttpp) cc_final: 0.5607 (ptmt) REVERT: F 120 PRO cc_start: 0.3791 (Cg_endo) cc_final: 0.3545 (Cg_exo) REVERT: F 265 LYS cc_start: 0.6964 (mmtm) cc_final: 0.6561 (mtmm) REVERT: F 274 ARG cc_start: 0.4518 (mtm-85) cc_final: 0.3961 (mtt90) REVERT: F 298 LYS cc_start: 0.6439 (mtmt) cc_final: 0.5896 (mppt) REVERT: F 333 LYS cc_start: 0.3879 (ttpp) cc_final: 0.3518 (ttpt) REVERT: F 337 GLU cc_start: 0.5806 (mm-30) cc_final: 0.5571 (mm-30) REVERT: F 384 MET cc_start: 0.5837 (mtp) cc_final: 0.5202 (ttm) REVERT: F 423 LYS cc_start: 0.6245 (mttm) cc_final: 0.5030 (pttm) REVERT: H 51 ARG cc_start: 0.4189 (mtt180) cc_final: 0.3769 (mtp180) REVERT: H 92 GLU cc_start: 0.5289 (tp30) cc_final: 0.4675 (tp30) REVERT: H 154 TRP cc_start: 0.2960 (m-90) cc_final: 0.2596 (m-90) REVERT: H 219 ILE cc_start: 0.5069 (pt) cc_final: 0.4641 (tt) REVERT: H 222 VAL cc_start: 0.5937 (OUTLIER) cc_final: 0.5572 (p) REVERT: H 271 GLU cc_start: 0.5978 (OUTLIER) cc_final: 0.5762 (mt-10) REVERT: H 278 ILE cc_start: 0.8067 (pp) cc_final: 0.7780 (mm) REVERT: H 303 ASP cc_start: 0.5251 (p0) cc_final: 0.4293 (p0) REVERT: H 305 ASN cc_start: 0.6480 (t0) cc_final: 0.6076 (p0) REVERT: H 308 ILE cc_start: 0.7789 (mt) cc_final: 0.7479 (pt) outliers start: 50 outliers final: 23 residues processed: 515 average time/residue: 0.3709 time to fit residues: 292.9361 Evaluate side-chains 390 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 364 time to evaluate : 3.508 ------------------------------------------------------------------------------- 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 C residue 313 LEU 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 5 optimal weight: 0.9990 chunk 199 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 280 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 257 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 253 HIS B 100 GLN B 200 ASN C 57 ASN C 100 GLN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN F 359 GLN F 403 GLN H 325 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.152718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.129538 restraints weight = 43395.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.130611 restraints weight = 32905.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.131926 restraints weight = 24978.359| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 24201 Z= 0.216 Angle : 0.731 10.350 32813 Z= 0.384 Chirality : 0.048 0.276 3647 Planarity : 0.005 0.055 4071 Dihedral : 10.883 175.456 3399 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.84 % Allowed : 13.79 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 2898 helix: 0.69 (0.13), residues: 1457 sheet: -0.52 (0.26), residues: 396 loop : -1.26 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP F 428 HIS 0.007 0.002 HIS A 43 PHE 0.027 0.003 PHE C 174 TYR 0.023 0.003 TYR B 312 ARG 0.010 0.001 ARG D 236 Details of bonding type rmsd hydrogen bonds : bond 0.04650 ( 1155) hydrogen bonds : angle 5.21822 ( 3303) metal coordination : bond 0.00883 ( 4) metal coordination : angle 5.81043 ( 6) covalent geometry : bond 0.00494 (24197) covalent geometry : angle 0.72649 (32807) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 426 time to evaluate : 2.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6497 (t0) cc_final: 0.5749 (m-30) REVERT: A 121 PRO cc_start: 0.5964 (Cg_exo) cc_final: 0.5757 (Cg_endo) REVERT: A 222 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7246 (tt) REVERT: A 385 LEU cc_start: 0.6570 (mt) cc_final: 0.6213 (tp) REVERT: A 417 PHE cc_start: 0.3224 (t80) cc_final: 0.3003 (t80) REVERT: A 425 ASN cc_start: 0.3601 (t160) cc_final: 0.3390 (t0) REVERT: B 418 LEU cc_start: 0.6677 (tp) cc_final: 0.6082 (tt) REVERT: C 47 TYR cc_start: 0.4979 (m-80) cc_final: 0.4608 (m-80) REVERT: D 1 MET cc_start: 0.6415 (ptm) cc_final: 0.5842 (ptm) REVERT: D 3 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6487 (tt0) REVERT: D 24 ASP cc_start: 0.6728 (OUTLIER) cc_final: 0.6492 (m-30) REVERT: D 41 LYS cc_start: 0.6613 (ttpp) cc_final: 0.5983 (pttp) REVERT: D 128 MET cc_start: 0.6964 (tpp) cc_final: 0.6540 (ttm) REVERT: D 165 TYR cc_start: 0.6494 (m-10) cc_final: 0.6239 (m-80) REVERT: D 200 ASN cc_start: 0.6016 (OUTLIER) cc_final: 0.5635 (t0) REVERT: E 32 PRO cc_start: 0.5204 (Cg_endo) cc_final: 0.5002 (Cg_exo) REVERT: E 76 LEU cc_start: 0.5822 (OUTLIER) cc_final: 0.5324 (mt) REVERT: E 331 THR cc_start: 0.6087 (m) cc_final: 0.5672 (t) REVERT: E 427 LYS cc_start: 0.6288 (ttpp) cc_final: 0.6010 (ptmt) REVERT: F 9 LEU cc_start: 0.6082 (OUTLIER) cc_final: 0.5765 (mp) REVERT: F 75 THR cc_start: 0.6741 (m) cc_final: 0.6492 (t) REVERT: F 139 ARG cc_start: 0.5854 (mtp-110) cc_final: 0.5604 (mtt-85) REVERT: F 236 ARG cc_start: 0.5584 (mtt-85) cc_final: 0.5328 (mtt90) REVERT: F 248 ASP cc_start: 0.5168 (m-30) cc_final: 0.4826 (m-30) REVERT: F 263 MET cc_start: 0.6572 (mmm) cc_final: 0.5882 (tmm) REVERT: F 265 LYS cc_start: 0.7083 (mmtm) cc_final: 0.6571 (mtmm) REVERT: F 274 ARG cc_start: 0.4528 (mtm-85) cc_final: 0.3956 (mtt90) REVERT: F 384 MET cc_start: 0.5846 (mtp) cc_final: 0.5624 (ttp) REVERT: F 423 LYS cc_start: 0.6388 (mttm) cc_final: 0.4682 (ptmm) REVERT: H 242 ILE cc_start: 0.5447 (mm) cc_final: 0.5043 (mm) REVERT: H 281 MET cc_start: 0.7292 (mtt) cc_final: 0.6853 (mmp) REVERT: H 294 TRP cc_start: 0.7143 (m100) cc_final: 0.6796 (m100) REVERT: H 303 ASP cc_start: 0.5059 (p0) cc_final: 0.4782 (p0) REVERT: H 311 GLU cc_start: 0.5160 (OUTLIER) cc_final: 0.4762 (mm-30) outliers start: 97 outliers final: 57 residues processed: 499 average time/residue: 0.3564 time to fit residues: 274.9626 Evaluate side-chains 392 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 329 time to evaluate : 2.632 ------------------------------------------------------------------------------- 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 222 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 142 LEU 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 B residue 380 THR Chi-restraints excluded: chain C residue 53 ILE 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 258 GLU 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 61 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 200 ASN 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 176 LEU 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 325 SER 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 9 LEU 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 147 ASP Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 401 ILE 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 248 ILE 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 306 ASP Chi-restraints excluded: chain H residue 311 GLU 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 87 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 275 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN B 200 ASN B 216 GLN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 ASN F 399 GLN H 71 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.153114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.130151 restraints weight = 43327.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.131615 restraints weight = 31700.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.132577 restraints weight = 24967.585| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24201 Z= 0.145 Angle : 0.585 8.449 32813 Z= 0.311 Chirality : 0.043 0.353 3647 Planarity : 0.004 0.041 4071 Dihedral : 10.688 177.435 3399 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.01 % Allowed : 15.26 % Favored : 81.73 % 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: 0.97 (0.14), residues: 1457 sheet: -0.51 (0.27), residues: 401 loop : -1.24 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP F 428 HIS 0.004 0.001 HIS A 43 PHE 0.016 0.002 PHE D 37 TYR 0.019 0.002 TYR F 15 ARG 0.005 0.001 ARG D 322 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 1155) hydrogen bonds : angle 4.91738 ( 3303) metal coordination : bond 0.00531 ( 4) metal coordination : angle 5.22116 ( 6) covalent geometry : bond 0.00327 (24197) covalent geometry : angle 0.58094 (32807) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 376 time to evaluate : 2.577 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: 0.6533 (t0) cc_final: 0.5789 (m-30) REVERT: A 38 LYS cc_start: 0.7568 (mmmm) cc_final: 0.6655 (mttm) REVERT: A 53 ILE cc_start: 0.7170 (mm) cc_final: 0.6342 (pt) REVERT: A 385 LEU cc_start: 0.6519 (mt) cc_final: 0.6191 (tp) REVERT: A 417 PHE cc_start: 0.3095 (t80) cc_final: 0.2884 (t80) REVERT: B 389 GLU cc_start: 0.4309 (OUTLIER) cc_final: 0.2984 (pp20) REVERT: B 418 LEU cc_start: 0.6671 (tp) cc_final: 0.6155 (tt) REVERT: C 47 TYR cc_start: 0.5035 (m-80) cc_final: 0.4597 (m-80) REVERT: C 76 LEU cc_start: 0.7452 (tt) cc_final: 0.7226 (tp) REVERT: C 165 TYR cc_start: 0.7465 (m-10) cc_final: 0.7233 (m-10) REVERT: C 389 GLU cc_start: 0.5288 (pt0) cc_final: 0.4998 (pm20) REVERT: C 428 TRP cc_start: 0.7200 (m-10) cc_final: 0.6922 (m100) REVERT: D 1 MET cc_start: 0.6445 (ptm) cc_final: 0.5916 (ptm) REVERT: D 3 GLU cc_start: 0.6770 (mt-10) cc_final: 0.6378 (tt0) REVERT: D 24 ASP cc_start: 0.6620 (OUTLIER) cc_final: 0.6314 (m-30) REVERT: D 41 LYS cc_start: 0.6668 (ttpp) cc_final: 0.6109 (pttp) REVERT: D 152 HIS cc_start: 0.5198 (t70) cc_final: 0.4327 (t-170) REVERT: D 165 TYR cc_start: 0.6426 (m-10) cc_final: 0.6197 (m-80) REVERT: D 236 ARG cc_start: 0.7007 (mtt180) cc_final: 0.6805 (mtt180) REVERT: E 32 PRO cc_start: 0.4954 (Cg_endo) cc_final: 0.4747 (Cg_exo) REVERT: E 76 LEU cc_start: 0.5869 (OUTLIER) cc_final: 0.5471 (mt) REVERT: E 181 LYS cc_start: 0.7222 (mmmt) cc_final: 0.7013 (ptmm) REVERT: E 228 MET cc_start: 0.6908 (ptt) cc_final: 0.6644 (ptp) REVERT: E 331 THR cc_start: 0.5961 (m) cc_final: 0.5440 (t) REVERT: E 427 LYS cc_start: 0.6434 (ttpp) cc_final: 0.6076 (ptmt) REVERT: F 9 LEU cc_start: 0.5869 (mt) cc_final: 0.5596 (mp) REVERT: F 48 HIS cc_start: 0.5190 (m90) cc_final: 0.4960 (m170) REVERT: F 79 LYS cc_start: 0.6745 (mttm) cc_final: 0.6445 (ttmm) REVERT: F 139 ARG cc_start: 0.5832 (mtp-110) cc_final: 0.5601 (mtt-85) REVERT: F 203 LYS cc_start: 0.4605 (OUTLIER) cc_final: 0.3173 (ttmt) REVERT: F 236 ARG cc_start: 0.5525 (mtt-85) cc_final: 0.5237 (mtt90) REVERT: F 263 MET cc_start: 0.6303 (mmm) cc_final: 0.5866 (tmm) REVERT: F 265 LYS cc_start: 0.7083 (mmtm) cc_final: 0.6553 (mmtp) REVERT: F 274 ARG cc_start: 0.4484 (mtm-85) cc_final: 0.3891 (mtt90) REVERT: F 384 MET cc_start: 0.5759 (mtp) cc_final: 0.5432 (ttm) REVERT: F 423 LYS cc_start: 0.6265 (mttm) cc_final: 0.4624 (ptmm) REVERT: H 154 TRP cc_start: 0.3006 (m-90) cc_final: 0.2580 (m-90) REVERT: H 242 ILE cc_start: 0.5249 (mm) cc_final: 0.4298 (tp) REVERT: H 255 LEU cc_start: 0.6238 (OUTLIER) cc_final: 0.5935 (mp) REVERT: H 294 TRP cc_start: 0.7078 (m100) cc_final: 0.6723 (m100) outliers start: 76 outliers final: 44 residues processed: 434 average time/residue: 0.3379 time to fit residues: 230.5881 Evaluate side-chains 376 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 327 time to evaluate : 2.468 ------------------------------------------------------------------------------- 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 178 ILE 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 389 GLU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 244 VAL 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 2 VAL Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 110 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 108 SER 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 310 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 387 VAL 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 103 MET Chi-restraints excluded: chain F residue 203 LYS 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 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 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 8 optimal weight: 9.9990 chunk 202 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 63 optimal weight: 20.0000 chunk 144 optimal weight: 1.9990 chunk 283 optimal weight: 0.3980 chunk 234 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 425 ASN B 100 GLN C 57 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.154688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.132533 restraints weight = 42896.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.132712 restraints weight = 31208.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.133763 restraints weight = 24978.076| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 24201 Z= 0.112 Angle : 0.538 9.036 32813 Z= 0.285 Chirality : 0.041 0.300 3647 Planarity : 0.003 0.038 4071 Dihedral : 10.506 178.452 3399 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.66 % Allowed : 16.33 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 2898 helix: 1.26 (0.14), residues: 1460 sheet: -0.43 (0.27), residues: 400 loop : -1.21 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP F 428 HIS 0.006 0.001 HIS A 43 PHE 0.016 0.001 PHE H 194 TYR 0.015 0.001 TYR A 312 ARG 0.004 0.000 ARG F 170 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 1155) hydrogen bonds : angle 4.71192 ( 3303) metal coordination : bond 0.00299 ( 4) metal coordination : angle 4.82662 ( 6) covalent geometry : bond 0.00242 (24197) covalent geometry : angle 0.53419 (32807) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 363 time to evaluate : 2.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6575 (t0) cc_final: 0.5948 (m-30) REVERT: A 80 LEU cc_start: 0.6136 (OUTLIER) cc_final: 0.5899 (mt) REVERT: A 385 LEU cc_start: 0.6509 (mt) cc_final: 0.6088 (tp) REVERT: B 79 LYS cc_start: 0.7116 (mmmt) cc_final: 0.6576 (mmtp) REVERT: B 418 LEU cc_start: 0.6800 (tp) cc_final: 0.6174 (tt) REVERT: C 1 MET cc_start: 0.7856 (ptm) cc_final: 0.7399 (ptt) REVERT: C 159 GLU cc_start: 0.6494 (mm-30) cc_final: 0.6196 (tt0) REVERT: D 1 MET cc_start: 0.6389 (ptm) cc_final: 0.5920 (ptm) REVERT: D 3 GLU cc_start: 0.6748 (mt-10) cc_final: 0.6331 (tt0) REVERT: D 15 TYR cc_start: 0.5636 (t80) cc_final: 0.5372 (t80) REVERT: D 24 ASP cc_start: 0.6604 (OUTLIER) cc_final: 0.6273 (m-30) REVERT: D 41 LYS cc_start: 0.6652 (ttpp) cc_final: 0.6185 (pttp) REVERT: D 48 HIS cc_start: 0.5251 (m90) cc_final: 0.4721 (m-70) REVERT: D 103 MET cc_start: 0.6430 (mmp) cc_final: 0.6193 (mmm) REVERT: D 128 MET cc_start: 0.6979 (tpp) cc_final: 0.6449 (ttm) REVERT: D 152 HIS cc_start: 0.5236 (t70) cc_final: 0.4387 (t-170) REVERT: D 236 ARG cc_start: 0.6955 (mtt180) cc_final: 0.6698 (mtt180) REVERT: D 303 PHE cc_start: 0.6561 (t80) cc_final: 0.6210 (t80) REVERT: D 419 MET cc_start: 0.6530 (tpp) cc_final: 0.5955 (tpt) REVERT: E 32 PRO cc_start: 0.5005 (Cg_endo) cc_final: 0.4793 (Cg_exo) REVERT: E 76 LEU cc_start: 0.5858 (OUTLIER) cc_final: 0.5456 (mm) REVERT: E 181 LYS cc_start: 0.7184 (mmmt) cc_final: 0.6965 (ptmm) REVERT: E 290 PHE cc_start: 0.6197 (m-80) cc_final: 0.5962 (m-80) REVERT: E 331 THR cc_start: 0.5902 (m) cc_final: 0.5373 (t) REVERT: E 427 LYS cc_start: 0.6531 (ttpp) cc_final: 0.6170 (ptmt) REVERT: F 9 LEU cc_start: 0.5781 (mt) cc_final: 0.5471 (mp) REVERT: F 79 LYS cc_start: 0.6779 (mttm) cc_final: 0.6565 (ttmm) REVERT: F 152 HIS cc_start: 0.6630 (t70) cc_final: 0.6385 (t-170) REVERT: F 263 MET cc_start: 0.6290 (mmm) cc_final: 0.5849 (tmm) REVERT: F 265 LYS cc_start: 0.7076 (mmtm) cc_final: 0.6538 (mmtp) REVERT: F 274 ARG cc_start: 0.4467 (mtm-85) cc_final: 0.3870 (mtt90) REVERT: F 337 GLU cc_start: 0.6059 (mm-30) cc_final: 0.5693 (mm-30) REVERT: F 384 MET cc_start: 0.5834 (mtp) cc_final: 0.5473 (ttm) REVERT: F 423 LYS cc_start: 0.6228 (mttm) cc_final: 0.4579 (ptmm) REVERT: H 49 LYS cc_start: 0.1528 (mttt) cc_final: 0.1191 (tptp) REVERT: H 154 TRP cc_start: 0.2922 (m-90) cc_final: 0.2569 (m-90) REVERT: H 242 ILE cc_start: 0.5309 (mm) cc_final: 0.4885 (mm) REVERT: H 255 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5878 (mp) outliers start: 67 outliers final: 36 residues processed: 411 average time/residue: 0.4297 time to fit residues: 278.1087 Evaluate side-chains 375 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 335 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 172 VAL 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 56 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 307 ILE Chi-restraints excluded: chain C residue 313 LEU 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 D residue 110 ILE 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 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 E residue 429 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 131 VAL 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 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 299 TRP 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 9 optimal weight: 0.9990 chunk 265 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 0.5980 chunk 88 optimal weight: 8.9990 chunk 272 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 B 100 GLN B 399 GLN ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.152809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.130342 restraints weight = 42825.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.130312 restraints weight = 31607.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.131201 restraints weight = 25336.752| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24201 Z= 0.140 Angle : 0.578 9.759 32813 Z= 0.304 Chirality : 0.043 0.292 3647 Planarity : 0.004 0.040 4071 Dihedral : 10.478 170.240 3399 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.77 % Allowed : 16.25 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.16), residues: 2898 helix: 1.19 (0.14), residues: 1459 sheet: -0.41 (0.27), residues: 400 loop : -1.25 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 428 HIS 0.007 0.001 HIS A 43 PHE 0.025 0.002 PHE A 417 TYR 0.018 0.002 TYR A 312 ARG 0.005 0.001 ARG D 161 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 1155) hydrogen bonds : angle 4.76958 ( 3303) metal coordination : bond 0.00474 ( 4) metal coordination : angle 5.53167 ( 6) covalent geometry : bond 0.00319 (24197) covalent geometry : angle 0.57348 (32807) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 375 time to evaluate : 2.662 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: 0.6686 (t0) cc_final: 0.6068 (m-30) REVERT: A 57 ASN cc_start: 0.6797 (t0) cc_final: 0.5921 (t0) REVERT: A 80 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.6009 (mt) REVERT: A 312 TYR cc_start: 0.4020 (OUTLIER) cc_final: 0.3483 (m-80) REVERT: A 380 THR cc_start: 0.7160 (p) cc_final: 0.6788 (t) REVERT: B 67 GLU cc_start: 0.5326 (mt-10) cc_final: 0.4946 (mt-10) REVERT: B 79 LYS cc_start: 0.7289 (mmmt) cc_final: 0.7074 (mmtp) REVERT: B 296 GLU cc_start: 0.5937 (tt0) cc_final: 0.5635 (tt0) REVERT: B 418 LEU cc_start: 0.6776 (tp) cc_final: 0.6204 (tt) REVERT: C 1 MET cc_start: 0.7897 (ptm) cc_final: 0.7430 (ptt) REVERT: C 400 LEU cc_start: 0.6810 (tp) cc_final: 0.6568 (tt) REVERT: D 1 MET cc_start: 0.6352 (ptm) cc_final: 0.5918 (ptm) REVERT: D 3 GLU cc_start: 0.6834 (mt-10) cc_final: 0.6400 (tt0) REVERT: D 23 MET cc_start: 0.7232 (mmp) cc_final: 0.6945 (mmp) REVERT: D 41 LYS cc_start: 0.6701 (ttpp) cc_final: 0.6199 (pttp) REVERT: D 48 HIS cc_start: 0.5344 (m90) cc_final: 0.4810 (m-70) REVERT: D 93 GLU cc_start: 0.6490 (mm-30) cc_final: 0.5994 (tp30) REVERT: D 103 MET cc_start: 0.6451 (mmp) cc_final: 0.6204 (mmm) REVERT: D 236 ARG cc_start: 0.7030 (mtt180) cc_final: 0.6783 (mtt180) REVERT: D 274 ARG cc_start: 0.5914 (mtm110) cc_final: 0.5676 (mtm-85) REVERT: D 419 MET cc_start: 0.6720 (tpp) cc_final: 0.6320 (tpt) REVERT: E 32 PRO cc_start: 0.4906 (Cg_endo) cc_final: 0.4674 (Cg_exo) REVERT: E 76 LEU cc_start: 0.5873 (OUTLIER) cc_final: 0.5460 (mm) REVERT: E 228 MET cc_start: 0.6823 (ptt) cc_final: 0.6471 (ptp) REVERT: E 264 GLU cc_start: 0.5448 (mt-10) cc_final: 0.5228 (mt-10) REVERT: E 290 PHE cc_start: 0.6143 (m-80) cc_final: 0.5919 (m-80) REVERT: E 331 THR cc_start: 0.5991 (m) cc_final: 0.5672 (t) REVERT: E 428 TRP cc_start: 0.7133 (m-10) cc_final: 0.6668 (m-10) REVERT: F 9 LEU cc_start: 0.5857 (mt) cc_final: 0.5608 (mp) REVERT: F 79 LYS cc_start: 0.6783 (mttm) cc_final: 0.6525 (ttmm) REVERT: F 152 HIS cc_start: 0.6709 (t70) cc_final: 0.6344 (t-170) REVERT: F 265 LYS cc_start: 0.7043 (mmtm) cc_final: 0.6521 (mmtp) REVERT: F 274 ARG cc_start: 0.4348 (mtm-85) cc_final: 0.3821 (mtt90) REVERT: F 384 MET cc_start: 0.5835 (mtp) cc_final: 0.5545 (ttm) REVERT: F 423 LYS cc_start: 0.6227 (mttm) cc_final: 0.5618 (mmmm) REVERT: H 18 HIS cc_start: 0.2784 (OUTLIER) cc_final: 0.1885 (p-80) REVERT: H 49 LYS cc_start: 0.1589 (mttt) cc_final: 0.1232 (tptp) REVERT: H 94 ARG cc_start: 0.5835 (mtp-110) cc_final: 0.5325 (mmm160) REVERT: H 154 TRP cc_start: 0.3189 (m-90) cc_final: 0.2705 (m-90) REVERT: H 242 ILE cc_start: 0.5353 (mm) cc_final: 0.4814 (mm) REVERT: H 255 LEU cc_start: 0.6188 (OUTLIER) cc_final: 0.5848 (mp) REVERT: H 294 TRP cc_start: 0.7071 (m100) cc_final: 0.6679 (m100) outliers start: 70 outliers final: 50 residues processed: 427 average time/residue: 0.3386 time to fit residues: 227.6986 Evaluate side-chains 394 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 339 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 312 TYR 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 56 LEU 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 313 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 155 MET 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 152 HIS Chi-restraints excluded: chain E residue 174 PHE 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 325 SER 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 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 90 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 131 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 255 LEU Chi-restraints excluded: chain H residue 299 TRP Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 273 optimal weight: 0.9980 chunk 253 optimal weight: 1.9990 chunk 218 optimal weight: 0.3980 chunk 191 optimal weight: 3.9990 chunk 206 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 268 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 B 100 GLN B 200 ASN ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 GLN H 48 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.154599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.131824 restraints weight = 42931.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.132102 restraints weight = 31388.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.132790 restraints weight = 24844.059| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24201 Z= 0.108 Angle : 0.541 9.681 32813 Z= 0.285 Chirality : 0.041 0.286 3647 Planarity : 0.003 0.038 4071 Dihedral : 10.289 167.524 3399 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.26 % Allowed : 17.28 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.16), residues: 2898 helix: 1.42 (0.14), residues: 1454 sheet: -0.32 (0.28), residues: 392 loop : -1.25 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 428 HIS 0.007 0.001 HIS A 43 PHE 0.019 0.001 PHE H 194 TYR 0.015 0.001 TYR A 165 ARG 0.004 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 1155) hydrogen bonds : angle 4.60528 ( 3303) metal coordination : bond 0.00231 ( 4) metal coordination : angle 4.85858 ( 6) covalent geometry : bond 0.00231 (24197) covalent geometry : angle 0.53744 (32807) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 372 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6688 (tpp) cc_final: 0.6254 (tpp) REVERT: A 12 ASP cc_start: 0.6656 (t0) cc_final: 0.6074 (m-30) REVERT: A 53 ILE cc_start: 0.6997 (OUTLIER) cc_final: 0.6647 (pt) REVERT: A 76 LEU cc_start: 0.5438 (OUTLIER) cc_final: 0.5158 (mm) REVERT: A 380 THR cc_start: 0.7112 (p) cc_final: 0.6735 (t) REVERT: B 67 GLU cc_start: 0.5222 (mt-10) cc_final: 0.4879 (mt-10) REVERT: B 163 LEU cc_start: 0.7343 (mm) cc_final: 0.6839 (tp) REVERT: B 296 GLU cc_start: 0.5970 (tt0) cc_final: 0.5605 (tt0) REVERT: C 1 MET cc_start: 0.7902 (ptm) cc_final: 0.7409 (ptt) REVERT: C 263 MET cc_start: 0.6650 (mmm) cc_final: 0.5952 (mtp) REVERT: D 1 MET cc_start: 0.6338 (ptm) cc_final: 0.5898 (ptm) REVERT: D 3 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6359 (tt0) REVERT: D 15 TYR cc_start: 0.5757 (t80) cc_final: 0.5533 (t80) REVERT: D 23 MET cc_start: 0.7193 (mmp) cc_final: 0.6844 (mmp) REVERT: D 24 ASP cc_start: 0.6520 (OUTLIER) cc_final: 0.6235 (m-30) REVERT: D 41 LYS cc_start: 0.6679 (ttpp) cc_final: 0.6137 (pttp) REVERT: D 48 HIS cc_start: 0.5270 (m90) cc_final: 0.4906 (m-70) REVERT: D 93 GLU cc_start: 0.6492 (mm-30) cc_final: 0.5992 (tp30) REVERT: D 236 ARG cc_start: 0.6885 (mtt180) cc_final: 0.6609 (mtt180) REVERT: D 419 MET cc_start: 0.6727 (tpp) cc_final: 0.6305 (tpt) REVERT: E 32 PRO cc_start: 0.4892 (Cg_endo) cc_final: 0.4679 (Cg_exo) REVERT: E 76 LEU cc_start: 0.5888 (OUTLIER) cc_final: 0.5450 (mm) REVERT: E 331 THR cc_start: 0.5872 (m) cc_final: 0.5563 (t) REVERT: F 9 LEU cc_start: 0.5757 (mt) cc_final: 0.5485 (mp) REVERT: F 152 HIS cc_start: 0.6630 (t70) cc_final: 0.5971 (t-170) REVERT: F 265 LYS cc_start: 0.7022 (mmtm) cc_final: 0.6512 (mmtp) REVERT: F 274 ARG cc_start: 0.4427 (mtm-85) cc_final: 0.3866 (mtt90) REVERT: F 337 GLU cc_start: 0.6021 (mm-30) cc_final: 0.5612 (mm-30) REVERT: F 384 MET cc_start: 0.5885 (mtp) cc_final: 0.5554 (ttm) REVERT: F 423 LYS cc_start: 0.6231 (mttm) cc_final: 0.4550 (ptmm) REVERT: H 49 LYS cc_start: 0.1676 (mttt) cc_final: 0.1262 (tptp) REVERT: H 94 ARG cc_start: 0.5719 (mtp-110) cc_final: 0.5349 (mmm160) REVERT: H 242 ILE cc_start: 0.5242 (mm) cc_final: 0.4760 (mm) REVERT: H 255 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5933 (mp) REVERT: H 268 LEU cc_start: 0.5662 (mt) cc_final: 0.5434 (mp) REVERT: H 281 MET cc_start: 0.7141 (mtt) cc_final: 0.6689 (mmp) outliers start: 57 outliers final: 35 residues processed: 414 average time/residue: 0.4014 time to fit residues: 261.6087 Evaluate side-chains 376 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 336 time to evaluate : 2.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE 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 142 LEU 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 C residue 244 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 243 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 174 PHE 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 325 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 19 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 208 CYS Chi-restraints excluded: chain F residue 327 ASN 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 255 LEU Chi-restraints excluded: chain H residue 299 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 57 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 112 optimal weight: 0.0070 chunk 265 optimal weight: 10.0000 chunk 177 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 134 optimal weight: 0.4980 overall best weight: 2.1004 ------------------------------------------------------------------------------- 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 B 100 GLN B 200 ASN ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.153242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.130627 restraints weight = 43097.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.130411 restraints weight = 32368.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.131329 restraints weight = 25384.644| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24201 Z= 0.134 Angle : 0.572 9.282 32813 Z= 0.301 Chirality : 0.042 0.290 3647 Planarity : 0.004 0.038 4071 Dihedral : 10.360 165.664 3399 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.42 % Allowed : 17.20 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2898 helix: 1.34 (0.14), residues: 1453 sheet: -0.31 (0.28), residues: 392 loop : -1.28 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 428 HIS 0.005 0.001 HIS A 43 PHE 0.020 0.002 PHE E 290 TYR 0.018 0.001 TYR F 15 ARG 0.006 0.000 ARG D 322 Details of bonding type rmsd hydrogen bonds : bond 0.03308 ( 1155) hydrogen bonds : angle 4.64517 ( 3303) metal coordination : bond 0.00371 ( 4) metal coordination : angle 5.27168 ( 6) covalent geometry : bond 0.00303 (24197) covalent geometry : angle 0.56748 (32807) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 348 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6722 (tpp) cc_final: 0.6285 (tpp) REVERT: A 12 ASP cc_start: 0.6679 (t0) cc_final: 0.6127 (m-30) REVERT: A 76 LEU cc_start: 0.5546 (OUTLIER) cc_final: 0.5221 (mm) REVERT: A 128 MET cc_start: 0.3694 (tpt) cc_final: 0.3291 (tpt) REVERT: A 380 THR cc_start: 0.7076 (p) cc_final: 0.6757 (t) REVERT: B 67 GLU cc_start: 0.5308 (mt-10) cc_final: 0.4948 (mt-10) REVERT: B 89 TRP cc_start: 0.6607 (t60) cc_final: 0.6342 (t60) REVERT: B 163 LEU cc_start: 0.7374 (mm) cc_final: 0.6842 (tp) REVERT: B 296 GLU cc_start: 0.5998 (tt0) cc_final: 0.5671 (tt0) REVERT: B 326 GLU cc_start: 0.4719 (tt0) cc_final: 0.3448 (mp0) REVERT: C 1 MET cc_start: 0.7799 (ptm) cc_final: 0.7407 (ptt) REVERT: C 112 GLU cc_start: 0.6433 (tt0) cc_final: 0.6099 (tt0) REVERT: D 1 MET cc_start: 0.6319 (ptm) cc_final: 0.5545 (ptm) REVERT: D 3 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6371 (tt0) REVERT: D 23 MET cc_start: 0.7180 (mmp) cc_final: 0.6894 (mmp) REVERT: D 41 LYS cc_start: 0.6839 (ttpp) cc_final: 0.6287 (pttp) REVERT: D 48 HIS cc_start: 0.5398 (m90) cc_final: 0.4991 (m-70) REVERT: D 52 SER cc_start: 0.7138 (p) cc_final: 0.6890 (t) REVERT: D 93 GLU cc_start: 0.6535 (mm-30) cc_final: 0.6083 (mm-30) REVERT: D 236 ARG cc_start: 0.7005 (mtt180) cc_final: 0.6764 (mtt180) REVERT: D 373 GLU cc_start: 0.4498 (pm20) cc_final: 0.3998 (pm20) REVERT: D 419 MET cc_start: 0.6770 (tpp) cc_final: 0.6355 (tpt) REVERT: E 18 LYS cc_start: 0.5941 (mmtm) cc_final: 0.5204 (tptt) REVERT: E 32 PRO cc_start: 0.4827 (Cg_endo) cc_final: 0.4611 (Cg_exo) REVERT: E 76 LEU cc_start: 0.5908 (OUTLIER) cc_final: 0.5446 (mm) REVERT: E 264 GLU cc_start: 0.5436 (mt-10) cc_final: 0.5153 (mt-10) REVERT: E 331 THR cc_start: 0.5972 (m) cc_final: 0.5679 (t) REVERT: E 429 VAL cc_start: 0.7970 (OUTLIER) cc_final: 0.7708 (p) REVERT: F 9 LEU cc_start: 0.5864 (mt) cc_final: 0.5596 (mp) REVERT: F 152 HIS cc_start: 0.6602 (t70) cc_final: 0.6010 (t-170) REVERT: F 265 LYS cc_start: 0.7040 (mmtm) cc_final: 0.6526 (mmtp) REVERT: F 274 ARG cc_start: 0.4366 (mtm-85) cc_final: 0.3812 (mtt90) REVERT: F 298 LYS cc_start: 0.6199 (mtmt) cc_final: 0.5991 (mtpt) REVERT: F 384 MET cc_start: 0.5907 (mtp) cc_final: 0.5606 (ttm) REVERT: F 419 MET cc_start: 0.3770 (ttt) cc_final: 0.3229 (ttt) REVERT: F 423 LYS cc_start: 0.6158 (mttm) cc_final: 0.4603 (ptmm) REVERT: H 18 HIS cc_start: 0.2862 (OUTLIER) cc_final: 0.1959 (p-80) REVERT: H 49 LYS cc_start: 0.1661 (mttt) cc_final: 0.1290 (tptp) REVERT: H 94 ARG cc_start: 0.5683 (mtp-110) cc_final: 0.5324 (mmm160) REVERT: H 242 ILE cc_start: 0.5395 (mm) cc_final: 0.4899 (mm) REVERT: H 255 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5930 (mp) REVERT: H 294 TRP cc_start: 0.7065 (m100) cc_final: 0.6730 (m100) outliers start: 61 outliers final: 45 residues processed: 395 average time/residue: 0.3880 time to fit residues: 241.3932 Evaluate side-chains 387 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 337 time to evaluate : 3.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 244 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 306 THR 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 110 ILE Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 422 GLN 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 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 199 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 325 SER 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 19 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 131 VAL 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 181 VAL 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 299 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 267 optimal weight: 6.9990 chunk 144 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 196 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 265 optimal weight: 1.9990 chunk 236 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 B 100 GLN B 200 ASN C 116 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.154291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.131758 restraints weight = 42699.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.131876 restraints weight = 30585.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.132678 restraints weight = 22171.743| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 24201 Z= 0.112 Angle : 0.555 11.283 32813 Z= 0.289 Chirality : 0.042 0.283 3647 Planarity : 0.003 0.036 4071 Dihedral : 10.268 163.964 3399 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.30 % Allowed : 17.76 % 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: 0.34 (0.16), residues: 2898 helix: 1.42 (0.14), residues: 1452 sheet: -0.26 (0.28), residues: 392 loop : -1.27 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 428 HIS 0.009 0.001 HIS A 43 PHE 0.023 0.001 PHE H 194 TYR 0.014 0.001 TYR A 165 ARG 0.006 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03109 ( 1155) hydrogen bonds : angle 4.59141 ( 3303) metal coordination : bond 0.00247 ( 4) metal coordination : angle 4.91849 ( 6) covalent geometry : bond 0.00247 (24197) covalent geometry : angle 0.55074 (32807) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 358 time to evaluate : 2.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6613 (tpp) cc_final: 0.6359 (tpp) REVERT: A 12 ASP cc_start: 0.6658 (t0) cc_final: 0.6153 (m-30) REVERT: A 53 ILE cc_start: 0.6944 (OUTLIER) cc_final: 0.6398 (pt) REVERT: A 76 LEU cc_start: 0.5469 (OUTLIER) cc_final: 0.5168 (mm) REVERT: A 128 MET cc_start: 0.3678 (tpt) cc_final: 0.3336 (tpt) REVERT: A 380 THR cc_start: 0.6918 (p) cc_final: 0.6603 (t) REVERT: B 67 GLU cc_start: 0.5290 (mt-10) cc_final: 0.4906 (mt-10) REVERT: B 89 TRP cc_start: 0.6585 (t60) cc_final: 0.6343 (t60) REVERT: B 163 LEU cc_start: 0.7309 (mm) cc_final: 0.6829 (tp) REVERT: B 296 GLU cc_start: 0.5951 (tt0) cc_final: 0.5604 (tt0) REVERT: B 326 GLU cc_start: 0.4640 (tt0) cc_final: 0.3421 (mp0) REVERT: C 1 MET cc_start: 0.7782 (ptm) cc_final: 0.7454 (ptt) REVERT: C 85 GLU cc_start: 0.6357 (OUTLIER) cc_final: 0.6038 (mm-30) REVERT: C 304 VAL cc_start: 0.7901 (t) cc_final: 0.7685 (p) REVERT: D 1 MET cc_start: 0.6277 (ptm) cc_final: 0.5514 (ptm) REVERT: D 3 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6372 (tt0) REVERT: D 23 MET cc_start: 0.7157 (mmp) cc_final: 0.6867 (mmp) REVERT: D 41 LYS cc_start: 0.6848 (ttpp) cc_final: 0.6275 (pttp) REVERT: D 48 HIS cc_start: 0.5400 (m90) cc_final: 0.5045 (m170) REVERT: D 52 SER cc_start: 0.7157 (p) cc_final: 0.6928 (t) REVERT: D 93 GLU cc_start: 0.6540 (mm-30) cc_final: 0.6082 (mm-30) REVERT: D 236 ARG cc_start: 0.6909 (mtt180) cc_final: 0.6614 (mtt180) REVERT: D 419 MET cc_start: 0.6782 (tpp) cc_final: 0.6381 (tpt) REVERT: E 18 LYS cc_start: 0.5923 (mmtm) cc_final: 0.5296 (tptt) REVERT: E 32 PRO cc_start: 0.4765 (Cg_endo) cc_final: 0.4544 (Cg_exo) REVERT: E 76 LEU cc_start: 0.5958 (OUTLIER) cc_final: 0.5456 (mm) REVERT: E 228 MET cc_start: 0.6780 (ptt) cc_final: 0.6438 (ptp) REVERT: E 264 GLU cc_start: 0.5383 (OUTLIER) cc_final: 0.5177 (mt-10) REVERT: E 331 THR cc_start: 0.5919 (m) cc_final: 0.5608 (t) REVERT: E 391 GLU cc_start: 0.5918 (pt0) cc_final: 0.5711 (pt0) REVERT: F 9 LEU cc_start: 0.5792 (mt) cc_final: 0.5511 (mp) REVERT: F 152 HIS cc_start: 0.6477 (t70) cc_final: 0.5957 (t-170) REVERT: F 236 ARG cc_start: 0.6115 (mtp85) cc_final: 0.5229 (mtp85) REVERT: F 265 LYS cc_start: 0.7024 (mmtm) cc_final: 0.6503 (mmtp) REVERT: F 274 ARG cc_start: 0.4382 (mtm-85) cc_final: 0.3819 (mtt90) REVERT: F 298 LYS cc_start: 0.6198 (mtmt) cc_final: 0.5983 (mtpt) REVERT: F 321 ILE cc_start: 0.4830 (mt) cc_final: 0.4558 (mp) REVERT: F 337 GLU cc_start: 0.6144 (mm-30) cc_final: 0.5663 (mm-30) REVERT: F 384 MET cc_start: 0.5923 (mtp) cc_final: 0.5646 (ttm) REVERT: H 18 HIS cc_start: 0.2935 (OUTLIER) cc_final: 0.2067 (p-80) REVERT: H 94 ARG cc_start: 0.5665 (mtp-110) cc_final: 0.5311 (mmm160) REVERT: H 242 ILE cc_start: 0.5345 (mm) cc_final: 0.4854 (mm) REVERT: H 255 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.6018 (mp) outliers start: 58 outliers final: 40 residues processed: 400 average time/residue: 0.3398 time to fit residues: 214.6577 Evaluate side-chains 381 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 334 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 53 ILE 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 200 ASN Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 131 VAL 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 313 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 422 GLN 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 174 PHE 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 264 GLU Chi-restraints excluded: chain E residue 325 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 19 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 208 CYS 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 181 VAL Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 255 LEU 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 93 optimal weight: 2.9990 chunk 290 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 193 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 279 optimal weight: 30.0000 chunk 48 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 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** ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 ASN H 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.151750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.129010 restraints weight = 43099.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.128884 restraints weight = 33748.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.129672 restraints weight = 24947.642| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6459 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24201 Z= 0.162 Angle : 0.630 12.310 32813 Z= 0.328 Chirality : 0.044 0.303 3647 Planarity : 0.004 0.038 4071 Dihedral : 10.529 167.978 3399 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.34 % Allowed : 18.03 % Favored : 79.63 % 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: 0.07 (0.16), residues: 2898 helix: 1.14 (0.14), residues: 1452 sheet: -0.29 (0.28), residues: 383 loop : -1.33 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 428 HIS 0.009 0.001 HIS A 43 PHE 0.026 0.002 PHE E 383 TYR 0.034 0.002 TYR D 15 ARG 0.005 0.001 ARG D 322 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 1155) hydrogen bonds : angle 4.77118 ( 3303) metal coordination : bond 0.00455 ( 4) metal coordination : angle 7.78169 ( 6) covalent geometry : bond 0.00370 (24197) covalent geometry : angle 0.62117 (32807) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 349 time to evaluate : 3.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6723 (tpp) cc_final: 0.6307 (tpp) REVERT: A 12 ASP cc_start: 0.6752 (t0) cc_final: 0.6200 (m-30) REVERT: A 76 LEU cc_start: 0.5625 (OUTLIER) cc_final: 0.5295 (mm) REVERT: A 128 MET cc_start: 0.3617 (tpt) cc_final: 0.3305 (tpt) REVERT: A 333 LYS cc_start: 0.6033 (tptt) cc_final: 0.5494 (tptt) REVERT: A 380 THR cc_start: 0.7057 (p) cc_final: 0.6717 (t) REVERT: B 67 GLU cc_start: 0.5329 (mt-10) cc_final: 0.4940 (mt-10) REVERT: B 103 MET cc_start: 0.6402 (mmp) cc_final: 0.6184 (mmm) REVERT: B 163 LEU cc_start: 0.7363 (mm) cc_final: 0.6826 (tp) REVERT: B 177 ARG cc_start: 0.6161 (mtm180) cc_final: 0.5947 (mtm-85) REVERT: C 85 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.6049 (mm-30) REVERT: D 1 MET cc_start: 0.6273 (ptm) cc_final: 0.5567 (ptm) REVERT: D 3 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6456 (tt0) REVERT: D 23 MET cc_start: 0.7163 (mmp) cc_final: 0.6882 (mmp) REVERT: D 41 LYS cc_start: 0.7158 (ttpp) cc_final: 0.6341 (pttp) REVERT: D 48 HIS cc_start: 0.5394 (m90) cc_final: 0.4982 (m-70) REVERT: D 93 GLU cc_start: 0.6546 (mm-30) cc_final: 0.6093 (mm-30) REVERT: D 236 ARG cc_start: 0.7002 (mtt180) cc_final: 0.6751 (mtt180) REVERT: E 18 LYS cc_start: 0.5918 (mmtm) cc_final: 0.5153 (tptt) REVERT: E 32 PRO cc_start: 0.4834 (Cg_endo) cc_final: 0.4625 (Cg_exo) REVERT: E 76 LEU cc_start: 0.5987 (OUTLIER) cc_final: 0.5458 (mm) REVERT: E 290 PHE cc_start: 0.6189 (m-80) cc_final: 0.5983 (m-80) REVERT: E 331 THR cc_start: 0.5981 (m) cc_final: 0.5665 (t) REVERT: F 9 LEU cc_start: 0.5874 (mt) cc_final: 0.5609 (mp) REVERT: F 152 HIS cc_start: 0.6419 (t70) cc_final: 0.5886 (t-170) REVERT: F 175 LYS cc_start: 0.5281 (tttt) cc_final: 0.4760 (tptp) REVERT: F 263 MET cc_start: 0.5781 (tmm) cc_final: 0.4402 (tmm) REVERT: F 265 LYS cc_start: 0.7044 (mmtm) cc_final: 0.6563 (mttm) REVERT: F 274 ARG cc_start: 0.4349 (mtm-85) cc_final: 0.3865 (mtt90) REVERT: F 321 ILE cc_start: 0.4776 (mt) cc_final: 0.4476 (mm) REVERT: F 358 LYS cc_start: 0.5458 (mtpt) cc_final: 0.4796 (mtmt) REVERT: F 384 MET cc_start: 0.5923 (mtp) cc_final: 0.5635 (ttm) REVERT: H 18 HIS cc_start: 0.3131 (OUTLIER) cc_final: 0.2128 (p-80) REVERT: H 94 ARG cc_start: 0.5604 (mtp-110) cc_final: 0.5184 (mmm160) REVERT: H 242 ILE cc_start: 0.5333 (mm) cc_final: 0.4835 (mm) REVERT: H 255 LEU cc_start: 0.6282 (OUTLIER) cc_final: 0.6075 (mp) REVERT: H 294 TRP cc_start: 0.7113 (m100) cc_final: 0.6729 (m100) outliers start: 59 outliers final: 44 residues processed: 395 average time/residue: 0.3569 time to fit residues: 223.9320 Evaluate side-chains 371 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 322 time to evaluate : 2.635 ------------------------------------------------------------------------------- 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 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 131 VAL 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 2 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 422 GLN 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 148 SER Chi-restraints excluded: chain E residue 174 PHE 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 310 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 208 CYS 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 181 VAL Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 255 LEU 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 164 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 203 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 B 200 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 ASN ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 ASN H 48 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.152090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.129556 restraints weight = 42892.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.129664 restraints weight = 31347.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.130214 restraints weight = 24742.895| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24201 Z= 0.140 Angle : 0.605 16.418 32813 Z= 0.314 Chirality : 0.043 0.297 3647 Planarity : 0.004 0.037 4071 Dihedral : 10.499 167.268 3399 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.30 % Allowed : 18.23 % Favored : 79.47 % 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: 0.11 (0.16), residues: 2898 helix: 1.20 (0.14), residues: 1454 sheet: -0.26 (0.28), residues: 384 loop : -1.36 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP C 428 HIS 0.010 0.001 HIS A 43 PHE 0.022 0.002 PHE E 383 TYR 0.024 0.002 TYR D 47 ARG 0.005 0.000 ARG D 322 Details of bonding type rmsd hydrogen bonds : bond 0.03406 ( 1155) hydrogen bonds : angle 4.73388 ( 3303) metal coordination : bond 0.00517 ( 4) metal coordination : angle 9.03255 ( 6) covalent geometry : bond 0.00319 (24197) covalent geometry : angle 0.59298 (32807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8261.31 seconds wall clock time: 147 minutes 36.25 seconds (8856.25 seconds total)