Starting phenix.real_space_refine on Sun Mar 17 10:04:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5g_30085/03_2024/6m5g_30085_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5g_30085/03_2024/6m5g_30085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5g_30085/03_2024/6m5g_30085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5g_30085/03_2024/6m5g_30085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5g_30085/03_2024/6m5g_30085_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5g_30085/03_2024/6m5g_30085_updated.pdb" } resolution = 3.6 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 108 5.16 5 C 10948 2.51 5 N 2981 2.21 5 O 3311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 28": "NH1" <-> "NH2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "E ARG 28": "NH1" <-> "NH2" Residue "E PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17363 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2881 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2879 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2885 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2873 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2876 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 943 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "G" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 943 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 943 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.55, per 1000 atoms: 0.55 Number of scatterers: 17363 At special positions: 0 Unit cell: (129.72, 89.7, 194.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 P 10 15.00 Mg 5 11.99 O 3311 8.00 N 2981 7.00 C 10948 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 - 3.50 Amino acid : False - 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: 6.58 Conformation dependent library (CDL) restraints added in 3.1 seconds 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4074 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 106 helices and 20 sheets defined 42.9% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 removed outlier: 3.853A pdb=" N GLU A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 139 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.610A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.690A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.739A pdb=" N THR A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 293 removed outlier: 3.860A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 335 through 348 removed outlier: 4.930A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.746A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.914A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.902A pdb=" N SER B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 196 removed outlier: 4.133A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 4.045A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 231 removed outlier: 3.717A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 264 through 267 removed outlier: 3.531A pdb=" N ILE B 267 " --> pdb=" O PRO B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 264 through 267' Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.656A pdb=" N THR B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 293 removed outlier: 3.795A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 338 through 348 removed outlier: 3.798A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.591A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 79 through 91 removed outlier: 3.794A pdb=" N GLU C 83 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.923A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 195 removed outlier: 4.801A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.827A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 252 through 254 No H-bonds generated for 'chain 'C' and resid 252 through 254' Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 264 through 267 removed outlier: 3.661A pdb=" N ILE C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 267' Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.562A pdb=" N THR C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 293 removed outlier: 3.972A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 307 through 318 removed outlier: 4.495A pdb=" N ALA C 310 " --> pdb=" O PRO C 307 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP C 311 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG C 312 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N MET C 313 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 352 through 354 No H-bonds generated for 'chain 'C' and resid 352 through 354' Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.867A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 79 through 91 removed outlier: 3.907A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 126 Processing helix chain 'D' and resid 137 through 145 removed outlier: 4.171A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 195 removed outlier: 4.182A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 4.156A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 231 removed outlier: 3.687A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.517A pdb=" N THR D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 293 removed outlier: 4.085A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 305 No H-bonds generated for 'chain 'D' and resid 303 through 305' Processing helix chain 'D' and resid 307 through 318 removed outlier: 4.548A pdb=" N ALA D 310 " --> pdb=" O PRO D 307 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP D 311 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG D 312 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N MET D 313 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 347 removed outlier: 4.691A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 354 removed outlier: 3.742A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 351 through 354' Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 373 Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 79 through 91 removed outlier: 3.829A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 145 removed outlier: 4.248A pdb=" N LEU E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 195 removed outlier: 3.509A pdb=" N LYS E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 removed outlier: 3.888A pdb=" N LYS E 215 " --> pdb=" O ASP E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 231 Processing helix chain 'E' and resid 274 through 283 removed outlier: 3.553A pdb=" N THR E 278 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 293 removed outlier: 4.250A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 305 Processing helix chain 'E' and resid 309 through 318 removed outlier: 3.884A pdb=" N GLN E 314 " --> pdb=" O ALA E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 348 Processing helix chain 'E' and resid 352 through 354 No H-bonds generated for 'chain 'E' and resid 352 through 354' Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 367 through 373 removed outlier: 3.589A pdb=" N VAL E 370 " --> pdb=" O PRO E 367 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS E 371 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 47 removed outlier: 3.862A pdb=" N LYS F 35 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER F 46 " --> pdb=" O ALA F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 112 through 116 removed outlier: 3.532A pdb=" N VAL F 116 " --> pdb=" O GLY F 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 112 through 116' Processing helix chain 'F' and resid 120 through 123 No H-bonds generated for 'chain 'F' and resid 120 through 123' Processing helix chain 'F' and resid 126 through 134 Processing helix chain 'G' and resid 21 through 47 removed outlier: 4.212A pdb=" N GLU G 28 " --> pdb=" O ARG G 25 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS G 35 " --> pdb=" O VAL G 32 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER G 46 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 74 removed outlier: 3.517A pdb=" N GLU G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 103 removed outlier: 4.165A pdb=" N ASN G 103 " --> pdb=" O VAL G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'G' and resid 120 through 123 No H-bonds generated for 'chain 'G' and resid 120 through 123' Processing helix chain 'G' and resid 125 through 134 Processing helix chain 'H' and resid 21 through 47 removed outlier: 3.984A pdb=" N LYS H 35 " --> pdb=" O VAL H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 74 removed outlier: 3.982A pdb=" N LEU H 69 " --> pdb=" O LYS H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 102 Processing helix chain 'H' and resid 113 through 116 No H-bonds generated for 'chain 'H' and resid 113 through 116' Processing helix chain 'H' and resid 120 through 123 No H-bonds generated for 'chain 'H' and resid 120 through 123' Processing helix chain 'H' and resid 126 through 134 removed outlier: 3.647A pdb=" N TRP H 134 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 8 through 12 removed outlier: 3.572A pdb=" N ALA A 19 " --> pdb=" O ALA A 29 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 103 through 107 Processing sheet with id= C, first strand: chain 'A' and resid 163 through 165 removed outlier: 3.558A pdb=" N VAL A 298 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 160 through 162 Processing sheet with id= E, first strand: chain 'B' and resid 8 through 10 removed outlier: 4.215A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 16 through 19 removed outlier: 3.674A pdb=" N ALA B 29 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 34 through 38 removed outlier: 3.740A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 150 through 152 removed outlier: 3.710A pdb=" N VAL B 152 " --> pdb=" O VAL B 163 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 7 through 10 removed outlier: 7.553A pdb=" N CYS C 10 " --> pdb=" O PRO C 102 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU C 104 " --> pdb=" O CYS C 10 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 16 through 19 removed outlier: 3.665A pdb=" N ALA C 19 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA C 29 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= L, first strand: chain 'C' and resid 150 through 155 removed outlier: 3.754A pdb=" N VAL C 152 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN C 162 " --> pdb=" O MET C 176 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 239 through 241 Processing sheet with id= N, first strand: chain 'D' and resid 16 through 19 removed outlier: 3.602A pdb=" N PHE D 31 " --> pdb=" O VAL D 17 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= P, first strand: chain 'D' and resid 103 through 107 Processing sheet with id= Q, first strand: chain 'D' and resid 150 through 154 removed outlier: 3.561A pdb=" N VAL D 152 " --> pdb=" O VAL D 163 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.618A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL E 9 " --> pdb=" O GLY E 20 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 150 through 154 removed outlier: 3.727A pdb=" N VAL E 152 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP E 154 " --> pdb=" O HIS E 161 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 238 through 241 removed outlier: 3.724A pdb=" N LYS E 238 " --> pdb=" O ILE E 250 " (cutoff:3.500A) 548 hydrogen bonds defined for protein. 1260 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: 4.70 Time building geometry restraints manager: 7.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5672 1.33 - 1.45: 2332 1.45 - 1.57: 9519 1.57 - 1.68: 15 1.68 - 1.80: 191 Bond restraints: 17729 Sorted by residual: bond pdb=" CA ARG E 335 " pdb=" C ARG E 335 " ideal model delta sigma weight residual 1.523 1.441 0.083 1.80e-02 3.09e+03 2.10e+01 bond pdb=" CA ALA C 310 " pdb=" C ALA C 310 " ideal model delta sigma weight residual 1.522 1.469 0.053 1.72e-02 3.38e+03 9.48e+00 bond pdb=" C GLN C 263 " pdb=" N PRO C 264 " ideal model delta sigma weight residual 1.334 1.310 0.023 8.40e-03 1.42e+04 7.70e+00 bond pdb=" C LEU D 171 " pdb=" N PRO D 172 " ideal model delta sigma weight residual 1.337 1.312 0.025 9.80e-03 1.04e+04 6.42e+00 bond pdb=" C TYR B 69 " pdb=" N PRO B 70 " ideal model delta sigma weight residual 1.336 1.310 0.026 1.20e-02 6.94e+03 4.73e+00 ... (remaining 17724 not shown) Histogram of bond angle deviations from ideal: 98.54 - 106.03: 488 106.03 - 113.52: 10266 113.52 - 121.01: 8557 121.01 - 128.51: 4573 128.51 - 136.00: 160 Bond angle restraints: 24044 Sorted by residual: angle pdb=" C GLY B 308 " pdb=" N ILE B 309 " pdb=" CA ILE B 309 " ideal model delta sigma weight residual 121.97 129.35 -7.38 1.80e+00 3.09e-01 1.68e+01 angle pdb=" C GLY A 308 " pdb=" N ILE A 309 " pdb=" CA ILE A 309 " ideal model delta sigma weight residual 121.97 129.19 -7.22 1.80e+00 3.09e-01 1.61e+01 angle pdb=" N GLY E 268 " pdb=" CA GLY E 268 " pdb=" C GLY E 268 " ideal model delta sigma weight residual 114.95 110.30 4.65 1.41e+00 5.03e-01 1.09e+01 angle pdb=" N ARG B 335 " pdb=" CA ARG B 335 " pdb=" C ARG B 335 " ideal model delta sigma weight residual 113.21 109.78 3.43 1.15e+00 7.56e-01 8.92e+00 angle pdb=" C HIS A 161 " pdb=" CA HIS A 161 " pdb=" CB HIS A 161 " ideal model delta sigma weight residual 112.99 106.93 6.06 2.10e+00 2.27e-01 8.34e+00 ... (remaining 24039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.51: 10150 25.51 - 51.02: 468 51.02 - 76.54: 40 76.54 - 102.05: 5 102.05 - 127.56: 2 Dihedral angle restraints: 10665 sinusoidal: 4315 harmonic: 6350 Sorted by residual: dihedral pdb=" C5' ADP C 402 " pdb=" O5' ADP C 402 " pdb=" PA ADP C 402 " pdb=" O2A ADP C 402 " ideal model delta sinusoidal sigma weight residual -60.00 67.56 -127.56 1 2.00e+01 2.50e-03 3.86e+01 dihedral pdb=" C5' ADP B 402 " pdb=" O5' ADP B 402 " pdb=" PA ADP B 402 " pdb=" O2A ADP B 402 " ideal model delta sinusoidal sigma weight residual -60.00 54.81 -114.80 1 2.00e+01 2.50e-03 3.41e+01 dihedral pdb=" CA GLY A 308 " pdb=" C GLY A 308 " pdb=" N ILE A 309 " pdb=" CA ILE A 309 " ideal model delta harmonic sigma weight residual -180.00 -153.72 -26.28 0 5.00e+00 4.00e-02 2.76e+01 ... (remaining 10662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1484 0.039 - 0.077: 874 0.077 - 0.116: 283 0.116 - 0.154: 39 0.154 - 0.192: 11 Chirality restraints: 2691 Sorted by residual: chirality pdb=" C2' ADP B 402 " pdb=" C1' ADP B 402 " pdb=" C3' ADP B 402 " pdb=" O2' ADP B 402 " both_signs ideal model delta sigma weight residual False -2.51 -2.70 0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CB ILE C 151 " pdb=" CA ILE C 151 " pdb=" CG1 ILE C 151 " pdb=" CG2 ILE C 151 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CB ILE D 151 " pdb=" CA ILE D 151 " pdb=" CG1 ILE D 151 " pdb=" CG2 ILE D 151 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 2688 not shown) Planarity restraints: 3070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 306 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.52e+00 pdb=" N PRO C 307 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 307 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 307 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 181 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.57e+00 pdb=" C ALA E 181 " 0.033 2.00e-02 2.50e+03 pdb=" O ALA E 181 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY E 182 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 306 " -0.031 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO B 307 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 307 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 307 " -0.025 5.00e-02 4.00e+02 ... (remaining 3067 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 186 2.54 - 3.13: 14816 3.13 - 3.72: 25643 3.72 - 4.31: 37786 4.31 - 4.90: 64204 Nonbonded interactions: 142635 Sorted by model distance: nonbonded pdb="MG MG E 401 " pdb=" O1B ADP E 402 " model vdw 1.951 2.170 nonbonded pdb="MG MG A 401 " pdb=" O1B ADP A 402 " model vdw 1.987 2.170 nonbonded pdb=" N ASP B 56 " pdb=" OD1 ASP B 56 " model vdw 2.127 2.520 nonbonded pdb=" N ASP A 56 " pdb=" OD1 ASP A 56 " model vdw 2.194 2.520 nonbonded pdb=" OG SER D 350 " pdb=" OE2 GLU F 81 " model vdw 2.199 2.440 ... (remaining 142630 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 204 or (resid 205 and (name N or \ name CA or name C or name O or name CB )) or resid 206 through 212 or (resid 21 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 214 through \ 233 or (resid 234 and (name N or name CA or name C or name O or name CB )) or re \ sid 235 through 245 or (resid 246 and (name N or name CA or name C or name O or \ name CB )) or resid 247 through 374 or resid 401 through 402)) selection = (chain 'B' and (resid 5 through 204 or (resid 205 and (name N or name CA or name \ C or name O or name CB )) or resid 206 through 212 or (resid 213 and (name N or \ name CA or name C or name O or name CB )) or resid 214 through 233 or (resid 23 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 235 through \ 258 or (resid 259 and (name N or name CA or name C or name O or name CB )) or re \ sid 260 through 374 or resid 401 through 402)) selection = (chain 'C' and (resid 5 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 204 or (resid 205 and (name N or \ name CA or name C or name O or name CB )) or resid 206 through 212 or (resid 21 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 214 through \ 233 or (resid 234 and (name N or name CA or name C or name O or name CB )) or re \ sid 235 through 245 or (resid 246 and (name N or name CA or name C or name O or \ name CB )) or resid 247 through 258 or (resid 259 and (name N or name CA or name \ C or name O or name CB )) or resid 260 through 374 or resid 401 through 402)) selection = (chain 'D' and (resid 5 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 233 or (resid 234 and (name N or \ name CA or name C or name O or name CB )) or resid 235 through 245 or (resid 24 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 247 through \ 374 or resid 401 through 402)) selection = (chain 'E' and (resid 5 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 245 or (resid 246 and (name N or \ name CA or name C or name O or name CB )) or resid 247 through 258 or (resid 25 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 260 through \ 374 or resid 401 through 402)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.800 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: 4.390 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 47.190 Find NCS groups from input model: 1.190 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: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 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 : 0.010 0.083 17729 Z= 0.678 Angle : 0.820 7.377 24044 Z= 0.430 Chirality : 0.050 0.192 2691 Planarity : 0.004 0.053 3070 Dihedral : 13.870 127.561 6591 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.41 % Favored : 90.40 % Rotamer: Outliers : 9.29 % Allowed : 10.58 % Favored : 80.13 % 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: -3.64 (0.15), residues: 2188 helix: -1.80 (0.15), residues: 923 sheet: -2.41 (0.30), residues: 265 loop : -3.00 (0.17), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 340 HIS 0.006 0.001 HIS A 371 PHE 0.017 0.002 PHE B 262 TYR 0.012 0.002 TYR C 69 ARG 0.005 0.001 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 244 time to evaluate : 2.214 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9387 (pt) REVERT: A 44 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8262 (mtt) REVERT: A 119 MET cc_start: 0.8865 (ttm) cc_final: 0.8624 (ttm) REVERT: A 162 ASN cc_start: 0.9294 (OUTLIER) cc_final: 0.8598 (m110) REVERT: A 227 MET cc_start: 0.8700 (mmm) cc_final: 0.8308 (mtp) REVERT: A 288 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8634 (m-30) REVERT: B 335 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8304 (ptt-90) REVERT: B 360 GLN cc_start: 0.8021 (tp40) cc_final: 0.7752 (tp-100) REVERT: C 50 LYS cc_start: 0.8074 (tptt) cc_final: 0.7848 (tptp) REVERT: C 176 MET cc_start: 0.8601 (mmm) cc_final: 0.8206 (mmt) REVERT: D 61 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8806 (mtmm) REVERT: D 92 ASN cc_start: 0.9292 (OUTLIER) cc_final: 0.8992 (m-40) REVERT: D 132 MET cc_start: 0.9235 (ppp) cc_final: 0.8918 (ptm) REVERT: D 249 THR cc_start: 0.9416 (OUTLIER) cc_final: 0.9091 (p) REVERT: D 283 MET cc_start: 0.8831 (mmm) cc_final: 0.7794 (mmt) REVERT: F 31 ASP cc_start: 0.8179 (m-30) cc_final: 0.7833 (m-30) REVERT: F 34 LYS cc_start: 0.8874 (tttt) cc_final: 0.8663 (tttp) REVERT: F 64 ARG cc_start: 0.8457 (mtm110) cc_final: 0.8230 (mtm110) REVERT: F 86 ARG cc_start: 0.7754 (ttt-90) cc_final: 0.7487 (ttt-90) REVERT: F 94 ASN cc_start: 0.8411 (t0) cc_final: 0.8172 (t0) REVERT: F 98 GLN cc_start: 0.8311 (mt0) cc_final: 0.8011 (mt0) REVERT: F 119 ASN cc_start: 0.9017 (t0) cc_final: 0.8802 (t0) REVERT: F 121 LYS cc_start: 0.8211 (ttmt) cc_final: 0.7784 (ttpt) REVERT: G 56 MET cc_start: 0.8853 (tpp) cc_final: 0.8464 (tpp) REVERT: G 71 GLU cc_start: 0.8864 (pt0) cc_final: 0.8182 (tt0) REVERT: G 81 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7522 (mm-30) REVERT: G 99 VAL cc_start: 0.9088 (m) cc_final: 0.8868 (p) REVERT: G 102 GLN cc_start: 0.8701 (mp10) cc_final: 0.8350 (mp10) REVERT: H 23 LYS cc_start: 0.8284 (mmmt) cc_final: 0.8009 (tppt) REVERT: H 24 SER cc_start: 0.9157 (m) cc_final: 0.8555 (p) REVERT: H 31 ASP cc_start: 0.8390 (m-30) cc_final: 0.8005 (m-30) REVERT: H 33 GLN cc_start: 0.8631 (mm110) cc_final: 0.8386 (mm-40) REVERT: H 60 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8719 (mp) REVERT: H 71 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8672 (tt0) outliers start: 174 outliers final: 117 residues processed: 407 average time/residue: 0.3101 time to fit residues: 187.1629 Evaluate side-chains 352 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 226 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 107 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 0.6980 chunk 165 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 197 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 162 ASN A 353 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS B 92 ASN B 162 ASN B 275 HIS C 12 ASN C 88 HIS C 111 ASN C 161 HIS ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS D 88 HIS E 88 HIS ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 162 ASN E 275 HIS F 88 HIS F 120 HIS F 135 GLN G 88 HIS G 120 HIS H 29 HIS H 33 GLN H 88 HIS H 102 GLN H 120 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17729 Z= 0.158 Angle : 0.594 6.617 24044 Z= 0.295 Chirality : 0.043 0.181 2691 Planarity : 0.004 0.043 3070 Dihedral : 10.687 109.817 2679 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.02 % Favored : 95.89 % Rotamer: Outliers : 6.36 % Allowed : 13.89 % Favored : 79.75 % 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: -2.22 (0.17), residues: 2188 helix: -0.60 (0.17), residues: 889 sheet: -1.95 (0.31), residues: 260 loop : -2.10 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 340 HIS 0.005 0.001 HIS G 133 PHE 0.010 0.001 PHE E 352 TYR 0.008 0.001 TYR A 362 ARG 0.007 0.000 ARG H 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 259 time to evaluate : 2.227 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9359 (pt) REVERT: A 44 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7811 (mtt) REVERT: A 93 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7889 (mm-30) REVERT: A 119 MET cc_start: 0.8768 (ttm) cc_final: 0.8366 (ttm) REVERT: A 132 MET cc_start: 0.9309 (tmm) cc_final: 0.9055 (tmm) REVERT: A 153 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8968 (tp) REVERT: A 161 HIS cc_start: 0.8533 (m170) cc_final: 0.8092 (m170) REVERT: A 162 ASN cc_start: 0.9219 (OUTLIER) cc_final: 0.8212 (m-40) REVERT: B 335 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8385 (ptt-90) REVERT: C 50 LYS cc_start: 0.7972 (tptt) cc_final: 0.7649 (tptp) REVERT: D 61 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8766 (mtmm) REVERT: D 132 MET cc_start: 0.9143 (ppp) cc_final: 0.8837 (ptm) REVERT: D 192 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8872 (tp) REVERT: D 283 MET cc_start: 0.8744 (mmm) cc_final: 0.7778 (mmt) REVERT: D 355 MET cc_start: 0.8118 (mtt) cc_final: 0.7914 (mtm) REVERT: E 312 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.7600 (ttt180) REVERT: F 31 ASP cc_start: 0.8304 (m-30) cc_final: 0.7877 (m-30) REVERT: F 56 MET cc_start: 0.8511 (tpp) cc_final: 0.8288 (tpp) REVERT: F 65 LYS cc_start: 0.7951 (mtpp) cc_final: 0.7744 (mtpp) REVERT: F 94 ASN cc_start: 0.8377 (t0) cc_final: 0.8093 (t0) REVERT: F 95 ARG cc_start: 0.8814 (tpp80) cc_final: 0.8203 (ttm110) REVERT: F 98 GLN cc_start: 0.8150 (mt0) cc_final: 0.7849 (pt0) REVERT: F 121 LYS cc_start: 0.8064 (ttmt) cc_final: 0.7523 (ttmm) REVERT: G 27 ASP cc_start: 0.8093 (m-30) cc_final: 0.7882 (m-30) REVERT: G 56 MET cc_start: 0.8909 (tpp) cc_final: 0.8635 (tpp) REVERT: G 62 ASP cc_start: 0.8556 (p0) cc_final: 0.8335 (p0) REVERT: G 64 ARG cc_start: 0.8474 (ttm-80) cc_final: 0.8016 (ttm-80) REVERT: G 71 GLU cc_start: 0.8759 (pt0) cc_final: 0.8307 (tt0) REVERT: G 81 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7656 (mm-30) REVERT: G 92 ASN cc_start: 0.9011 (m-40) cc_final: 0.8679 (m-40) REVERT: H 71 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8591 (tt0) REVERT: H 102 GLN cc_start: 0.9152 (mt0) cc_final: 0.8894 (mp10) outliers start: 119 outliers final: 73 residues processed: 366 average time/residue: 0.3123 time to fit residues: 171.5164 Evaluate side-chains 322 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 240 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 107 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 0.0970 chunk 164 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 176 optimal weight: 0.8980 chunk 196 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 275 HIS D 161 HIS G 120 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17729 Z= 0.146 Angle : 0.553 6.505 24044 Z= 0.270 Chirality : 0.042 0.307 2691 Planarity : 0.004 0.037 3070 Dihedral : 9.296 92.983 2568 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.38 % Rotamer: Outliers : 5.72 % Allowed : 15.06 % Favored : 79.22 % 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: -1.85 (0.18), residues: 2188 helix: -0.36 (0.17), residues: 912 sheet: -2.12 (0.27), residues: 330 loop : -1.66 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 356 HIS 0.006 0.001 HIS G 133 PHE 0.012 0.001 PHE G 37 TYR 0.007 0.001 TYR C 166 ARG 0.009 0.000 ARG G 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 248 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9674 (OUTLIER) cc_final: 0.9342 (pt) REVERT: A 44 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.7981 (mtt) REVERT: A 153 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8774 (tp) REVERT: A 162 ASN cc_start: 0.9196 (OUTLIER) cc_final: 0.7998 (m-40) REVERT: B 335 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8370 (ptt-90) REVERT: C 50 LYS cc_start: 0.7962 (tptt) cc_final: 0.7709 (tptp) REVERT: C 132 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8902 (ptm) REVERT: D 61 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8734 (mtmm) REVERT: D 132 MET cc_start: 0.9124 (ppp) cc_final: 0.8806 (ptm) REVERT: D 192 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8814 (tp) REVERT: D 283 MET cc_start: 0.8685 (mmm) cc_final: 0.7670 (mmt) REVERT: E 312 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.7490 (ttt180) REVERT: F 31 ASP cc_start: 0.8371 (m-30) cc_final: 0.8033 (m-30) REVERT: F 62 ASP cc_start: 0.7709 (p0) cc_final: 0.7329 (p0) REVERT: F 64 ARG cc_start: 0.8207 (mtm110) cc_final: 0.7897 (ttp-110) REVERT: F 95 ARG cc_start: 0.8774 (tpp80) cc_final: 0.8343 (ttm110) REVERT: F 98 GLN cc_start: 0.8144 (mt0) cc_final: 0.7762 (pt0) REVERT: F 102 GLN cc_start: 0.9070 (mt0) cc_final: 0.8803 (mt0) REVERT: G 56 MET cc_start: 0.8910 (tpp) cc_final: 0.8500 (tpp) REVERT: G 62 ASP cc_start: 0.8460 (p0) cc_final: 0.8131 (p0) REVERT: G 71 GLU cc_start: 0.8840 (pt0) cc_final: 0.8525 (tt0) REVERT: H 71 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8759 (tt0) REVERT: H 95 ARG cc_start: 0.8102 (ttm110) cc_final: 0.7856 (ttm110) REVERT: H 98 GLN cc_start: 0.8535 (mt0) cc_final: 0.8240 (mt0) outliers start: 107 outliers final: 71 residues processed: 338 average time/residue: 0.2975 time to fit residues: 149.6431 Evaluate side-chains 317 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 237 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 107 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 195 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 188 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN G 29 HIS G 42 ASN ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 HIS H 101 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17729 Z= 0.294 Angle : 0.603 6.568 24044 Z= 0.294 Chirality : 0.045 0.342 2691 Planarity : 0.004 0.040 3070 Dihedral : 9.188 97.132 2545 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.48 % Favored : 94.47 % Rotamer: Outliers : 6.62 % Allowed : 15.60 % Favored : 77.78 % 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: -1.76 (0.18), residues: 2188 helix: -0.33 (0.18), residues: 912 sheet: -2.12 (0.26), residues: 330 loop : -1.53 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 340 HIS 0.007 0.001 HIS H 101 PHE 0.009 0.001 PHE B 262 TYR 0.008 0.001 TYR C 69 ARG 0.004 0.000 ARG G 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 242 time to evaluate : 1.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9680 (OUTLIER) cc_final: 0.9377 (pt) REVERT: A 44 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8027 (mtt) REVERT: B 47 MET cc_start: 0.8589 (mmm) cc_final: 0.8242 (mmm) REVERT: B 335 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8182 (ptt-90) REVERT: C 50 LYS cc_start: 0.7962 (tptt) cc_final: 0.7706 (tptp) REVERT: D 61 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8783 (mtmm) REVERT: D 132 MET cc_start: 0.9145 (ppp) cc_final: 0.8829 (ptm) REVERT: D 192 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8910 (tp) REVERT: D 283 MET cc_start: 0.8664 (mmm) cc_final: 0.7603 (mmt) REVERT: E 312 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7451 (ttt-90) REVERT: F 30 ASN cc_start: 0.8739 (m-40) cc_final: 0.8431 (m110) REVERT: F 31 ASP cc_start: 0.8288 (m-30) cc_final: 0.7922 (m-30) REVERT: F 62 ASP cc_start: 0.7780 (p0) cc_final: 0.7281 (p0) REVERT: F 64 ARG cc_start: 0.8291 (mtm110) cc_final: 0.7806 (ttm110) REVERT: F 98 GLN cc_start: 0.8175 (mt0) cc_final: 0.7844 (pt0) REVERT: G 32 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8606 (m) REVERT: G 56 MET cc_start: 0.8861 (tpp) cc_final: 0.8486 (tpp) REVERT: G 62 ASP cc_start: 0.8500 (p0) cc_final: 0.8201 (p0) REVERT: G 71 GLU cc_start: 0.8855 (pt0) cc_final: 0.8535 (tt0) REVERT: G 81 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6811 (mm-30) REVERT: G 92 ASN cc_start: 0.9047 (m-40) cc_final: 0.8751 (m-40) REVERT: H 71 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8780 (tt0) REVERT: H 98 GLN cc_start: 0.8562 (mt0) cc_final: 0.7691 (mt0) REVERT: H 102 GLN cc_start: 0.9135 (mt0) cc_final: 0.8871 (mp10) outliers start: 124 outliers final: 95 residues processed: 345 average time/residue: 0.3052 time to fit residues: 156.5012 Evaluate side-chains 337 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 235 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 107 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 175 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 53 optimal weight: 0.2980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN F 33 GLN F 109 ASN ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17729 Z= 0.184 Angle : 0.557 9.322 24044 Z= 0.270 Chirality : 0.042 0.285 2691 Planarity : 0.004 0.043 3070 Dihedral : 8.729 89.881 2538 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.48 % Favored : 95.48 % Rotamer: Outliers : 5.72 % Allowed : 16.93 % Favored : 77.35 % 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: -1.51 (0.18), residues: 2188 helix: -0.15 (0.18), residues: 912 sheet: -2.01 (0.26), residues: 330 loop : -1.36 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 340 HIS 0.004 0.001 HIS G 133 PHE 0.007 0.001 PHE D 255 TYR 0.009 0.001 TYR B 53 ARG 0.010 0.000 ARG H 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 242 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9659 (OUTLIER) cc_final: 0.9324 (pt) REVERT: A 44 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.7935 (mtt) REVERT: B 47 MET cc_start: 0.8676 (mmm) cc_final: 0.8313 (mmm) REVERT: B 335 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8410 (ptt-90) REVERT: C 50 LYS cc_start: 0.7956 (tptt) cc_final: 0.7695 (tptp) REVERT: C 132 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8853 (ptm) REVERT: D 61 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8763 (mtmm) REVERT: D 132 MET cc_start: 0.9118 (ppp) cc_final: 0.8488 (ppp) REVERT: D 192 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8875 (tp) REVERT: D 283 MET cc_start: 0.8605 (mmm) cc_final: 0.7533 (mmt) REVERT: E 312 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7348 (ttt-90) REVERT: F 30 ASN cc_start: 0.8759 (m-40) cc_final: 0.8453 (m110) REVERT: F 31 ASP cc_start: 0.8248 (m-30) cc_final: 0.7649 (m-30) REVERT: F 62 ASP cc_start: 0.7763 (p0) cc_final: 0.7456 (p0) REVERT: F 95 ARG cc_start: 0.8264 (ttm110) cc_final: 0.8024 (ttm110) REVERT: F 98 GLN cc_start: 0.8171 (mt0) cc_final: 0.7789 (pt0) REVERT: F 102 GLN cc_start: 0.9125 (mt0) cc_final: 0.8909 (mt0) REVERT: G 30 ASN cc_start: 0.7853 (m110) cc_final: 0.7341 (m110) REVERT: G 32 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8567 (m) REVERT: G 56 MET cc_start: 0.8907 (tpp) cc_final: 0.8450 (tpp) REVERT: G 62 ASP cc_start: 0.8471 (p0) cc_final: 0.8180 (p0) REVERT: G 71 GLU cc_start: 0.8848 (pt0) cc_final: 0.8518 (tt0) REVERT: G 92 ASN cc_start: 0.9036 (m-40) cc_final: 0.8745 (m-40) REVERT: H 98 GLN cc_start: 0.8609 (mt0) cc_final: 0.7780 (mt0) REVERT: H 121 LYS cc_start: 0.7920 (ttmt) cc_final: 0.7168 (tttt) outliers start: 107 outliers final: 82 residues processed: 330 average time/residue: 0.3155 time to fit residues: 154.8909 Evaluate side-chains 326 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 236 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 107 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 70 optimal weight: 4.9990 chunk 189 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 210 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 GLN ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 17729 Z= 0.406 Angle : 0.649 8.635 24044 Z= 0.319 Chirality : 0.046 0.314 2691 Planarity : 0.004 0.040 3070 Dihedral : 8.864 100.837 2529 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.17 % Favored : 93.78 % Rotamer: Outliers : 6.94 % Allowed : 16.35 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.18), residues: 2188 helix: -0.25 (0.18), residues: 906 sheet: -1.95 (0.28), residues: 300 loop : -1.42 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 HIS 0.004 0.001 HIS A 371 PHE 0.012 0.001 PHE B 262 TYR 0.010 0.001 TYR C 69 ARG 0.004 0.000 ARG G 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 241 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9658 (OUTLIER) cc_final: 0.9367 (pt) REVERT: A 44 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8170 (mtt) REVERT: A 93 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7836 (mt-10) REVERT: B 47 MET cc_start: 0.8682 (mmm) cc_final: 0.8354 (mmm) REVERT: B 335 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8374 (ptt-90) REVERT: D 61 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8784 (mtmm) REVERT: D 132 MET cc_start: 0.9162 (ppp) cc_final: 0.8473 (ppp) REVERT: D 192 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8964 (tp) REVERT: D 283 MET cc_start: 0.8672 (mmm) cc_final: 0.7638 (mmt) REVERT: E 312 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7544 (ttt-90) REVERT: F 30 ASN cc_start: 0.8611 (m-40) cc_final: 0.8291 (m110) REVERT: F 31 ASP cc_start: 0.8327 (m-30) cc_final: 0.7696 (m-30) REVERT: F 62 ASP cc_start: 0.7804 (p0) cc_final: 0.7448 (p0) REVERT: F 98 GLN cc_start: 0.8208 (mt0) cc_final: 0.7786 (pt0) REVERT: F 102 GLN cc_start: 0.9128 (mt0) cc_final: 0.8909 (mt0) REVERT: G 30 ASN cc_start: 0.7901 (m110) cc_final: 0.7368 (m110) REVERT: G 32 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8606 (m) REVERT: G 56 MET cc_start: 0.8857 (tpp) cc_final: 0.8446 (tpp) REVERT: G 62 ASP cc_start: 0.8482 (p0) cc_final: 0.8196 (p0) REVERT: G 68 ASP cc_start: 0.8187 (p0) cc_final: 0.7982 (p0) REVERT: G 71 GLU cc_start: 0.8768 (pt0) cc_final: 0.8535 (tt0) REVERT: G 81 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6798 (mm-30) REVERT: G 92 ASN cc_start: 0.9034 (m-40) cc_final: 0.8713 (m-40) REVERT: G 114 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8411 (m-30) REVERT: H 98 GLN cc_start: 0.8662 (mt0) cc_final: 0.8178 (mt0) REVERT: H 102 GLN cc_start: 0.9320 (mp10) cc_final: 0.8572 (mp10) REVERT: H 121 LYS cc_start: 0.7811 (ttmt) cc_final: 0.7099 (tttt) outliers start: 130 outliers final: 107 residues processed: 342 average time/residue: 0.2966 time to fit residues: 151.7121 Evaluate side-chains 355 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 239 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 135 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 203 optimal weight: 10.0000 chunk 23 optimal weight: 0.1980 chunk 120 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 210 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS B 59 GLN ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 17729 Z= 0.135 Angle : 0.543 8.771 24044 Z= 0.264 Chirality : 0.042 0.253 2691 Planarity : 0.004 0.047 3070 Dihedral : 8.287 83.341 2529 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.07 % Favored : 95.89 % Rotamer: Outliers : 5.13 % Allowed : 17.84 % Favored : 77.03 % 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: -1.28 (0.18), residues: 2188 helix: -0.02 (0.18), residues: 906 sheet: -1.86 (0.27), residues: 330 loop : -1.17 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 340 HIS 0.003 0.000 HIS G 133 PHE 0.007 0.001 PHE E 352 TYR 0.007 0.001 TYR B 53 ARG 0.012 0.000 ARG H 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 246 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9646 (OUTLIER) cc_final: 0.9300 (pt) REVERT: A 44 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8067 (mtt) REVERT: A 93 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7733 (mm-30) REVERT: B 47 MET cc_start: 0.8669 (mmm) cc_final: 0.8292 (mmm) REVERT: C 132 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8882 (ptm) REVERT: D 61 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8758 (mtmm) REVERT: D 132 MET cc_start: 0.9113 (ppp) cc_final: 0.8414 (ppp) REVERT: D 192 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8856 (tp) REVERT: D 283 MET cc_start: 0.8575 (mmm) cc_final: 0.7519 (mmt) REVERT: E 312 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7283 (ttt-90) REVERT: F 30 ASN cc_start: 0.8579 (m-40) cc_final: 0.8239 (m110) REVERT: F 31 ASP cc_start: 0.8363 (m-30) cc_final: 0.7772 (m-30) REVERT: F 62 ASP cc_start: 0.7685 (p0) cc_final: 0.7378 (p0) REVERT: F 64 ARG cc_start: 0.7795 (ttp-110) cc_final: 0.7080 (ttp-110) REVERT: F 98 GLN cc_start: 0.8186 (mt0) cc_final: 0.7761 (pt0) REVERT: F 102 GLN cc_start: 0.9093 (mt0) cc_final: 0.8828 (mt0) REVERT: G 30 ASN cc_start: 0.7897 (m110) cc_final: 0.7353 (m110) REVERT: G 32 VAL cc_start: 0.8804 (OUTLIER) cc_final: 0.8526 (m) REVERT: G 56 MET cc_start: 0.8892 (tpp) cc_final: 0.8466 (tpp) REVERT: G 62 ASP cc_start: 0.8456 (p0) cc_final: 0.8182 (p0) REVERT: G 71 GLU cc_start: 0.8753 (pt0) cc_final: 0.8202 (tt0) REVERT: G 81 GLU cc_start: 0.7459 (mm-30) cc_final: 0.6796 (mm-30) REVERT: G 92 ASN cc_start: 0.9017 (m-40) cc_final: 0.8703 (m-40) REVERT: G 119 ASN cc_start: 0.9025 (t0) cc_final: 0.8573 (t0) REVERT: H 31 ASP cc_start: 0.8367 (m-30) cc_final: 0.8158 (m-30) REVERT: H 80 LYS cc_start: 0.8392 (mmtt) cc_final: 0.8110 (mmtt) REVERT: H 98 GLN cc_start: 0.8682 (mt0) cc_final: 0.8358 (mt0) REVERT: H 121 LYS cc_start: 0.7813 (ttmt) cc_final: 0.7084 (tttt) outliers start: 96 outliers final: 75 residues processed: 326 average time/residue: 0.2974 time to fit residues: 144.4467 Evaluate side-chains 322 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 239 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 78 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 129 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 143 optimal weight: 0.1980 chunk 103 optimal weight: 4.9990 chunk 19 optimal weight: 0.0050 chunk 165 optimal weight: 5.9990 overall best weight: 1.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17729 Z= 0.185 Angle : 0.552 11.117 24044 Z= 0.267 Chirality : 0.042 0.257 2691 Planarity : 0.003 0.039 3070 Dihedral : 8.008 80.826 2520 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.57 % Favored : 95.38 % Rotamer: Outliers : 5.02 % Allowed : 18.06 % Favored : 76.92 % 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: -1.10 (0.18), residues: 2188 helix: 0.06 (0.18), residues: 891 sheet: -1.70 (0.29), residues: 300 loop : -1.04 (0.21), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 340 HIS 0.003 0.001 HIS G 133 PHE 0.007 0.001 PHE D 255 TYR 0.007 0.001 TYR B 53 ARG 0.005 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 243 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9649 (OUTLIER) cc_final: 0.9294 (pt) REVERT: A 93 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7771 (mm-30) REVERT: A 122 ILE cc_start: 0.9329 (mt) cc_final: 0.9085 (mt) REVERT: B 47 MET cc_start: 0.8649 (mmm) cc_final: 0.8290 (mmm) REVERT: C 132 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8836 (ptm) REVERT: D 61 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8751 (mtmm) REVERT: D 132 MET cc_start: 0.9118 (ppp) cc_final: 0.8446 (ppp) REVERT: D 192 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8868 (tp) REVERT: D 283 MET cc_start: 0.8575 (mmm) cc_final: 0.7550 (mmt) REVERT: E 312 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7303 (ttt-90) REVERT: F 30 ASN cc_start: 0.8600 (m-40) cc_final: 0.8267 (m110) REVERT: F 31 ASP cc_start: 0.8407 (m-30) cc_final: 0.7798 (m-30) REVERT: F 47 LYS cc_start: 0.8591 (mptt) cc_final: 0.8342 (mmtt) REVERT: F 62 ASP cc_start: 0.7688 (p0) cc_final: 0.7272 (p0) REVERT: F 98 GLN cc_start: 0.8188 (mt0) cc_final: 0.7769 (pt0) REVERT: F 102 GLN cc_start: 0.9049 (mt0) cc_final: 0.8806 (mt0) REVERT: G 30 ASN cc_start: 0.7887 (m110) cc_final: 0.7344 (m110) REVERT: G 32 VAL cc_start: 0.8772 (OUTLIER) cc_final: 0.8478 (m) REVERT: G 56 MET cc_start: 0.8825 (tpp) cc_final: 0.8431 (tpp) REVERT: G 62 ASP cc_start: 0.8451 (p0) cc_final: 0.8173 (p0) REVERT: G 71 GLU cc_start: 0.8764 (pt0) cc_final: 0.8194 (tt0) REVERT: G 81 GLU cc_start: 0.7462 (mm-30) cc_final: 0.6785 (mm-30) REVERT: G 92 ASN cc_start: 0.9039 (m-40) cc_final: 0.8710 (m-40) REVERT: G 119 ASN cc_start: 0.9051 (t0) cc_final: 0.8579 (t0) REVERT: H 31 ASP cc_start: 0.8434 (m-30) cc_final: 0.8226 (m-30) REVERT: H 98 GLN cc_start: 0.8623 (mt0) cc_final: 0.8305 (mt0) REVERT: H 121 LYS cc_start: 0.7788 (ttmt) cc_final: 0.7076 (tttt) outliers start: 94 outliers final: 77 residues processed: 321 average time/residue: 0.2996 time to fit residues: 144.0524 Evaluate side-chains 325 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 241 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 78 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 191 optimal weight: 20.0000 chunk 201 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 117 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 176 optimal weight: 0.0170 chunk 185 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 overall best weight: 2.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 ASN F 120 HIS ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17729 Z= 0.312 Angle : 0.604 10.441 24044 Z= 0.294 Chirality : 0.045 0.404 2691 Planarity : 0.004 0.040 3070 Dihedral : 8.015 86.522 2514 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.71 % Favored : 94.24 % Rotamer: Outliers : 5.29 % Allowed : 18.16 % Favored : 76.55 % 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: -1.22 (0.18), residues: 2188 helix: -0.03 (0.18), residues: 906 sheet: -1.70 (0.29), residues: 300 loop : -1.16 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 340 HIS 0.006 0.001 HIS B 161 PHE 0.009 0.001 PHE B 262 TYR 0.008 0.001 TYR D 69 ARG 0.005 0.000 ARG D 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 242 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9661 (OUTLIER) cc_final: 0.9333 (pt) REVERT: B 47 MET cc_start: 0.8693 (mmm) cc_final: 0.8362 (mmm) REVERT: C 132 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8844 (ptm) REVERT: D 61 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8773 (mtmm) REVERT: D 132 MET cc_start: 0.9135 (ppp) cc_final: 0.8481 (ppp) REVERT: D 192 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8939 (tp) REVERT: D 283 MET cc_start: 0.8606 (mmm) cc_final: 0.7552 (mmt) REVERT: E 312 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7401 (ttt-90) REVERT: F 30 ASN cc_start: 0.8616 (m-40) cc_final: 0.8290 (m110) REVERT: F 31 ASP cc_start: 0.8406 (m-30) cc_final: 0.7811 (m-30) REVERT: F 33 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7267 (mt0) REVERT: F 47 LYS cc_start: 0.8573 (mptt) cc_final: 0.8309 (mmtt) REVERT: F 98 GLN cc_start: 0.8204 (mt0) cc_final: 0.7771 (pt0) REVERT: F 102 GLN cc_start: 0.9064 (mt0) cc_final: 0.8817 (mt0) REVERT: G 30 ASN cc_start: 0.7941 (m110) cc_final: 0.7402 (m110) REVERT: G 32 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8506 (m) REVERT: G 56 MET cc_start: 0.8850 (tpp) cc_final: 0.8449 (tpp) REVERT: G 62 ASP cc_start: 0.8469 (p0) cc_final: 0.8194 (p0) REVERT: G 71 GLU cc_start: 0.8772 (pt0) cc_final: 0.8368 (tt0) REVERT: G 81 GLU cc_start: 0.7427 (mm-30) cc_final: 0.6731 (mm-30) REVERT: H 31 ASP cc_start: 0.8422 (m-30) cc_final: 0.8210 (m-30) REVERT: H 98 GLN cc_start: 0.8626 (mt0) cc_final: 0.8261 (mt0) REVERT: H 121 LYS cc_start: 0.7783 (ttmt) cc_final: 0.7079 (tttt) outliers start: 99 outliers final: 82 residues processed: 323 average time/residue: 0.3024 time to fit residues: 145.5260 Evaluate side-chains 329 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 241 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 207 optimal weight: 0.3980 chunk 126 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 217 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17729 Z= 0.153 Angle : 0.552 10.309 24044 Z= 0.268 Chirality : 0.042 0.373 2691 Planarity : 0.003 0.041 3070 Dihedral : 7.683 77.112 2514 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.25 % Favored : 95.70 % Rotamer: Outliers : 4.65 % Allowed : 19.02 % Favored : 76.34 % 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: -0.98 (0.18), residues: 2188 helix: 0.13 (0.18), residues: 891 sheet: -1.56 (0.29), residues: 300 loop : -0.98 (0.21), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 356 HIS 0.004 0.001 HIS B 161 PHE 0.006 0.001 PHE D 255 TYR 0.006 0.001 TYR B 53 ARG 0.007 0.000 ARG H 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 242 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9254 (pt) REVERT: A 122 ILE cc_start: 0.9273 (mt) cc_final: 0.9006 (mt) REVERT: B 47 MET cc_start: 0.8686 (mmm) cc_final: 0.8371 (mmm) REVERT: C 132 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8873 (ptm) REVERT: D 61 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8728 (mtmm) REVERT: D 132 MET cc_start: 0.9111 (ppp) cc_final: 0.8436 (ppp) REVERT: D 192 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8857 (tp) REVERT: D 283 MET cc_start: 0.8517 (mmm) cc_final: 0.7526 (mmt) REVERT: E 190 MET cc_start: 0.8617 (ttm) cc_final: 0.8374 (ttm) REVERT: E 312 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7216 (ttt-90) REVERT: F 30 ASN cc_start: 0.8635 (m-40) cc_final: 0.8317 (m110) REVERT: F 31 ASP cc_start: 0.8543 (m-30) cc_final: 0.7962 (m-30) REVERT: F 33 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7217 (mt0) REVERT: F 40 TRP cc_start: 0.8102 (t60) cc_final: 0.7812 (t60) REVERT: F 47 LYS cc_start: 0.8511 (mptt) cc_final: 0.8211 (mmtt) REVERT: F 98 GLN cc_start: 0.8196 (mt0) cc_final: 0.7758 (pt0) REVERT: F 102 GLN cc_start: 0.9059 (mt0) cc_final: 0.8809 (mt0) REVERT: G 30 ASN cc_start: 0.7921 (m110) cc_final: 0.7393 (m110) REVERT: G 32 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8575 (m) REVERT: G 56 MET cc_start: 0.8907 (tpp) cc_final: 0.8443 (tpp) REVERT: G 62 ASP cc_start: 0.8461 (p0) cc_final: 0.8163 (p0) REVERT: G 71 GLU cc_start: 0.8779 (pt0) cc_final: 0.8195 (tt0) REVERT: G 81 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7016 (mm-30) REVERT: G 92 ASN cc_start: 0.8947 (m-40) cc_final: 0.8684 (m-40) REVERT: G 119 ASN cc_start: 0.9029 (t0) cc_final: 0.8538 (t0) REVERT: H 31 ASP cc_start: 0.8435 (m-30) cc_final: 0.8230 (m-30) REVERT: H 98 GLN cc_start: 0.8625 (mt0) cc_final: 0.8326 (mt0) REVERT: H 121 LYS cc_start: 0.7806 (ttmt) cc_final: 0.7070 (tttt) outliers start: 87 outliers final: 72 residues processed: 314 average time/residue: 0.2937 time to fit residues: 137.6862 Evaluate side-chains 317 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 239 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 0.5980 chunk 52 optimal weight: 8.9990 chunk 159 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 21 optimal weight: 0.0970 chunk 31 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 29 HIS ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.072065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.057312 restraints weight = 45056.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.058693 restraints weight = 21970.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.059252 restraints weight = 15426.828| |-----------------------------------------------------------------------------| r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17729 Z= 0.166 Angle : 0.553 10.345 24044 Z= 0.268 Chirality : 0.043 0.391 2691 Planarity : 0.003 0.040 3070 Dihedral : 7.361 71.729 2507 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.62 % Favored : 95.34 % Rotamer: Outliers : 3.90 % Allowed : 19.87 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.19), residues: 2188 helix: 0.21 (0.18), residues: 891 sheet: -1.51 (0.29), residues: 300 loop : -0.92 (0.21), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 340 HIS 0.004 0.001 HIS B 161 PHE 0.007 0.001 PHE E 352 TYR 0.007 0.001 TYR B 53 ARG 0.006 0.000 ARG H 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3536.15 seconds wall clock time: 64 minutes 45.68 seconds (3885.68 seconds total)