Starting phenix.real_space_refine on Sun Mar 10 14:45:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vec_21155/03_2024/6vec_21155_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vec_21155/03_2024/6vec_21155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vec_21155/03_2024/6vec_21155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vec_21155/03_2024/6vec_21155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vec_21155/03_2024/6vec_21155_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vec_21155/03_2024/6vec_21155_updated.pdb" } resolution = 3.9 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= 0.011 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 22 5.49 5 Mg 11 5.21 5 S 341 5.16 5 C 33517 2.51 5 N 9031 2.21 5 O 10142 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 27": "OD1" <-> "OD2" Residue "A TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 27": "OD1" <-> "OD2" Residue "C TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 27": "OD1" <-> "OD2" Residue "D TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 27": "OD1" <-> "OD2" Residue "E TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 27": "OD1" <-> "OD2" Residue "F TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 27": "OD1" <-> "OD2" Residue "G TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 27": "OD1" <-> "OD2" Residue "H TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 27": "OD1" <-> "OD2" Residue "I TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 27": "OD1" <-> "OD2" Residue "J TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 27": "OD1" <-> "OD2" Residue "K TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 391": "OE1" <-> "OE2" Residue "a ARG 412": "NH1" <-> "NH2" Residue "a GLU 533": "OE1" <-> "OE2" Residue "a ASP 567": "OD1" <-> "OD2" Residue "b GLU 391": "OE1" <-> "OE2" Residue "b ARG 412": "NH1" <-> "NH2" Residue "b GLU 533": "OE1" <-> "OE2" Residue "b ASP 567": "OD1" <-> "OD2" Residue "c GLU 391": "OE1" <-> "OE2" Residue "c ARG 412": "NH1" <-> "NH2" Residue "c GLU 533": "OE1" <-> "OE2" Residue "c ASP 567": "OD1" <-> "OD2" Residue "d GLU 391": "OE1" <-> "OE2" Residue "d ARG 412": "NH1" <-> "NH2" Residue "d GLU 533": "OE1" <-> "OE2" Residue "d ASP 567": "OD1" <-> "OD2" Residue "e GLU 391": "OE1" <-> "OE2" Residue "e ARG 412": "NH1" <-> "NH2" Residue "e GLU 533": "OE1" <-> "OE2" Residue "e ASP 567": "OD1" <-> "OD2" Residue "f GLU 391": "OE1" <-> "OE2" Residue "f ARG 412": "NH1" <-> "NH2" Residue "f GLU 533": "OE1" <-> "OE2" Residue "f ASP 567": "OD1" <-> "OD2" Residue "g GLU 391": "OE1" <-> "OE2" Residue "g ARG 412": "NH1" <-> "NH2" Residue "g GLU 533": "OE1" <-> "OE2" Residue "g ASP 567": "OD1" <-> "OD2" Residue "h GLU 391": "OE1" <-> "OE2" Residue "h ARG 412": "NH1" <-> "NH2" Residue "h GLU 533": "OE1" <-> "OE2" Residue "h ASP 567": "OD1" <-> "OD2" Residue "i GLU 391": "OE1" <-> "OE2" Residue "i ARG 412": "NH1" <-> "NH2" Residue "i GLU 533": "OE1" <-> "OE2" Residue "i ASP 567": "OD1" <-> "OD2" Residue "j GLU 391": "OE1" <-> "OE2" Residue "j ARG 412": "NH1" <-> "NH2" Residue "j GLU 533": "OE1" <-> "OE2" Residue "j ASP 567": "OD1" <-> "OD2" Residue "k GLU 391": "OE1" <-> "OE2" Residue "k ARG 412": "NH1" <-> "NH2" Residue "k GLU 533": "OE1" <-> "OE2" Residue "k ASP 567": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 53064 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2887 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "B" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2887 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "C" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2887 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "D" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2887 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "E" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2887 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "F" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2887 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "G" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2887 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "H" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2887 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "I" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2887 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "J" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2887 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "K" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2887 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "a" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1909 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 10, 'TRANS': 230} Chain: "b" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1909 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 10, 'TRANS': 230} Chain: "c" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1909 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 10, 'TRANS': 230} Chain: "d" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1909 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 10, 'TRANS': 230} Chain: "e" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1909 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 10, 'TRANS': 230} Chain: "f" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1909 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 10, 'TRANS': 230} Chain: "g" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1909 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 10, 'TRANS': 230} Chain: "h" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1909 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 10, 'TRANS': 230} Chain: "i" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1909 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 10, 'TRANS': 230} Chain: "j" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1909 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 10, 'TRANS': 230} Chain: "k" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1909 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 10, 'TRANS': 230} 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} Chain: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: 20.95, per 1000 atoms: 0.39 Number of scatterers: 53064 At special positions: 0 Unit cell: (165.2, 170.8, 373.8, 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 341 16.00 P 22 15.00 Mg 11 11.99 O 10142 8.00 N 9031 7.00 C 33517 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: 17.28 Conformation dependent library (CDL) restraints added in 7.2 seconds 13354 Ramachandran restraints generated. 6677 Oldfield, 0 Emsley, 6677 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12452 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 363 helices and 44 sheets defined 48.6% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.36 Creating SS restraints... Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 81 through 93 Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 139 through 147 removed outlier: 3.933A pdb=" N SER A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 184 through 198 removed outlier: 3.896A pdb=" N THR A 196 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU A 197 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 218 removed outlier: 3.646A pdb=" N LYS A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 Processing helix chain 'A' and resid 254 through 258 removed outlier: 3.574A pdb=" N ARG A 258 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 263 Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 276 through 285 removed outlier: 3.824A pdb=" N TYR A 281 " --> pdb=" O HIS A 277 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 298 removed outlier: 4.546A pdb=" N LYS A 293 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 311 through 317 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 340 through 350 removed outlier: 3.548A pdb=" N SER A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 357 Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.519A pdb=" N VAL A 372 " --> pdb=" O PRO A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 81 through 93 Processing helix chain 'B' and resid 115 through 128 Processing helix chain 'B' and resid 139 through 147 removed outlier: 3.934A pdb=" N SER B 143 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR B 145 " --> pdb=" O VAL B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 184 through 198 removed outlier: 3.897A pdb=" N THR B 196 " --> pdb=" O MET B 192 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU B 197 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 218 removed outlier: 3.645A pdb=" N LYS B 217 " --> pdb=" O ASP B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 234 Processing helix chain 'B' and resid 254 through 258 removed outlier: 3.574A pdb=" N ARG B 258 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 263 Processing helix chain 'B' and resid 266 through 269 Processing helix chain 'B' and resid 276 through 285 removed outlier: 3.824A pdb=" N TYR B 281 " --> pdb=" O HIS B 277 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 284 " --> pdb=" O THR B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 298 removed outlier: 4.546A pdb=" N LYS B 293 " --> pdb=" O ASP B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 307 Processing helix chain 'B' and resid 311 through 317 Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 340 through 350 removed outlier: 3.549A pdb=" N SER B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 357 Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.518A pdb=" N VAL B 372 " --> pdb=" O PRO B 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 81 through 93 Processing helix chain 'C' and resid 115 through 128 Processing helix chain 'C' and resid 139 through 147 removed outlier: 3.933A pdb=" N SER C 143 " --> pdb=" O GLN C 139 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR C 145 " --> pdb=" O VAL C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 184 through 198 removed outlier: 3.896A pdb=" N THR C 196 " --> pdb=" O MET C 192 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU C 197 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG C 198 " --> pdb=" O ILE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 218 removed outlier: 3.646A pdb=" N LYS C 217 " --> pdb=" O ASP C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 234 Processing helix chain 'C' and resid 254 through 258 removed outlier: 3.572A pdb=" N ARG C 258 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 263 Processing helix chain 'C' and resid 266 through 269 Processing helix chain 'C' and resid 276 through 285 removed outlier: 3.824A pdb=" N TYR C 281 " --> pdb=" O HIS C 277 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 284 " --> pdb=" O THR C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 298 removed outlier: 4.546A pdb=" N LYS C 293 " --> pdb=" O ASP C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 307 Processing helix chain 'C' and resid 311 through 317 Processing helix chain 'C' and resid 319 through 321 No H-bonds generated for 'chain 'C' and resid 319 through 321' Processing helix chain 'C' and resid 340 through 350 removed outlier: 3.549A pdb=" N SER C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 357 Processing helix chain 'C' and resid 361 through 367 Processing helix chain 'C' and resid 369 through 374 removed outlier: 3.518A pdb=" N VAL C 372 " --> pdb=" O PRO C 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 81 through 93 Processing helix chain 'D' and resid 115 through 128 Processing helix chain 'D' and resid 139 through 147 removed outlier: 3.933A pdb=" N SER D 143 " --> pdb=" O GLN D 139 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU D 144 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR D 145 " --> pdb=" O VAL D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 176 No H-bonds generated for 'chain 'D' and resid 174 through 176' Processing helix chain 'D' and resid 184 through 198 removed outlier: 3.897A pdb=" N THR D 196 " --> pdb=" O MET D 192 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU D 197 " --> pdb=" O LYS D 193 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG D 198 " --> pdb=" O ILE D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 218 removed outlier: 3.646A pdb=" N LYS D 217 " --> pdb=" O ASP D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 234 Processing helix chain 'D' and resid 254 through 258 removed outlier: 3.572A pdb=" N ARG D 258 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 263 Processing helix chain 'D' and resid 266 through 269 Processing helix chain 'D' and resid 276 through 285 removed outlier: 3.824A pdb=" N TYR D 281 " --> pdb=" O HIS D 277 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D 284 " --> pdb=" O THR D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 298 removed outlier: 4.547A pdb=" N LYS D 293 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 307 Processing helix chain 'D' and resid 311 through 317 Processing helix chain 'D' and resid 319 through 321 No H-bonds generated for 'chain 'D' and resid 319 through 321' Processing helix chain 'D' and resid 340 through 350 removed outlier: 3.548A pdb=" N SER D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 357 Processing helix chain 'D' and resid 361 through 367 Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.519A pdb=" N VAL D 372 " --> pdb=" O PRO D 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 62 Processing helix chain 'E' and resid 64 through 66 No H-bonds generated for 'chain 'E' and resid 64 through 66' Processing helix chain 'E' and resid 81 through 93 Processing helix chain 'E' and resid 115 through 128 Processing helix chain 'E' and resid 139 through 147 removed outlier: 3.933A pdb=" N SER E 143 " --> pdb=" O GLN E 139 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR E 145 " --> pdb=" O VAL E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 176 No H-bonds generated for 'chain 'E' and resid 174 through 176' Processing helix chain 'E' and resid 184 through 198 removed outlier: 3.897A pdb=" N THR E 196 " --> pdb=" O MET E 192 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU E 197 " --> pdb=" O LYS E 193 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG E 198 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 218 removed outlier: 3.646A pdb=" N LYS E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 234 Processing helix chain 'E' and resid 254 through 258 removed outlier: 3.573A pdb=" N ARG E 258 " --> pdb=" O GLU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 263 Processing helix chain 'E' and resid 266 through 269 Processing helix chain 'E' and resid 276 through 285 removed outlier: 3.824A pdb=" N TYR E 281 " --> pdb=" O HIS E 277 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE E 284 " --> pdb=" O THR E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 298 removed outlier: 4.547A pdb=" N LYS E 293 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 307 Processing helix chain 'E' and resid 311 through 317 Processing helix chain 'E' and resid 319 through 321 No H-bonds generated for 'chain 'E' and resid 319 through 321' Processing helix chain 'E' and resid 340 through 350 removed outlier: 3.549A pdb=" N SER E 350 " --> pdb=" O SER E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 357 Processing helix chain 'E' and resid 361 through 367 Processing helix chain 'E' and resid 369 through 374 removed outlier: 3.518A pdb=" N VAL E 372 " --> pdb=" O PRO E 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 62 Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'F' and resid 81 through 93 Processing helix chain 'F' and resid 115 through 128 Processing helix chain 'F' and resid 139 through 147 removed outlier: 3.933A pdb=" N SER F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU F 144 " --> pdb=" O ALA F 140 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR F 145 " --> pdb=" O VAL F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 176 No H-bonds generated for 'chain 'F' and resid 174 through 176' Processing helix chain 'F' and resid 184 through 198 removed outlier: 3.897A pdb=" N THR F 196 " --> pdb=" O MET F 192 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU F 197 " --> pdb=" O LYS F 193 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG F 198 " --> pdb=" O ILE F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 218 removed outlier: 3.645A pdb=" N LYS F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 234 Processing helix chain 'F' and resid 254 through 258 removed outlier: 3.573A pdb=" N ARG F 258 " --> pdb=" O GLU F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 263 Processing helix chain 'F' and resid 266 through 269 Processing helix chain 'F' and resid 276 through 285 removed outlier: 3.824A pdb=" N TYR F 281 " --> pdb=" O HIS F 277 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE F 284 " --> pdb=" O THR F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 298 removed outlier: 4.546A pdb=" N LYS F 293 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 307 Processing helix chain 'F' and resid 311 through 317 Processing helix chain 'F' and resid 319 through 321 No H-bonds generated for 'chain 'F' and resid 319 through 321' Processing helix chain 'F' and resid 340 through 350 removed outlier: 3.549A pdb=" N SER F 350 " --> pdb=" O SER F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 357 Processing helix chain 'F' and resid 361 through 367 Processing helix chain 'F' and resid 369 through 374 removed outlier: 3.518A pdb=" N VAL F 372 " --> pdb=" O PRO F 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 81 through 93 Processing helix chain 'G' and resid 115 through 128 Processing helix chain 'G' and resid 139 through 147 removed outlier: 3.933A pdb=" N SER G 143 " --> pdb=" O GLN G 139 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU G 144 " --> pdb=" O ALA G 140 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR G 145 " --> pdb=" O VAL G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 176 No H-bonds generated for 'chain 'G' and resid 174 through 176' Processing helix chain 'G' and resid 184 through 198 removed outlier: 3.897A pdb=" N THR G 196 " --> pdb=" O MET G 192 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU G 197 " --> pdb=" O LYS G 193 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG G 198 " --> pdb=" O ILE G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 218 removed outlier: 3.646A pdb=" N LYS G 217 " --> pdb=" O ASP G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 234 Processing helix chain 'G' and resid 254 through 258 removed outlier: 3.574A pdb=" N ARG G 258 " --> pdb=" O GLU G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 263 Processing helix chain 'G' and resid 266 through 269 Processing helix chain 'G' and resid 276 through 285 removed outlier: 3.824A pdb=" N TYR G 281 " --> pdb=" O HIS G 277 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE G 284 " --> pdb=" O THR G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 298 removed outlier: 4.546A pdb=" N LYS G 293 " --> pdb=" O ASP G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 307 Processing helix chain 'G' and resid 311 through 317 Processing helix chain 'G' and resid 319 through 321 No H-bonds generated for 'chain 'G' and resid 319 through 321' Processing helix chain 'G' and resid 340 through 350 removed outlier: 3.549A pdb=" N SER G 350 " --> pdb=" O SER G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 357 Processing helix chain 'G' and resid 361 through 367 Processing helix chain 'G' and resid 369 through 374 removed outlier: 3.518A pdb=" N VAL G 372 " --> pdb=" O PRO G 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 62 Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 81 through 93 Processing helix chain 'H' and resid 115 through 128 Processing helix chain 'H' and resid 139 through 147 removed outlier: 3.932A pdb=" N SER H 143 " --> pdb=" O GLN H 139 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU H 144 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR H 145 " --> pdb=" O VAL H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 176 No H-bonds generated for 'chain 'H' and resid 174 through 176' Processing helix chain 'H' and resid 184 through 198 removed outlier: 3.897A pdb=" N THR H 196 " --> pdb=" O MET H 192 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU H 197 " --> pdb=" O LYS H 193 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG H 198 " --> pdb=" O ILE H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 218 removed outlier: 3.645A pdb=" N LYS H 217 " --> pdb=" O ASP H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 234 Processing helix chain 'H' and resid 254 through 258 removed outlier: 3.572A pdb=" N ARG H 258 " --> pdb=" O GLU H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 260 through 263 Processing helix chain 'H' and resid 266 through 269 Processing helix chain 'H' and resid 276 through 285 removed outlier: 3.824A pdb=" N TYR H 281 " --> pdb=" O HIS H 277 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE H 284 " --> pdb=" O THR H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 289 through 298 removed outlier: 4.547A pdb=" N LYS H 293 " --> pdb=" O ASP H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 307 Processing helix chain 'H' and resid 311 through 317 Processing helix chain 'H' and resid 319 through 321 No H-bonds generated for 'chain 'H' and resid 319 through 321' Processing helix chain 'H' and resid 340 through 350 removed outlier: 3.548A pdb=" N SER H 350 " --> pdb=" O SER H 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 353 through 357 Processing helix chain 'H' and resid 361 through 367 Processing helix chain 'H' and resid 369 through 374 removed outlier: 3.519A pdb=" N VAL H 372 " --> pdb=" O PRO H 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 62 Processing helix chain 'I' and resid 64 through 66 No H-bonds generated for 'chain 'I' and resid 64 through 66' Processing helix chain 'I' and resid 81 through 93 Processing helix chain 'I' and resid 115 through 128 Processing helix chain 'I' and resid 139 through 147 removed outlier: 3.933A pdb=" N SER I 143 " --> pdb=" O GLN I 139 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU I 144 " --> pdb=" O ALA I 140 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR I 145 " --> pdb=" O VAL I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 176 No H-bonds generated for 'chain 'I' and resid 174 through 176' Processing helix chain 'I' and resid 184 through 198 removed outlier: 3.897A pdb=" N THR I 196 " --> pdb=" O MET I 192 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU I 197 " --> pdb=" O LYS I 193 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG I 198 " --> pdb=" O ILE I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 218 removed outlier: 3.646A pdb=" N LYS I 217 " --> pdb=" O ASP I 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 234 Processing helix chain 'I' and resid 254 through 258 removed outlier: 3.573A pdb=" N ARG I 258 " --> pdb=" O GLU I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 260 through 263 Processing helix chain 'I' and resid 266 through 269 Processing helix chain 'I' and resid 276 through 285 removed outlier: 3.825A pdb=" N TYR I 281 " --> pdb=" O HIS I 277 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE I 284 " --> pdb=" O THR I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 289 through 298 removed outlier: 4.547A pdb=" N LYS I 293 " --> pdb=" O ASP I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 307 Processing helix chain 'I' and resid 311 through 317 Processing helix chain 'I' and resid 319 through 321 No H-bonds generated for 'chain 'I' and resid 319 through 321' Processing helix chain 'I' and resid 340 through 350 removed outlier: 3.549A pdb=" N SER I 350 " --> pdb=" O SER I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 353 through 357 Processing helix chain 'I' and resid 361 through 367 Processing helix chain 'I' and resid 369 through 374 removed outlier: 3.519A pdb=" N VAL I 372 " --> pdb=" O PRO I 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 62 Processing helix chain 'J' and resid 64 through 66 No H-bonds generated for 'chain 'J' and resid 64 through 66' Processing helix chain 'J' and resid 81 through 93 Processing helix chain 'J' and resid 115 through 128 Processing helix chain 'J' and resid 139 through 147 removed outlier: 3.933A pdb=" N SER J 143 " --> pdb=" O GLN J 139 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU J 144 " --> pdb=" O ALA J 140 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR J 145 " --> pdb=" O VAL J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 176 No H-bonds generated for 'chain 'J' and resid 174 through 176' Processing helix chain 'J' and resid 184 through 198 removed outlier: 3.897A pdb=" N THR J 196 " --> pdb=" O MET J 192 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU J 197 " --> pdb=" O LYS J 193 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG J 198 " --> pdb=" O ILE J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 218 removed outlier: 3.646A pdb=" N LYS J 217 " --> pdb=" O ASP J 213 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 234 Processing helix chain 'J' and resid 254 through 258 removed outlier: 3.573A pdb=" N ARG J 258 " --> pdb=" O GLU J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 260 through 263 Processing helix chain 'J' and resid 266 through 269 Processing helix chain 'J' and resid 276 through 285 removed outlier: 3.824A pdb=" N TYR J 281 " --> pdb=" O HIS J 277 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE J 284 " --> pdb=" O THR J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 298 removed outlier: 4.546A pdb=" N LYS J 293 " --> pdb=" O ASP J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 304 through 307 Processing helix chain 'J' and resid 311 through 317 Processing helix chain 'J' and resid 319 through 321 No H-bonds generated for 'chain 'J' and resid 319 through 321' Processing helix chain 'J' and resid 340 through 350 removed outlier: 3.548A pdb=" N SER J 350 " --> pdb=" O SER J 346 " (cutoff:3.500A) Processing helix chain 'J' and resid 353 through 357 Processing helix chain 'J' and resid 361 through 367 Processing helix chain 'J' and resid 369 through 374 removed outlier: 3.518A pdb=" N VAL J 372 " --> pdb=" O PRO J 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 62 Processing helix chain 'K' and resid 64 through 66 No H-bonds generated for 'chain 'K' and resid 64 through 66' Processing helix chain 'K' and resid 81 through 93 Processing helix chain 'K' and resid 115 through 128 Processing helix chain 'K' and resid 139 through 147 removed outlier: 3.933A pdb=" N SER K 143 " --> pdb=" O GLN K 139 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU K 144 " --> pdb=" O ALA K 140 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR K 145 " --> pdb=" O VAL K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 176 No H-bonds generated for 'chain 'K' and resid 174 through 176' Processing helix chain 'K' and resid 184 through 198 removed outlier: 3.897A pdb=" N THR K 196 " --> pdb=" O MET K 192 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU K 197 " --> pdb=" O LYS K 193 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG K 198 " --> pdb=" O ILE K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 218 removed outlier: 3.645A pdb=" N LYS K 217 " --> pdb=" O ASP K 213 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 234 Processing helix chain 'K' and resid 254 through 258 removed outlier: 3.573A pdb=" N ARG K 258 " --> pdb=" O GLU K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 260 through 263 Processing helix chain 'K' and resid 266 through 269 Processing helix chain 'K' and resid 276 through 285 removed outlier: 3.823A pdb=" N TYR K 281 " --> pdb=" O HIS K 277 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE K 284 " --> pdb=" O THR K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 289 through 298 removed outlier: 4.547A pdb=" N LYS K 293 " --> pdb=" O ASP K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 307 Processing helix chain 'K' and resid 311 through 317 Processing helix chain 'K' and resid 319 through 321 No H-bonds generated for 'chain 'K' and resid 319 through 321' Processing helix chain 'K' and resid 340 through 350 removed outlier: 3.549A pdb=" N SER K 350 " --> pdb=" O SER K 346 " (cutoff:3.500A) Processing helix chain 'K' and resid 353 through 357 Processing helix chain 'K' and resid 361 through 367 Processing helix chain 'K' and resid 369 through 374 removed outlier: 3.518A pdb=" N VAL K 372 " --> pdb=" O PRO K 369 " (cutoff:3.500A) Processing helix chain 'a' and resid 395 through 406 removed outlier: 3.551A pdb=" N THR a 399 " --> pdb=" O ARG a 395 " (cutoff:3.500A) Processing helix chain 'a' and resid 416 through 419 No H-bonds generated for 'chain 'a' and resid 416 through 419' Processing helix chain 'a' and resid 424 through 433 removed outlier: 3.925A pdb=" N GLU a 431 " --> pdb=" O PHE a 427 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS a 432 " --> pdb=" O GLN a 428 " (cutoff:3.500A) Processing helix chain 'a' and resid 453 through 468 Processing helix chain 'a' and resid 480 through 484 Processing helix chain 'a' and resid 488 through 510 removed outlier: 4.362A pdb=" N LEU a 492 " --> pdb=" O ARG a 488 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN a 497 " --> pdb=" O ALA a 493 " (cutoff:3.500A) Processing helix chain 'a' and resid 518 through 531 Processing helix chain 'a' and resid 544 through 548 Processing helix chain 'a' and resid 550 through 559 Processing helix chain 'a' and resid 576 through 593 Processing helix chain 'a' and resid 601 through 604 No H-bonds generated for 'chain 'a' and resid 601 through 604' Processing helix chain 'a' and resid 609 through 621 Processing helix chain 'b' and resid 395 through 406 removed outlier: 3.551A pdb=" N THR b 399 " --> pdb=" O ARG b 395 " (cutoff:3.500A) Processing helix chain 'b' and resid 416 through 419 No H-bonds generated for 'chain 'b' and resid 416 through 419' Processing helix chain 'b' and resid 424 through 433 removed outlier: 3.926A pdb=" N GLU b 431 " --> pdb=" O PHE b 427 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS b 432 " --> pdb=" O GLN b 428 " (cutoff:3.500A) Processing helix chain 'b' and resid 453 through 468 Processing helix chain 'b' and resid 480 through 484 Processing helix chain 'b' and resid 488 through 510 removed outlier: 4.362A pdb=" N LEU b 492 " --> pdb=" O ARG b 488 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN b 497 " --> pdb=" O ALA b 493 " (cutoff:3.500A) Processing helix chain 'b' and resid 518 through 531 Processing helix chain 'b' and resid 544 through 548 Processing helix chain 'b' and resid 550 through 559 Processing helix chain 'b' and resid 576 through 593 Processing helix chain 'b' and resid 601 through 604 No H-bonds generated for 'chain 'b' and resid 601 through 604' Processing helix chain 'b' and resid 609 through 621 Processing helix chain 'c' and resid 395 through 406 removed outlier: 3.551A pdb=" N THR c 399 " --> pdb=" O ARG c 395 " (cutoff:3.500A) Processing helix chain 'c' and resid 416 through 419 No H-bonds generated for 'chain 'c' and resid 416 through 419' Processing helix chain 'c' and resid 424 through 433 removed outlier: 3.925A pdb=" N GLU c 431 " --> pdb=" O PHE c 427 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS c 432 " --> pdb=" O GLN c 428 " (cutoff:3.500A) Processing helix chain 'c' and resid 453 through 468 Processing helix chain 'c' and resid 480 through 484 Processing helix chain 'c' and resid 488 through 510 removed outlier: 4.362A pdb=" N LEU c 492 " --> pdb=" O ARG c 488 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN c 497 " --> pdb=" O ALA c 493 " (cutoff:3.500A) Processing helix chain 'c' and resid 518 through 531 Processing helix chain 'c' and resid 544 through 548 Processing helix chain 'c' and resid 550 through 559 Processing helix chain 'c' and resid 576 through 593 Processing helix chain 'c' and resid 601 through 604 No H-bonds generated for 'chain 'c' and resid 601 through 604' Processing helix chain 'c' and resid 609 through 621 Processing helix chain 'd' and resid 395 through 406 removed outlier: 3.551A pdb=" N THR d 399 " --> pdb=" O ARG d 395 " (cutoff:3.500A) Processing helix chain 'd' and resid 416 through 419 No H-bonds generated for 'chain 'd' and resid 416 through 419' Processing helix chain 'd' and resid 424 through 433 removed outlier: 3.925A pdb=" N GLU d 431 " --> pdb=" O PHE d 427 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS d 432 " --> pdb=" O GLN d 428 " (cutoff:3.500A) Processing helix chain 'd' and resid 453 through 468 Processing helix chain 'd' and resid 480 through 484 Processing helix chain 'd' and resid 488 through 510 removed outlier: 4.363A pdb=" N LEU d 492 " --> pdb=" O ARG d 488 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN d 497 " --> pdb=" O ALA d 493 " (cutoff:3.500A) Processing helix chain 'd' and resid 518 through 531 Processing helix chain 'd' and resid 544 through 548 Processing helix chain 'd' and resid 550 through 559 Processing helix chain 'd' and resid 576 through 593 Processing helix chain 'd' and resid 601 through 604 No H-bonds generated for 'chain 'd' and resid 601 through 604' Processing helix chain 'd' and resid 609 through 621 Processing helix chain 'e' and resid 395 through 406 removed outlier: 3.551A pdb=" N THR e 399 " --> pdb=" O ARG e 395 " (cutoff:3.500A) Processing helix chain 'e' and resid 416 through 419 No H-bonds generated for 'chain 'e' and resid 416 through 419' Processing helix chain 'e' and resid 424 through 433 removed outlier: 3.925A pdb=" N GLU e 431 " --> pdb=" O PHE e 427 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS e 432 " --> pdb=" O GLN e 428 " (cutoff:3.500A) Processing helix chain 'e' and resid 453 through 468 Processing helix chain 'e' and resid 480 through 484 Processing helix chain 'e' and resid 488 through 510 removed outlier: 4.362A pdb=" N LEU e 492 " --> pdb=" O ARG e 488 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN e 497 " --> pdb=" O ALA e 493 " (cutoff:3.500A) Processing helix chain 'e' and resid 518 through 531 Processing helix chain 'e' and resid 544 through 548 Processing helix chain 'e' and resid 550 through 559 Processing helix chain 'e' and resid 576 through 593 Processing helix chain 'e' and resid 601 through 604 No H-bonds generated for 'chain 'e' and resid 601 through 604' Processing helix chain 'e' and resid 609 through 621 Processing helix chain 'f' and resid 395 through 406 removed outlier: 3.551A pdb=" N THR f 399 " --> pdb=" O ARG f 395 " (cutoff:3.500A) Processing helix chain 'f' and resid 416 through 419 No H-bonds generated for 'chain 'f' and resid 416 through 419' Processing helix chain 'f' and resid 424 through 433 removed outlier: 3.925A pdb=" N GLU f 431 " --> pdb=" O PHE f 427 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS f 432 " --> pdb=" O GLN f 428 " (cutoff:3.500A) Processing helix chain 'f' and resid 453 through 468 Processing helix chain 'f' and resid 480 through 484 Processing helix chain 'f' and resid 488 through 510 removed outlier: 4.362A pdb=" N LEU f 492 " --> pdb=" O ARG f 488 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN f 497 " --> pdb=" O ALA f 493 " (cutoff:3.500A) Processing helix chain 'f' and resid 518 through 531 Processing helix chain 'f' and resid 544 through 548 Processing helix chain 'f' and resid 550 through 559 Processing helix chain 'f' and resid 576 through 593 Processing helix chain 'f' and resid 601 through 604 No H-bonds generated for 'chain 'f' and resid 601 through 604' Processing helix chain 'f' and resid 609 through 621 Processing helix chain 'g' and resid 395 through 406 removed outlier: 3.551A pdb=" N THR g 399 " --> pdb=" O ARG g 395 " (cutoff:3.500A) Processing helix chain 'g' and resid 416 through 419 No H-bonds generated for 'chain 'g' and resid 416 through 419' Processing helix chain 'g' and resid 424 through 433 removed outlier: 3.925A pdb=" N GLU g 431 " --> pdb=" O PHE g 427 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS g 432 " --> pdb=" O GLN g 428 " (cutoff:3.500A) Processing helix chain 'g' and resid 453 through 468 Processing helix chain 'g' and resid 480 through 484 Processing helix chain 'g' and resid 488 through 510 removed outlier: 4.362A pdb=" N LEU g 492 " --> pdb=" O ARG g 488 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN g 497 " --> pdb=" O ALA g 493 " (cutoff:3.500A) Processing helix chain 'g' and resid 518 through 531 Processing helix chain 'g' and resid 544 through 548 Processing helix chain 'g' and resid 550 through 559 Processing helix chain 'g' and resid 576 through 593 Processing helix chain 'g' and resid 601 through 604 No H-bonds generated for 'chain 'g' and resid 601 through 604' Processing helix chain 'g' and resid 609 through 621 Processing helix chain 'h' and resid 395 through 406 removed outlier: 3.551A pdb=" N THR h 399 " --> pdb=" O ARG h 395 " (cutoff:3.500A) Processing helix chain 'h' and resid 416 through 419 No H-bonds generated for 'chain 'h' and resid 416 through 419' Processing helix chain 'h' and resid 424 through 433 removed outlier: 3.925A pdb=" N GLU h 431 " --> pdb=" O PHE h 427 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS h 432 " --> pdb=" O GLN h 428 " (cutoff:3.500A) Processing helix chain 'h' and resid 453 through 468 Processing helix chain 'h' and resid 480 through 484 Processing helix chain 'h' and resid 488 through 510 removed outlier: 4.363A pdb=" N LEU h 492 " --> pdb=" O ARG h 488 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN h 497 " --> pdb=" O ALA h 493 " (cutoff:3.500A) Processing helix chain 'h' and resid 518 through 531 Processing helix chain 'h' and resid 544 through 548 Processing helix chain 'h' and resid 550 through 559 Processing helix chain 'h' and resid 576 through 593 Processing helix chain 'h' and resid 601 through 604 No H-bonds generated for 'chain 'h' and resid 601 through 604' Processing helix chain 'h' and resid 609 through 621 Processing helix chain 'i' and resid 395 through 406 removed outlier: 3.551A pdb=" N THR i 399 " --> pdb=" O ARG i 395 " (cutoff:3.500A) Processing helix chain 'i' and resid 416 through 419 No H-bonds generated for 'chain 'i' and resid 416 through 419' Processing helix chain 'i' and resid 424 through 433 removed outlier: 3.925A pdb=" N GLU i 431 " --> pdb=" O PHE i 427 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS i 432 " --> pdb=" O GLN i 428 " (cutoff:3.500A) Processing helix chain 'i' and resid 453 through 468 Processing helix chain 'i' and resid 480 through 484 Processing helix chain 'i' and resid 488 through 510 removed outlier: 4.362A pdb=" N LEU i 492 " --> pdb=" O ARG i 488 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN i 497 " --> pdb=" O ALA i 493 " (cutoff:3.500A) Processing helix chain 'i' and resid 518 through 531 Processing helix chain 'i' and resid 544 through 548 Processing helix chain 'i' and resid 550 through 559 Processing helix chain 'i' and resid 576 through 593 Processing helix chain 'i' and resid 601 through 604 No H-bonds generated for 'chain 'i' and resid 601 through 604' Processing helix chain 'i' and resid 609 through 621 Processing helix chain 'j' and resid 395 through 406 removed outlier: 3.551A pdb=" N THR j 399 " --> pdb=" O ARG j 395 " (cutoff:3.500A) Processing helix chain 'j' and resid 416 through 419 No H-bonds generated for 'chain 'j' and resid 416 through 419' Processing helix chain 'j' and resid 424 through 433 removed outlier: 3.925A pdb=" N GLU j 431 " --> pdb=" O PHE j 427 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS j 432 " --> pdb=" O GLN j 428 " (cutoff:3.500A) Processing helix chain 'j' and resid 453 through 468 Processing helix chain 'j' and resid 480 through 484 Processing helix chain 'j' and resid 488 through 510 removed outlier: 4.362A pdb=" N LEU j 492 " --> pdb=" O ARG j 488 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN j 497 " --> pdb=" O ALA j 493 " (cutoff:3.500A) Processing helix chain 'j' and resid 518 through 531 Processing helix chain 'j' and resid 544 through 548 Processing helix chain 'j' and resid 550 through 559 Processing helix chain 'j' and resid 576 through 593 Processing helix chain 'j' and resid 601 through 604 No H-bonds generated for 'chain 'j' and resid 601 through 604' Processing helix chain 'j' and resid 609 through 621 Processing helix chain 'k' and resid 395 through 406 removed outlier: 3.551A pdb=" N THR k 399 " --> pdb=" O ARG k 395 " (cutoff:3.500A) Processing helix chain 'k' and resid 416 through 419 No H-bonds generated for 'chain 'k' and resid 416 through 419' Processing helix chain 'k' and resid 424 through 433 removed outlier: 3.926A pdb=" N GLU k 431 " --> pdb=" O PHE k 427 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS k 432 " --> pdb=" O GLN k 428 " (cutoff:3.500A) Processing helix chain 'k' and resid 453 through 468 Processing helix chain 'k' and resid 480 through 484 Processing helix chain 'k' and resid 488 through 510 removed outlier: 4.361A pdb=" N LEU k 492 " --> pdb=" O ARG k 488 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN k 497 " --> pdb=" O ALA k 493 " (cutoff:3.500A) Processing helix chain 'k' and resid 518 through 531 Processing helix chain 'k' and resid 544 through 548 Processing helix chain 'k' and resid 550 through 559 Processing helix chain 'k' and resid 576 through 593 Processing helix chain 'k' and resid 601 through 604 No H-bonds generated for 'chain 'k' and resid 601 through 604' Processing helix chain 'k' and resid 609 through 621 Processing sheet with id= A, first strand: chain 'A' and resid 134 through 138 removed outlier: 6.788A pdb=" N THR A 105 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ALA A 137 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU A 107 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 10 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N THR A 108 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS A 12 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 22 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA A 31 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 37 through 40 Processing sheet with id= C, first strand: chain 'A' and resid 299 through 302 removed outlier: 5.745A pdb=" N ILE A 153 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N SER A 302 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU A 155 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 240 through 243 Processing sheet with id= E, first strand: chain 'B' and resid 134 through 138 removed outlier: 6.789A pdb=" N THR B 105 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ALA B 137 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU B 107 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU B 10 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N THR B 108 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS B 12 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY B 22 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA B 31 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 37 through 40 Processing sheet with id= G, first strand: chain 'B' and resid 299 through 302 removed outlier: 5.744A pdb=" N ILE B 153 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER B 302 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU B 155 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 240 through 243 Processing sheet with id= I, first strand: chain 'C' and resid 134 through 138 removed outlier: 6.789A pdb=" N THR C 105 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ALA C 137 " --> pdb=" O THR C 105 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU C 107 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU C 10 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N THR C 108 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS C 12 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C 22 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA C 31 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 37 through 40 Processing sheet with id= K, first strand: chain 'C' and resid 299 through 302 removed outlier: 5.744A pdb=" N ILE C 153 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER C 302 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU C 155 " --> pdb=" O SER C 302 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 240 through 243 Processing sheet with id= M, first strand: chain 'D' and resid 134 through 138 removed outlier: 6.789A pdb=" N THR D 105 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ALA D 137 " --> pdb=" O THR D 105 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU D 107 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU D 10 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N THR D 108 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS D 12 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY D 22 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA D 31 " --> pdb=" O ALA D 21 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 37 through 40 Processing sheet with id= O, first strand: chain 'D' and resid 299 through 302 removed outlier: 5.744A pdb=" N ILE D 153 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER D 302 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU D 155 " --> pdb=" O SER D 302 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 240 through 243 Processing sheet with id= Q, first strand: chain 'E' and resid 134 through 138 removed outlier: 6.789A pdb=" N THR E 105 " --> pdb=" O TYR E 135 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ALA E 137 " --> pdb=" O THR E 105 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU E 107 " --> pdb=" O ALA E 137 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU E 10 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N THR E 108 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N CYS E 12 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY E 22 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA E 31 " --> pdb=" O ALA E 21 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 37 through 40 Processing sheet with id= S, first strand: chain 'E' and resid 299 through 302 removed outlier: 5.744A pdb=" N ILE E 153 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER E 302 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU E 155 " --> pdb=" O SER E 302 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 240 through 243 Processing sheet with id= U, first strand: chain 'F' and resid 134 through 138 removed outlier: 6.788A pdb=" N THR F 105 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ALA F 137 " --> pdb=" O THR F 105 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU F 107 " --> pdb=" O ALA F 137 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU F 10 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N THR F 108 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS F 12 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY F 22 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA F 31 " --> pdb=" O ALA F 21 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 37 through 40 Processing sheet with id= W, first strand: chain 'F' and resid 299 through 302 removed outlier: 5.744A pdb=" N ILE F 153 " --> pdb=" O VAL F 300 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER F 302 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU F 155 " --> pdb=" O SER F 302 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 240 through 243 Processing sheet with id= Y, first strand: chain 'G' and resid 134 through 138 removed outlier: 6.789A pdb=" N THR G 105 " --> pdb=" O TYR G 135 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ALA G 137 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU G 107 " --> pdb=" O ALA G 137 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU G 10 " --> pdb=" O LEU G 106 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N THR G 108 " --> pdb=" O LEU G 10 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS G 12 " --> pdb=" O THR G 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY G 22 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA G 31 " --> pdb=" O ALA G 21 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 37 through 40 Processing sheet with id= AA, first strand: chain 'G' and resid 299 through 302 removed outlier: 5.745A pdb=" N ILE G 153 " --> pdb=" O VAL G 300 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER G 302 " --> pdb=" O ILE G 153 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU G 155 " --> pdb=" O SER G 302 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 240 through 243 Processing sheet with id= AC, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.788A pdb=" N THR H 105 " --> pdb=" O TYR H 135 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ALA H 137 " --> pdb=" O THR H 105 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU H 107 " --> pdb=" O ALA H 137 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU H 10 " --> pdb=" O LEU H 106 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N THR H 108 " --> pdb=" O LEU H 10 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N CYS H 12 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY H 22 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA H 31 " --> pdb=" O ALA H 21 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 37 through 40 Processing sheet with id= AE, first strand: chain 'H' and resid 299 through 302 removed outlier: 5.744A pdb=" N ILE H 153 " --> pdb=" O VAL H 300 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER H 302 " --> pdb=" O ILE H 153 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU H 155 " --> pdb=" O SER H 302 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 240 through 243 Processing sheet with id= AG, first strand: chain 'I' and resid 134 through 138 removed outlier: 6.789A pdb=" N THR I 105 " --> pdb=" O TYR I 135 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ALA I 137 " --> pdb=" O THR I 105 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU I 107 " --> pdb=" O ALA I 137 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU I 10 " --> pdb=" O LEU I 106 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N THR I 108 " --> pdb=" O LEU I 10 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS I 12 " --> pdb=" O THR I 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY I 22 " --> pdb=" O VAL I 11 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA I 31 " --> pdb=" O ALA I 21 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 37 through 40 Processing sheet with id= AI, first strand: chain 'I' and resid 299 through 302 removed outlier: 5.745A pdb=" N ILE I 153 " --> pdb=" O VAL I 300 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER I 302 " --> pdb=" O ILE I 153 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU I 155 " --> pdb=" O SER I 302 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 240 through 243 Processing sheet with id= AK, first strand: chain 'J' and resid 134 through 138 removed outlier: 6.788A pdb=" N THR J 105 " --> pdb=" O TYR J 135 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ALA J 137 " --> pdb=" O THR J 105 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU J 107 " --> pdb=" O ALA J 137 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU J 10 " --> pdb=" O LEU J 106 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N THR J 108 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS J 12 " --> pdb=" O THR J 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY J 22 " --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA J 31 " --> pdb=" O ALA J 21 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'J' and resid 37 through 40 Processing sheet with id= AM, first strand: chain 'J' and resid 299 through 302 removed outlier: 5.744A pdb=" N ILE J 153 " --> pdb=" O VAL J 300 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER J 302 " --> pdb=" O ILE J 153 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU J 155 " --> pdb=" O SER J 302 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'J' and resid 240 through 243 Processing sheet with id= AO, first strand: chain 'K' and resid 134 through 138 removed outlier: 6.789A pdb=" N THR K 105 " --> pdb=" O TYR K 135 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ALA K 137 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU K 107 " --> pdb=" O ALA K 137 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU K 10 " --> pdb=" O LEU K 106 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N THR K 108 " --> pdb=" O LEU K 10 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS K 12 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY K 22 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA K 31 " --> pdb=" O ALA K 21 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'K' and resid 37 through 40 Processing sheet with id= AQ, first strand: chain 'K' and resid 299 through 302 removed outlier: 5.745A pdb=" N ILE K 153 " --> pdb=" O VAL K 300 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER K 302 " --> pdb=" O ILE K 153 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU K 155 " --> pdb=" O SER K 302 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'K' and resid 240 through 243 1980 hydrogen bonds defined for protein. 5247 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: 18.32 Time building geometry restraints manager: 18.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 17382 1.34 - 1.46: 12240 1.46 - 1.59: 23860 1.59 - 1.71: 33 1.71 - 1.83: 605 Bond restraints: 54120 Sorted by residual: bond pdb=" CA VAL f 435 " pdb=" C VAL f 435 " ideal model delta sigma weight residual 1.524 1.494 0.029 8.30e-03 1.45e+04 1.25e+01 bond pdb=" CA VAL h 435 " pdb=" C VAL h 435 " ideal model delta sigma weight residual 1.524 1.494 0.029 8.30e-03 1.45e+04 1.25e+01 bond pdb=" CA VAL e 435 " pdb=" C VAL e 435 " ideal model delta sigma weight residual 1.524 1.495 0.029 8.30e-03 1.45e+04 1.23e+01 bond pdb=" CA VAL c 435 " pdb=" C VAL c 435 " ideal model delta sigma weight residual 1.524 1.495 0.029 8.30e-03 1.45e+04 1.22e+01 bond pdb=" CA VAL i 435 " pdb=" C VAL i 435 " ideal model delta sigma weight residual 1.524 1.495 0.029 8.30e-03 1.45e+04 1.21e+01 ... (remaining 54115 not shown) Histogram of bond angle deviations from ideal: 95.48 - 104.33: 1095 104.33 - 113.18: 29717 113.18 - 122.03: 30980 122.03 - 130.88: 11279 130.88 - 139.72: 266 Bond angle restraints: 73337 Sorted by residual: angle pdb=" C LEU c 390 " pdb=" N GLU c 391 " pdb=" CA GLU c 391 " ideal model delta sigma weight residual 122.21 139.72 -17.51 1.48e+00 4.57e-01 1.40e+02 angle pdb=" C LEU h 390 " pdb=" N GLU h 391 " pdb=" CA GLU h 391 " ideal model delta sigma weight residual 122.21 139.72 -17.51 1.48e+00 4.57e-01 1.40e+02 angle pdb=" C LEU j 390 " pdb=" N GLU j 391 " pdb=" CA GLU j 391 " ideal model delta sigma weight residual 122.21 139.71 -17.50 1.48e+00 4.57e-01 1.40e+02 angle pdb=" C LEU f 390 " pdb=" N GLU f 391 " pdb=" CA GLU f 391 " ideal model delta sigma weight residual 122.21 139.71 -17.50 1.48e+00 4.57e-01 1.40e+02 angle pdb=" C LEU d 390 " pdb=" N GLU d 391 " pdb=" CA GLU d 391 " ideal model delta sigma weight residual 122.21 139.71 -17.50 1.48e+00 4.57e-01 1.40e+02 ... (remaining 73332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 31512 17.45 - 34.89: 1026 34.89 - 52.34: 220 52.34 - 69.79: 11 69.79 - 87.24: 44 Dihedral angle restraints: 32813 sinusoidal: 13398 harmonic: 19415 Sorted by residual: dihedral pdb=" CA MET j 620 " pdb=" C MET j 620 " pdb=" N GLY j 621 " pdb=" CA GLY j 621 " ideal model delta harmonic sigma weight residual 180.00 143.38 36.62 0 5.00e+00 4.00e-02 5.36e+01 dihedral pdb=" CA MET g 620 " pdb=" C MET g 620 " pdb=" N GLY g 621 " pdb=" CA GLY g 621 " ideal model delta harmonic sigma weight residual 180.00 143.39 36.61 0 5.00e+00 4.00e-02 5.36e+01 dihedral pdb=" CA MET e 620 " pdb=" C MET e 620 " pdb=" N GLY e 621 " pdb=" CA GLY e 621 " ideal model delta harmonic sigma weight residual 180.00 143.40 36.60 0 5.00e+00 4.00e-02 5.36e+01 ... (remaining 32810 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 4621 0.035 - 0.070: 2305 0.070 - 0.105: 939 0.105 - 0.140: 243 0.140 - 0.175: 76 Chirality restraints: 8184 Sorted by residual: chirality pdb=" CB ILE h 559 " pdb=" CA ILE h 559 " pdb=" CG1 ILE h 559 " pdb=" CG2 ILE h 559 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CB ILE b 559 " pdb=" CA ILE b 559 " pdb=" CG1 ILE b 559 " pdb=" CG2 ILE b 559 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" CB ILE e 559 " pdb=" CA ILE e 559 " pdb=" CG1 ILE e 559 " pdb=" CG2 ILE e 559 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 8181 not shown) Planarity restraints: 9405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR g 585 " 0.028 2.00e-02 2.50e+03 1.68e-02 5.62e+00 pdb=" CG TYR g 585 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR g 585 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR g 585 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR g 585 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR g 585 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR g 585 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR g 585 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR c 585 " 0.028 2.00e-02 2.50e+03 1.67e-02 5.56e+00 pdb=" CG TYR c 585 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR c 585 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR c 585 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR c 585 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR c 585 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR c 585 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR c 585 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR d 585 " -0.028 2.00e-02 2.50e+03 1.67e-02 5.55e+00 pdb=" CG TYR d 585 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR d 585 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR d 585 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR d 585 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR d 585 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR d 585 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR d 585 " -0.012 2.00e-02 2.50e+03 ... (remaining 9402 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 369 2.52 - 3.11: 42952 3.11 - 3.71: 78333 3.71 - 4.30: 114506 4.30 - 4.90: 186409 Nonbonded interactions: 422569 Sorted by model distance: nonbonded pdb=" OG SER A 157 " pdb=" OG1 THR A 305 " model vdw 1.923 2.440 nonbonded pdb=" OG SER E 157 " pdb=" OG1 THR E 305 " model vdw 1.924 2.440 nonbonded pdb=" OG SER C 157 " pdb=" OG1 THR C 305 " model vdw 1.924 2.440 nonbonded pdb=" OG SER F 157 " pdb=" OG1 THR F 305 " model vdw 1.924 2.440 nonbonded pdb=" OG SER G 157 " pdb=" OG1 THR G 305 " model vdw 1.924 2.440 ... (remaining 422564 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' } 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: 0.690 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: 0.040 Extract box with map and model: 5.880 Check model and map are aligned: 0.580 Set scattering table: 0.370 Process input model: 110.780 Find NCS groups from input model: 2.860 Set up NCS constraints: 0.540 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 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 : 0.008 0.087 54120 Z= 0.510 Angle : 1.024 20.065 73337 Z= 0.542 Chirality : 0.049 0.175 8184 Planarity : 0.006 0.044 9405 Dihedral : 10.317 87.236 20361 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.17 % Favored : 92.33 % Rotamer: Outliers : 0.95 % Allowed : 1.53 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -3.21 (0.09), residues: 6677 helix: -2.07 (0.07), residues: 3135 sheet: -2.23 (0.17), residues: 638 loop : -2.00 (0.12), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP H 88 HIS 0.009 0.002 HIS D 373 PHE 0.033 0.002 PHE G 354 TYR 0.035 0.003 TYR b 585 ARG 0.005 0.000 ARG K 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13354 Ramachandran restraints generated. 6677 Oldfield, 0 Emsley, 6677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13354 Ramachandran restraints generated. 6677 Oldfield, 0 Emsley, 6677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 983 residues out of total 5764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 928 time to evaluate : 4.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8599 (tpt) cc_final: 0.8065 (tpp) REVERT: A 371 ILE cc_start: 0.8708 (mt) cc_final: 0.8442 (tp) REVERT: B 11 VAL cc_start: 0.9092 (p) cc_final: 0.8866 (p) REVERT: B 159 ASP cc_start: 0.7350 (m-30) cc_final: 0.6370 (t0) REVERT: F 84 MET cc_start: 0.8577 (tpt) cc_final: 0.8353 (tpt) REVERT: F 121 MET cc_start: 0.8115 (mtm) cc_final: 0.7865 (mtm) REVERT: F 327 MET cc_start: 0.8476 (tpt) cc_final: 0.8052 (tpt) REVERT: H 307 MET cc_start: 0.8312 (mmm) cc_final: 0.7928 (tpp) REVERT: I 182 LEU cc_start: 0.9214 (mp) cc_final: 0.9001 (mt) REVERT: K 125 MET cc_start: 0.7984 (mmt) cc_final: 0.7600 (mmp) REVERT: a 614 THR cc_start: 0.8716 (m) cc_final: 0.8130 (m) REVERT: a 620 MET cc_start: 0.7697 (mmp) cc_final: 0.6203 (mmm) REVERT: b 391 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.5899 (pm20) REVERT: b 596 ARG cc_start: 0.7764 (mmm160) cc_final: 0.7421 (mmm160) REVERT: b 614 THR cc_start: 0.9064 (m) cc_final: 0.8821 (m) REVERT: c 391 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6814 (pm20) REVERT: d 478 ILE cc_start: 0.8544 (mt) cc_final: 0.8132 (mt) REVERT: d 560 GLN cc_start: 0.8177 (mm110) cc_final: 0.7448 (pp30) REVERT: e 614 THR cc_start: 0.8760 (m) cc_final: 0.8316 (m) REVERT: f 625 LYS cc_start: 0.6280 (OUTLIER) cc_final: 0.6078 (ttpt) REVERT: g 391 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.5871 (pp20) REVERT: g 454 MET cc_start: 0.8350 (mmp) cc_final: 0.8105 (mmp) REVERT: g 614 THR cc_start: 0.8640 (m) cc_final: 0.8260 (m) REVERT: h 533 GLU cc_start: 0.7248 (mp0) cc_final: 0.7023 (pp20) REVERT: h 625 LYS cc_start: 0.6468 (OUTLIER) cc_final: 0.6124 (ptpp) REVERT: j 470 GLN cc_start: 0.8390 (mp10) cc_final: 0.8025 (mp10) outliers start: 55 outliers final: 7 residues processed: 967 average time/residue: 0.5697 time to fit residues: 878.0714 Evaluate side-chains 459 residues out of total 5764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 447 time to evaluate : 4.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain G residue 157 SER Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain J residue 157 SER Chi-restraints excluded: chain a residue 625 LYS Chi-restraints excluded: chain b residue 391 GLU Chi-restraints excluded: chain c residue 391 GLU Chi-restraints excluded: chain f residue 625 LYS Chi-restraints excluded: chain g residue 391 GLU Chi-restraints excluded: chain h residue 391 GLU Chi-restraints excluded: chain h residue 625 LYS Chi-restraints excluded: chain i residue 625 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 671 random chunks: chunk 566 optimal weight: 4.9990 chunk 508 optimal weight: 0.0370 chunk 282 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 343 optimal weight: 7.9990 chunk 271 optimal weight: 1.9990 chunk 525 optimal weight: 7.9990 chunk 203 optimal weight: 0.9990 chunk 319 optimal weight: 8.9990 chunk 391 optimal weight: 8.9990 chunk 609 optimal weight: 7.9990 overall best weight: 1.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 89 HIS ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN B 89 HIS ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 ASN C 89 HIS ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN D 14 ASN D 89 HIS D 227 ASN E 14 ASN E 89 HIS ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN F 89 HIS ** F 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 HIS ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 GLN H 89 HIS ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 ASN I 89 HIS ** I 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 ASN J 61 GLN J 89 HIS ** J 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 HIS ** K 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 523 ASN c 523 ASN d 523 ASN e 469 ASN ** e 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 523 ASN f 523 ASN g 469 ASN h 523 ASN i 405 ASN ** i 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 514 GLN j 415 HIS j 469 ASN j 523 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 54120 Z= 0.210 Angle : 0.657 7.760 73337 Z= 0.332 Chirality : 0.044 0.194 8184 Planarity : 0.005 0.045 9405 Dihedral : 6.592 86.195 7435 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.22 % Favored : 95.45 % Rotamer: Outliers : 1.54 % Allowed : 6.09 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -1.61 (0.10), residues: 6677 helix: -0.50 (0.08), residues: 3267 sheet: -1.15 (0.19), residues: 649 loop : -1.63 (0.12), residues: 2761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP d 403 HIS 0.006 0.001 HIS A 373 PHE 0.032 0.002 PHE i 400 TYR 0.032 0.002 TYR d 585 ARG 0.007 0.000 ARG j 591 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13354 Ramachandran restraints generated. 6677 Oldfield, 0 Emsley, 6677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13354 Ramachandran restraints generated. 6677 Oldfield, 0 Emsley, 6677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 5764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 465 time to evaluate : 4.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8488 (tpt) cc_final: 0.8178 (tpp) REVERT: A 371 ILE cc_start: 0.8803 (mt) cc_final: 0.8490 (tp) REVERT: C 354 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.8152 (m-10) REVERT: D 182 LEU cc_start: 0.8728 (mt) cc_final: 0.8416 (tp) REVERT: D 229 MET cc_start: 0.8837 (tpt) cc_final: 0.8500 (mmm) REVERT: G 229 MET cc_start: 0.8422 (tpp) cc_final: 0.7828 (tpp) REVERT: H 49 MET cc_start: 0.7556 (mmt) cc_final: 0.7182 (ptm) REVERT: H 229 MET cc_start: 0.8156 (mmm) cc_final: 0.7841 (mmm) REVERT: H 285 MET cc_start: 0.8584 (mmp) cc_final: 0.8149 (mmp) REVERT: H 307 MET cc_start: 0.8462 (mmm) cc_final: 0.8114 (tpp) REVERT: I 182 LEU cc_start: 0.9085 (mp) cc_final: 0.8807 (mt) REVERT: I 307 MET cc_start: 0.8987 (mtt) cc_final: 0.8775 (mtt) REVERT: J 285 MET cc_start: 0.8421 (mmp) cc_final: 0.8067 (mmp) REVERT: K 121 MET cc_start: 0.8584 (mtm) cc_final: 0.8325 (mtp) REVERT: b 391 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.6262 (pm20) REVERT: b 624 MET cc_start: 0.7893 (mpp) cc_final: 0.7654 (mpp) REVERT: d 528 THR cc_start: 0.7776 (m) cc_final: 0.7537 (t) REVERT: d 560 GLN cc_start: 0.8190 (mm110) cc_final: 0.7539 (pp30) REVERT: d 566 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.6541 (t80) REVERT: d 614 THR cc_start: 0.8873 (m) cc_final: 0.8398 (m) REVERT: d 625 LYS cc_start: 0.4970 (OUTLIER) cc_final: 0.4265 (mmtt) REVERT: f 624 MET cc_start: 0.8164 (mtt) cc_final: 0.7935 (mmt) REVERT: g 454 MET cc_start: 0.8513 (mmp) cc_final: 0.8013 (mmt) REVERT: g 577 ASP cc_start: 0.8487 (t0) cc_final: 0.8190 (t0) REVERT: g 614 THR cc_start: 0.8827 (m) cc_final: 0.8505 (m) REVERT: i 624 MET cc_start: 0.4834 (OUTLIER) cc_final: 0.3032 (ptm) REVERT: j 415 HIS cc_start: 0.8204 (OUTLIER) cc_final: 0.7878 (p90) REVERT: j 499 MET cc_start: 0.8856 (tmm) cc_final: 0.8547 (tmm) REVERT: j 585 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.6832 (t80) REVERT: k 499 MET cc_start: 0.8588 (ttm) cc_final: 0.8125 (ttm) REVERT: k 620 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.7080 (mpp) REVERT: k 624 MET cc_start: 0.5112 (mtp) cc_final: 0.4848 (mtm) REVERT: k 625 LYS cc_start: 0.6112 (OUTLIER) cc_final: 0.5708 (mtmm) outliers start: 89 outliers final: 39 residues processed: 533 average time/residue: 0.4980 time to fit residues: 451.7845 Evaluate side-chains 427 residues out of total 5764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 379 time to evaluate : 4.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 354 PHE Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 61 GLN Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 354 PHE Chi-restraints excluded: chain I residue 20 LYS Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 240 LYS Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain a residue 507 LEU Chi-restraints excluded: chain b residue 391 GLU Chi-restraints excluded: chain b residue 398 ARG Chi-restraints excluded: chain d residue 485 GLU Chi-restraints excluded: chain d residue 566 TYR Chi-restraints excluded: chain d residue 567 ASP Chi-restraints excluded: chain d residue 625 LYS Chi-restraints excluded: chain e residue 442 VAL Chi-restraints excluded: chain e residue 507 LEU Chi-restraints excluded: chain h residue 391 GLU Chi-restraints excluded: chain h residue 571 THR Chi-restraints excluded: chain i residue 442 VAL Chi-restraints excluded: chain i residue 576 ASP Chi-restraints excluded: chain i residue 604 LEU Chi-restraints excluded: chain i residue 624 MET Chi-restraints excluded: chain j residue 415 HIS Chi-restraints excluded: chain j residue 566 TYR Chi-restraints excluded: chain j residue 585 TYR Chi-restraints excluded: chain k residue 566 TYR Chi-restraints excluded: chain k residue 620 MET Chi-restraints excluded: chain k residue 625 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 671 random chunks: chunk 338 optimal weight: 8.9990 chunk 189 optimal weight: 10.0000 chunk 507 optimal weight: 3.9990 chunk 414 optimal weight: 10.0000 chunk 168 optimal weight: 8.9990 chunk 610 optimal weight: 8.9990 chunk 659 optimal weight: 5.9990 chunk 543 optimal weight: 0.5980 chunk 605 optimal weight: 8.9990 chunk 208 optimal weight: 0.2980 chunk 489 optimal weight: 9.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 ASN E 227 ASN F 113 ASN G 75 HIS ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 HIS J 113 ASN ** J 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 470 GLN ** i 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 484 ASN k 505 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 54120 Z= 0.330 Angle : 0.696 9.079 73337 Z= 0.347 Chirality : 0.046 0.227 8184 Planarity : 0.005 0.062 9405 Dihedral : 6.118 89.142 7409 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.88 % Favored : 94.79 % Rotamer: Outliers : 1.75 % Allowed : 7.10 % Favored : 91.15 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.86 (0.10), residues: 6677 helix: 0.10 (0.09), residues: 3245 sheet: -0.27 (0.20), residues: 649 loop : -1.37 (0.12), residues: 2783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP i 524 HIS 0.019 0.001 HIS j 415 PHE 0.052 0.002 PHE J 354 TYR 0.026 0.002 TYR j 417 ARG 0.012 0.001 ARG i 441 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13354 Ramachandran restraints generated. 6677 Oldfield, 0 Emsley, 6677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13354 Ramachandran restraints generated. 6677 Oldfield, 0 Emsley, 6677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 5764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 388 time to evaluate : 4.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8855 (tpt) cc_final: 0.8595 (tpp) REVERT: A 371 ILE cc_start: 0.9026 (mt) cc_final: 0.8823 (tp) REVERT: C 354 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8321 (m-10) REVERT: D 182 LEU cc_start: 0.8780 (mt) cc_final: 0.8474 (tp) REVERT: F 354 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.6934 (m-80) REVERT: G 229 MET cc_start: 0.8589 (tpp) cc_final: 0.7855 (tpp) REVERT: H 49 MET cc_start: 0.7529 (mmt) cc_final: 0.7197 (ptm) REVERT: H 229 MET cc_start: 0.8399 (mmm) cc_final: 0.7961 (mmm) REVERT: H 307 MET cc_start: 0.8667 (mmm) cc_final: 0.8317 (tpp) REVERT: H 354 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.8047 (m-80) REVERT: I 182 LEU cc_start: 0.9201 (mp) cc_final: 0.8875 (mt) REVERT: I 354 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: J 121 MET cc_start: 0.8393 (mtm) cc_final: 0.8185 (ttm) REVERT: K 121 MET cc_start: 0.8699 (mtm) cc_final: 0.8223 (mtp) REVERT: K 125 MET cc_start: 0.8470 (mmt) cc_final: 0.7905 (mmp) REVERT: a 613 MET cc_start: 0.8666 (ppp) cc_final: 0.8434 (tmm) REVERT: c 624 MET cc_start: 0.7292 (mmm) cc_final: 0.6924 (mmm) REVERT: f 404 MET cc_start: 0.9013 (mtt) cc_final: 0.8554 (mtm) REVERT: f 613 MET cc_start: 0.8666 (tmm) cc_final: 0.8442 (tmm) REVERT: g 454 MET cc_start: 0.8658 (mmp) cc_final: 0.8212 (mmt) REVERT: g 577 ASP cc_start: 0.8579 (t0) cc_final: 0.8285 (t0) REVERT: j 499 MET cc_start: 0.8805 (tmm) cc_final: 0.8334 (tmm) REVERT: k 499 MET cc_start: 0.8572 (ttm) cc_final: 0.8129 (ttm) REVERT: k 620 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.7190 (mpp) REVERT: k 624 MET cc_start: 0.5644 (mtp) cc_final: 0.5408 (mtm) REVERT: k 625 LYS cc_start: 0.5998 (OUTLIER) cc_final: 0.5544 (mtmm) outliers start: 101 outliers final: 59 residues processed: 468 average time/residue: 0.4669 time to fit residues: 381.8568 Evaluate side-chains 417 residues out of total 5764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 352 time to evaluate : 4.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 354 PHE Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 354 PHE Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 354 PHE Chi-restraints excluded: chain I residue 20 LYS Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 354 PHE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain J residue 354 PHE Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain a residue 481 GLN Chi-restraints excluded: chain a residue 507 LEU Chi-restraints excluded: chain a residue 618 CYS Chi-restraints excluded: chain a residue 624 MET Chi-restraints excluded: chain b residue 398 ARG Chi-restraints excluded: chain b residue 485 GLU Chi-restraints excluded: chain b residue 589 MET Chi-restraints excluded: chain b residue 604 LEU Chi-restraints excluded: chain c residue 567 ASP Chi-restraints excluded: chain c residue 604 LEU Chi-restraints excluded: chain d residue 407 LEU Chi-restraints excluded: chain d residue 481 GLN Chi-restraints excluded: chain d residue 485 GLU Chi-restraints excluded: chain d residue 567 ASP Chi-restraints excluded: chain d residue 625 LYS Chi-restraints excluded: chain e residue 442 VAL Chi-restraints excluded: chain e residue 507 LEU Chi-restraints excluded: chain g residue 552 VAL Chi-restraints excluded: chain g residue 604 LEU Chi-restraints excluded: chain h residue 571 THR Chi-restraints excluded: chain i residue 442 VAL Chi-restraints excluded: chain i residue 491 THR Chi-restraints excluded: chain i residue 559 ILE Chi-restraints excluded: chain i residue 604 LEU Chi-restraints excluded: chain j residue 494 LEU Chi-restraints excluded: chain k residue 491 THR Chi-restraints excluded: chain k residue 620 MET Chi-restraints excluded: chain k residue 625 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 671 random chunks: chunk 603 optimal weight: 3.9990 chunk 458 optimal weight: 7.9990 chunk 316 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 291 optimal weight: 3.9990 chunk 409 optimal weight: 0.0970 chunk 612 optimal weight: 8.9990 chunk 648 optimal weight: 20.0000 chunk 320 optimal weight: 5.9990 chunk 580 optimal weight: 0.4980 chunk 174 optimal weight: 0.0060 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 227 ASN B 14 ASN ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 ASN E 227 ASN ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 470 GLN h 469 ASN ** i 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 415 HIS j 484 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 54120 Z= 0.149 Angle : 0.579 9.795 73337 Z= 0.284 Chirality : 0.042 0.170 8184 Planarity : 0.004 0.035 9405 Dihedral : 5.593 59.967 7403 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.21 % Favored : 95.48 % Rotamer: Outliers : 1.25 % Allowed : 8.55 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.29 (0.10), residues: 6677 helix: 0.65 (0.09), residues: 3179 sheet: -0.02 (0.20), residues: 649 loop : -1.16 (0.12), residues: 2849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 342 HIS 0.007 0.001 HIS j 415 PHE 0.025 0.001 PHE J 354 TYR 0.020 0.001 TYR j 585 ARG 0.004 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13354 Ramachandran restraints generated. 6677 Oldfield, 0 Emsley, 6677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13354 Ramachandran restraints generated. 6677 Oldfield, 0 Emsley, 6677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 5764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 387 time to evaluate : 4.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8646 (tpt) cc_final: 0.8368 (tpp) REVERT: A 371 ILE cc_start: 0.9010 (mt) cc_final: 0.8713 (tp) REVERT: B 159 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.5599 (t0) REVERT: C 354 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8082 (m-10) REVERT: D 182 LEU cc_start: 0.8760 (mt) cc_final: 0.8410 (tp) REVERT: F 354 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.6783 (m-80) REVERT: G 229 MET cc_start: 0.8497 (tpp) cc_final: 0.7811 (tpp) REVERT: H 49 MET cc_start: 0.7680 (mmt) cc_final: 0.7238 (ptm) REVERT: H 229 MET cc_start: 0.8336 (mmm) cc_final: 0.7933 (mmm) REVERT: H 354 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7853 (m-80) REVERT: I 182 LEU cc_start: 0.9116 (mp) cc_final: 0.8854 (mt) REVERT: I 354 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.7985 (m-80) REVERT: J 121 MET cc_start: 0.8484 (mtm) cc_final: 0.8260 (ttm) REVERT: K 121 MET cc_start: 0.8590 (mtm) cc_final: 0.7987 (mtp) REVERT: K 125 MET cc_start: 0.8438 (mmt) cc_final: 0.7744 (mmp) REVERT: a 613 MET cc_start: 0.8584 (ppp) cc_final: 0.8375 (tmm) REVERT: a 620 MET cc_start: 0.6871 (mmm) cc_final: 0.6603 (mmm) REVERT: b 620 MET cc_start: 0.7388 (mmm) cc_final: 0.7088 (tpt) REVERT: c 624 MET cc_start: 0.7093 (mmm) cc_final: 0.6481 (mmm) REVERT: d 624 MET cc_start: 0.5950 (mmm) cc_final: 0.5260 (mmm) REVERT: d 625 LYS cc_start: 0.6469 (OUTLIER) cc_final: 0.4899 (mmmt) REVERT: e 407 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.7982 (tt) REVERT: f 613 MET cc_start: 0.8551 (tmm) cc_final: 0.8203 (tmm) REVERT: g 577 ASP cc_start: 0.8444 (t0) cc_final: 0.8155 (t0) REVERT: h 407 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8502 (tt) REVERT: h 624 MET cc_start: 0.6271 (mtm) cc_final: 0.6059 (mtt) REVERT: i 620 MET cc_start: 0.8257 (mmp) cc_final: 0.8022 (mmm) REVERT: j 499 MET cc_start: 0.8846 (tmm) cc_final: 0.8256 (tmm) REVERT: k 499 MET cc_start: 0.8579 (ttm) cc_final: 0.8313 (ttm) REVERT: k 624 MET cc_start: 0.5983 (mtp) cc_final: 0.5689 (mtm) outliers start: 72 outliers final: 39 residues processed: 439 average time/residue: 0.4752 time to fit residues: 364.5415 Evaluate side-chains 396 residues out of total 5764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 349 time to evaluate : 5.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 354 PHE Chi-restraints excluded: chain F residue 354 PHE Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 354 PHE Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 354 PHE Chi-restraints excluded: chain I residue 20 LYS Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 354 PHE Chi-restraints excluded: chain J residue 354 PHE Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain a residue 407 LEU Chi-restraints excluded: chain a residue 481 GLN Chi-restraints excluded: chain b residue 398 ARG Chi-restraints excluded: chain b residue 485 GLU Chi-restraints excluded: chain b residue 589 MET Chi-restraints excluded: chain b residue 604 LEU Chi-restraints excluded: chain c residue 481 GLN Chi-restraints excluded: chain c residue 567 ASP Chi-restraints excluded: chain d residue 407 LEU Chi-restraints excluded: chain d residue 481 GLN Chi-restraints excluded: chain d residue 485 GLU Chi-restraints excluded: chain d residue 567 ASP Chi-restraints excluded: chain d residue 625 LYS Chi-restraints excluded: chain e residue 407 LEU Chi-restraints excluded: chain e residue 442 VAL Chi-restraints excluded: chain g residue 407 LEU Chi-restraints excluded: chain g residue 604 LEU Chi-restraints excluded: chain g residue 614 THR Chi-restraints excluded: chain h residue 407 LEU Chi-restraints excluded: chain i residue 442 VAL Chi-restraints excluded: chain i residue 482 ASP Chi-restraints excluded: chain i residue 604 LEU Chi-restraints excluded: chain j residue 494 LEU Chi-restraints excluded: chain j residue 566 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 671 random chunks: chunk 540 optimal weight: 5.9990 chunk 368 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 482 optimal weight: 10.0000 chunk 267 optimal weight: 10.0000 chunk 553 optimal weight: 1.9990 chunk 448 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 331 optimal weight: 10.0000 chunk 582 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 ASN C 355 GLN ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 355 GLN ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 355 GLN ** I 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 ASN ** J 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 469 ASN ** e 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 402 ASN ** i 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.134 54120 Z= 0.328 Angle : 0.651 8.152 73337 Z= 0.321 Chirality : 0.044 0.191 8184 Planarity : 0.004 0.041 9405 Dihedral : 5.658 56.366 7403 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.83 % Favored : 93.86 % Rotamer: Outliers : 1.68 % Allowed : 8.71 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.10), residues: 6677 helix: 0.74 (0.10), residues: 3146 sheet: 0.13 (0.20), residues: 649 loop : -1.08 (0.12), residues: 2882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP f 524 HIS 0.006 0.001 HIS I 373 PHE 0.035 0.002 PHE J 354 TYR 0.020 0.002 TYR G 145 ARG 0.007 0.001 ARG D 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13354 Ramachandran restraints generated. 6677 Oldfield, 0 Emsley, 6677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13354 Ramachandran restraints generated. 6677 Oldfield, 0 Emsley, 6677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 5764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 356 time to evaluate : 4.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8908 (tpt) cc_final: 0.8618 (tpp) REVERT: C 11 VAL cc_start: 0.9283 (OUTLIER) cc_final: 0.9039 (m) REVERT: C 354 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8459 (m-80) REVERT: D 182 LEU cc_start: 0.8887 (mt) cc_final: 0.8552 (tp) REVERT: E 354 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8153 (m-80) REVERT: F 354 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7028 (m-80) REVERT: G 229 MET cc_start: 0.8569 (tpp) cc_final: 0.7844 (tpp) REVERT: H 49 MET cc_start: 0.7890 (mmt) cc_final: 0.7295 (ptm) REVERT: H 229 MET cc_start: 0.8505 (mmm) cc_final: 0.8059 (mmm) REVERT: H 354 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.8185 (m-80) REVERT: H 357 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8585 (mmt) REVERT: I 182 LEU cc_start: 0.9105 (mp) cc_final: 0.8810 (mt) REVERT: I 354 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8363 (m-80) REVERT: J 121 MET cc_start: 0.8328 (mtm) cc_final: 0.8047 (ttm) REVERT: J 125 MET cc_start: 0.9019 (mmm) cc_final: 0.8798 (mmm) REVERT: K 121 MET cc_start: 0.8638 (mtm) cc_final: 0.8017 (mtp) REVERT: K 125 MET cc_start: 0.8493 (mmt) cc_final: 0.7779 (mmp) REVERT: a 585 TYR cc_start: 0.7829 (t80) cc_final: 0.7611 (t80) REVERT: a 613 MET cc_start: 0.8603 (ppp) cc_final: 0.8384 (tmm) REVERT: b 620 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.7024 (tpt) REVERT: b 624 MET cc_start: 0.8053 (mpp) cc_final: 0.7506 (mpp) REVERT: c 624 MET cc_start: 0.7188 (mmm) cc_final: 0.6730 (mmm) REVERT: d 614 THR cc_start: 0.9302 (p) cc_final: 0.9058 (p) REVERT: d 624 MET cc_start: 0.6234 (mmm) cc_final: 0.5447 (mmm) REVERT: d 625 LYS cc_start: 0.6556 (OUTLIER) cc_final: 0.4921 (mmmt) REVERT: e 407 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8110 (tt) REVERT: e 613 MET cc_start: 0.9115 (ppp) cc_final: 0.8832 (ppp) REVERT: f 613 MET cc_start: 0.8571 (tmm) cc_final: 0.8117 (tmm) REVERT: g 454 MET cc_start: 0.8803 (mmp) cc_final: 0.8316 (mmp) REVERT: g 577 ASP cc_start: 0.8335 (t0) cc_final: 0.8078 (t0) REVERT: h 407 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8532 (tt) REVERT: i 613 MET cc_start: 0.8943 (ppp) cc_final: 0.8678 (ppp) REVERT: j 450 LEU cc_start: 0.7775 (mt) cc_final: 0.7558 (pp) REVERT: j 499 MET cc_start: 0.8946 (tmm) cc_final: 0.8340 (tmm) REVERT: j 624 MET cc_start: 0.6451 (mpp) cc_final: 0.6247 (mpp) REVERT: k 499 MET cc_start: 0.8696 (ttm) cc_final: 0.8397 (ttm) REVERT: k 620 MET cc_start: 0.6778 (ptp) cc_final: 0.6394 (ptp) outliers start: 97 outliers final: 55 residues processed: 430 average time/residue: 0.4702 time to fit residues: 353.3072 Evaluate side-chains 405 residues out of total 5764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 339 time to evaluate : 4.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 354 PHE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 354 PHE Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 354 PHE Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 354 PHE Chi-restraints excluded: chain H residue 357 MET Chi-restraints excluded: chain I residue 20 LYS Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 354 PHE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain a residue 407 LEU Chi-restraints excluded: chain a residue 481 GLN Chi-restraints excluded: chain a residue 507 LEU Chi-restraints excluded: chain b residue 407 LEU Chi-restraints excluded: chain b residue 604 LEU Chi-restraints excluded: chain b residue 620 MET Chi-restraints excluded: chain c residue 407 LEU Chi-restraints excluded: chain c residue 481 GLN Chi-restraints excluded: chain c residue 567 ASP Chi-restraints excluded: chain d residue 481 GLN Chi-restraints excluded: chain d residue 485 GLU Chi-restraints excluded: chain d residue 567 ASP Chi-restraints excluded: chain d residue 625 LYS Chi-restraints excluded: chain e residue 407 LEU Chi-restraints excluded: chain e residue 442 VAL Chi-restraints excluded: chain e residue 507 LEU Chi-restraints excluded: chain f residue 552 VAL Chi-restraints excluded: chain g residue 407 LEU Chi-restraints excluded: chain g residue 552 VAL Chi-restraints excluded: chain g residue 604 LEU Chi-restraints excluded: chain g residue 614 THR Chi-restraints excluded: chain h residue 407 LEU Chi-restraints excluded: chain h residue 571 THR Chi-restraints excluded: chain i residue 442 VAL Chi-restraints excluded: chain i residue 481 GLN Chi-restraints excluded: chain i residue 482 ASP Chi-restraints excluded: chain i residue 483 LEU Chi-restraints excluded: chain i residue 491 THR Chi-restraints excluded: chain j residue 564 ILE Chi-restraints excluded: chain j residue 566 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 671 random chunks: chunk 218 optimal weight: 5.9990 chunk 584 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 380 optimal weight: 20.0000 chunk 160 optimal weight: 1.9990 chunk 649 optimal weight: 0.0020 chunk 538 optimal weight: 0.9980 chunk 300 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 214 optimal weight: 4.9990 chunk 340 optimal weight: 6.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 ASN D 14 ASN G 89 HIS ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 54120 Z= 0.179 Angle : 0.579 13.927 73337 Z= 0.283 Chirality : 0.042 0.197 8184 Planarity : 0.004 0.040 9405 Dihedral : 5.470 57.066 7403 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.72 % Favored : 94.98 % Rotamer: Outliers : 1.47 % Allowed : 9.25 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.11), residues: 6677 helix: 1.01 (0.10), residues: 3135 sheet: 0.12 (0.19), residues: 759 loop : -1.02 (0.12), residues: 2783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP f 524 HIS 0.005 0.001 HIS I 373 PHE 0.030 0.001 PHE J 354 TYR 0.019 0.001 TYR b 585 ARG 0.005 0.000 ARG D 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13354 Ramachandran restraints generated. 6677 Oldfield, 0 Emsley, 6677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13354 Ramachandran restraints generated. 6677 Oldfield, 0 Emsley, 6677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 5764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 360 time to evaluate : 4.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8723 (tpt) cc_final: 0.8435 (tpp) REVERT: A 327 MET cc_start: 0.8813 (tpt) cc_final: 0.8589 (tpt) REVERT: B 84 MET cc_start: 0.8812 (tpt) cc_final: 0.8473 (tpt) REVERT: C 354 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8363 (m-80) REVERT: D 182 LEU cc_start: 0.8796 (mt) cc_final: 0.8430 (tp) REVERT: E 354 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7951 (m-80) REVERT: F 354 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7063 (m-80) REVERT: G 229 MET cc_start: 0.8491 (tpp) cc_final: 0.7794 (tpp) REVERT: H 49 MET cc_start: 0.7894 (mmt) cc_final: 0.7292 (ptm) REVERT: H 229 MET cc_start: 0.8437 (mmm) cc_final: 0.8098 (mmm) REVERT: H 354 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.7996 (m-80) REVERT: I 84 MET cc_start: 0.8330 (tpp) cc_final: 0.8008 (tpp) REVERT: I 182 LEU cc_start: 0.9016 (mp) cc_final: 0.8618 (tp) REVERT: I 285 MET cc_start: 0.7445 (mmp) cc_final: 0.6926 (mmm) REVERT: I 354 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8263 (m-80) REVERT: J 121 MET cc_start: 0.8391 (mtm) cc_final: 0.8124 (ttm) REVERT: K 125 MET cc_start: 0.8441 (mmt) cc_final: 0.7815 (mmp) REVERT: a 585 TYR cc_start: 0.7683 (t80) cc_final: 0.7476 (t80) REVERT: a 613 MET cc_start: 0.8446 (ppp) cc_final: 0.8217 (tmm) REVERT: b 620 MET cc_start: 0.7257 (mmm) cc_final: 0.6890 (tpt) REVERT: b 624 MET cc_start: 0.7957 (mpp) cc_final: 0.7452 (mpp) REVERT: c 614 THR cc_start: 0.8683 (m) cc_final: 0.8342 (m) REVERT: d 624 MET cc_start: 0.6221 (mmm) cc_final: 0.5467 (mmm) REVERT: d 625 LYS cc_start: 0.6518 (OUTLIER) cc_final: 0.5140 (mmmt) REVERT: e 404 MET cc_start: 0.8724 (mtp) cc_final: 0.8406 (mtm) REVERT: e 407 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8093 (tt) REVERT: e 524 TRP cc_start: 0.7010 (t60) cc_final: 0.6641 (t60) REVERT: e 620 MET cc_start: 0.8359 (mmp) cc_final: 0.7820 (mmp) REVERT: f 478 ILE cc_start: 0.9059 (mt) cc_final: 0.8835 (mt) REVERT: f 613 MET cc_start: 0.8446 (tmm) cc_final: 0.7970 (tmm) REVERT: g 454 MET cc_start: 0.8750 (mmp) cc_final: 0.8243 (mmp) REVERT: g 577 ASP cc_start: 0.8204 (t0) cc_final: 0.7988 (t0) REVERT: h 407 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8505 (tt) REVERT: i 613 MET cc_start: 0.8874 (ppp) cc_final: 0.8671 (ppp) REVERT: j 450 LEU cc_start: 0.7754 (mt) cc_final: 0.7510 (pp) REVERT: j 499 MET cc_start: 0.8967 (tmm) cc_final: 0.8256 (tmm) REVERT: k 499 MET cc_start: 0.8761 (ttm) cc_final: 0.8364 (ttm) outliers start: 85 outliers final: 55 residues processed: 432 average time/residue: 0.4674 time to fit residues: 353.5000 Evaluate side-chains 405 residues out of total 5764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 342 time to evaluate : 4.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 315 MET Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 354 PHE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 354 PHE Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 354 PHE Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain H residue 354 PHE Chi-restraints excluded: chain I residue 20 LYS Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 354 PHE Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 313 ASP Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain a residue 407 LEU Chi-restraints excluded: chain a residue 481 GLN Chi-restraints excluded: chain b residue 407 LEU Chi-restraints excluded: chain b residue 564 ILE Chi-restraints excluded: chain b residue 604 LEU Chi-restraints excluded: chain c residue 407 LEU Chi-restraints excluded: chain c residue 481 GLN Chi-restraints excluded: chain c residue 510 ILE Chi-restraints excluded: chain c residue 567 ASP Chi-restraints excluded: chain c residue 618 CYS Chi-restraints excluded: chain d residue 481 GLN Chi-restraints excluded: chain d residue 485 GLU Chi-restraints excluded: chain d residue 567 ASP Chi-restraints excluded: chain d residue 625 LYS Chi-restraints excluded: chain e residue 394 THR Chi-restraints excluded: chain e residue 407 LEU Chi-restraints excluded: chain e residue 442 VAL Chi-restraints excluded: chain e residue 510 ILE Chi-restraints excluded: chain f residue 454 MET Chi-restraints excluded: chain f residue 552 VAL Chi-restraints excluded: chain g residue 407 LEU Chi-restraints excluded: chain g residue 604 LEU Chi-restraints excluded: chain h residue 407 LEU Chi-restraints excluded: chain i residue 442 VAL Chi-restraints excluded: chain i residue 481 GLN Chi-restraints excluded: chain i residue 482 ASP Chi-restraints excluded: chain i residue 483 LEU Chi-restraints excluded: chain j residue 415 HIS Chi-restraints excluded: chain j residue 494 LEU Chi-restraints excluded: chain j residue 564 ILE Chi-restraints excluded: chain j residue 566 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 671 random chunks: chunk 625 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 369 optimal weight: 7.9990 chunk 474 optimal weight: 7.9990 chunk 367 optimal weight: 7.9990 chunk 546 optimal weight: 0.8980 chunk 362 optimal weight: 10.0000 chunk 646 optimal weight: 1.9990 chunk 404 optimal weight: 10.0000 chunk 394 optimal weight: 20.0000 chunk 298 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 ASN ** K 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 469 ASN ** e 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 484 ASN h 560 GLN ** i 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 54120 Z= 0.384 Angle : 0.696 10.734 73337 Z= 0.344 Chirality : 0.045 0.197 8184 Planarity : 0.004 0.049 9405 Dihedral : 5.758 54.099 7403 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.56 % Favored : 93.13 % Rotamer: Outliers : 1.82 % Allowed : 9.59 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.11), residues: 6677 helix: 0.84 (0.10), residues: 3124 sheet: 0.11 (0.19), residues: 759 loop : -1.07 (0.12), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP i 403 HIS 0.007 0.001 HIS I 373 PHE 0.029 0.002 PHE E 354 TYR 0.021 0.002 TYR b 585 ARG 0.005 0.001 ARG D 179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13354 Ramachandran restraints generated. 6677 Oldfield, 0 Emsley, 6677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13354 Ramachandran restraints generated. 6677 Oldfield, 0 Emsley, 6677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 5764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 344 time to evaluate : 5.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8892 (tpt) cc_final: 0.8594 (tpp) REVERT: C 354 PHE cc_start: 0.9115 (OUTLIER) cc_final: 0.8463 (m-80) REVERT: D 207 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8323 (mm-30) REVERT: E 354 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.7961 (m-80) REVERT: F 354 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7206 (m-80) REVERT: G 229 MET cc_start: 0.8508 (tpp) cc_final: 0.8075 (tpp) REVERT: H 49 MET cc_start: 0.7935 (mmt) cc_final: 0.7303 (ptm) REVERT: H 134 MET cc_start: 0.8768 (tmm) cc_final: 0.8385 (tmm) REVERT: H 229 MET cc_start: 0.8391 (mmm) cc_final: 0.7998 (mmm) REVERT: H 354 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8373 (m-80) REVERT: H 357 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8489 (mmt) REVERT: I 84 MET cc_start: 0.8501 (tpp) cc_final: 0.8196 (tpp) REVERT: I 182 LEU cc_start: 0.9070 (mp) cc_final: 0.8801 (mt) REVERT: I 354 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8796 (t80) REVERT: J 49 MET cc_start: 0.3754 (ttp) cc_final: 0.3540 (ttp) REVERT: J 121 MET cc_start: 0.8385 (mtm) cc_final: 0.8113 (ttm) REVERT: J 125 MET cc_start: 0.8969 (mmm) cc_final: 0.8731 (mmm) REVERT: K 121 MET cc_start: 0.8704 (mtm) cc_final: 0.8344 (mtp) REVERT: K 125 MET cc_start: 0.8474 (mmt) cc_final: 0.7844 (mmp) REVERT: a 613 MET cc_start: 0.8489 (ppp) cc_final: 0.8285 (tmm) REVERT: b 620 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.7150 (mmm) REVERT: c 614 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8439 (m) REVERT: c 620 MET cc_start: 0.8232 (mpp) cc_final: 0.7711 (mpp) REVERT: d 624 MET cc_start: 0.6675 (mmm) cc_final: 0.5757 (mmm) REVERT: d 625 LYS cc_start: 0.6056 (OUTLIER) cc_final: 0.5128 (mmmt) REVERT: e 404 MET cc_start: 0.8838 (mtp) cc_final: 0.8507 (mtm) REVERT: e 407 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8029 (tt) REVERT: f 478 ILE cc_start: 0.9084 (mt) cc_final: 0.8710 (tt) REVERT: f 613 MET cc_start: 0.8452 (tmm) cc_final: 0.8045 (tmm) REVERT: g 454 MET cc_start: 0.8574 (mmp) cc_final: 0.7995 (mmp) REVERT: g 577 ASP cc_start: 0.8452 (t0) cc_final: 0.8150 (t0) REVERT: g 625 LYS cc_start: 0.4981 (OUTLIER) cc_final: 0.4717 (mtmm) REVERT: h 407 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8487 (tt) REVERT: h 624 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6319 (mpp) REVERT: i 613 MET cc_start: 0.8877 (ppp) cc_final: 0.8651 (tmm) REVERT: j 394 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7937 (p) REVERT: j 450 LEU cc_start: 0.7951 (mt) cc_final: 0.7613 (pp) REVERT: j 499 MET cc_start: 0.8941 (tmm) cc_final: 0.8219 (tmm) REVERT: k 499 MET cc_start: 0.8861 (ttm) cc_final: 0.8391 (ttm) outliers start: 105 outliers final: 67 residues processed: 426 average time/residue: 0.4669 time to fit residues: 348.8724 Evaluate side-chains 415 residues out of total 5764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 333 time to evaluate : 6.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 315 MET Chi-restraints excluded: chain E residue 354 PHE Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 354 PHE Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 354 PHE Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 88 TRP Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain H residue 354 PHE Chi-restraints excluded: chain H residue 357 MET Chi-restraints excluded: chain I residue 20 LYS Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 354 PHE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 313 ASP Chi-restraints excluded: chain a residue 407 LEU Chi-restraints excluded: chain a residue 481 GLN Chi-restraints excluded: chain a residue 507 LEU Chi-restraints excluded: chain a residue 577 ASP Chi-restraints excluded: chain b residue 407 LEU Chi-restraints excluded: chain b residue 564 ILE Chi-restraints excluded: chain b residue 604 LEU Chi-restraints excluded: chain b residue 620 MET Chi-restraints excluded: chain c residue 394 THR Chi-restraints excluded: chain c residue 407 LEU Chi-restraints excluded: chain c residue 481 GLN Chi-restraints excluded: chain c residue 510 ILE Chi-restraints excluded: chain c residue 567 ASP Chi-restraints excluded: chain c residue 614 THR Chi-restraints excluded: chain d residue 481 GLN Chi-restraints excluded: chain d residue 485 GLU Chi-restraints excluded: chain d residue 567 ASP Chi-restraints excluded: chain d residue 625 LYS Chi-restraints excluded: chain e residue 394 THR Chi-restraints excluded: chain e residue 407 LEU Chi-restraints excluded: chain e residue 442 VAL Chi-restraints excluded: chain e residue 510 ILE Chi-restraints excluded: chain f residue 454 MET Chi-restraints excluded: chain f residue 552 VAL Chi-restraints excluded: chain g residue 407 LEU Chi-restraints excluded: chain g residue 604 LEU Chi-restraints excluded: chain g residue 614 THR Chi-restraints excluded: chain g residue 625 LYS Chi-restraints excluded: chain h residue 407 LEU Chi-restraints excluded: chain h residue 519 ASP Chi-restraints excluded: chain h residue 624 MET Chi-restraints excluded: chain i residue 442 VAL Chi-restraints excluded: chain i residue 481 GLN Chi-restraints excluded: chain i residue 482 ASP Chi-restraints excluded: chain i residue 491 THR Chi-restraints excluded: chain i residue 604 LEU Chi-restraints excluded: chain j residue 394 THR Chi-restraints excluded: chain j residue 415 HIS Chi-restraints excluded: chain j residue 494 LEU Chi-restraints excluded: chain j residue 519 ASP Chi-restraints excluded: chain j residue 564 ILE Chi-restraints excluded: chain j residue 566 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 671 random chunks: chunk 400 optimal weight: 1.9990 chunk 258 optimal weight: 5.9990 chunk 386 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 411 optimal weight: 0.0870 chunk 440 optimal weight: 10.0000 chunk 319 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 508 optimal weight: 5.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 ASN F 14 ASN ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 560 GLN b 484 ASN e 514 GLN ** h 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 54120 Z= 0.142 Angle : 0.581 10.471 73337 Z= 0.282 Chirality : 0.042 0.200 8184 Planarity : 0.004 0.040 9405 Dihedral : 5.411 56.545 7403 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.46 % Favored : 95.22 % Rotamer: Outliers : 1.15 % Allowed : 10.29 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.29 (0.11), residues: 6677 helix: 1.16 (0.10), residues: 3124 sheet: 0.22 (0.19), residues: 759 loop : -0.90 (0.12), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP f 524 HIS 0.007 0.001 HIS G 277 PHE 0.018 0.001 PHE E 354 TYR 0.031 0.001 TYR a 585 ARG 0.015 0.000 ARG i 530 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13354 Ramachandran restraints generated. 6677 Oldfield, 0 Emsley, 6677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13354 Ramachandran restraints generated. 6677 Oldfield, 0 Emsley, 6677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 5764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 366 time to evaluate : 4.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8706 (tpt) cc_final: 0.8412 (tpp) REVERT: C 354 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8329 (m-80) REVERT: D 182 LEU cc_start: 0.8866 (mt) cc_final: 0.8462 (tp) REVERT: E 354 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.8032 (m-80) REVERT: F 354 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7130 (m-80) REVERT: G 229 MET cc_start: 0.8422 (tpp) cc_final: 0.7786 (ttm) REVERT: H 49 MET cc_start: 0.7983 (mmt) cc_final: 0.7453 (ttt) REVERT: H 84 MET cc_start: 0.8566 (tpt) cc_final: 0.8154 (tpt) REVERT: H 134 MET cc_start: 0.8859 (tmm) cc_final: 0.8542 (tmm) REVERT: H 229 MET cc_start: 0.8483 (mmm) cc_final: 0.8153 (mmm) REVERT: H 354 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8101 (m-80) REVERT: I 84 MET cc_start: 0.8353 (tpp) cc_final: 0.8106 (tpp) REVERT: I 182 LEU cc_start: 0.8965 (mp) cc_final: 0.8472 (tp) REVERT: I 354 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8827 (t80) REVERT: J 49 MET cc_start: 0.3694 (ttp) cc_final: 0.3469 (ttp) REVERT: J 125 MET cc_start: 0.8936 (mmm) cc_final: 0.8668 (mmm) REVERT: J 156 ASP cc_start: 0.8085 (t0) cc_final: 0.7817 (t0) REVERT: K 125 MET cc_start: 0.8342 (mmt) cc_final: 0.7693 (mmp) REVERT: a 613 MET cc_start: 0.8463 (ppp) cc_final: 0.8225 (tmm) REVERT: b 478 ILE cc_start: 0.8775 (mt) cc_final: 0.8304 (tt) REVERT: b 603 ASP cc_start: 0.8417 (m-30) cc_final: 0.8188 (m-30) REVERT: d 624 MET cc_start: 0.6763 (mmm) cc_final: 0.5438 (mmm) REVERT: d 625 LYS cc_start: 0.6201 (OUTLIER) cc_final: 0.5336 (mmmt) REVERT: e 407 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7910 (tt) REVERT: e 488 ARG cc_start: 0.7961 (mtp180) cc_final: 0.7699 (ttm-80) REVERT: e 611 MET cc_start: 0.8401 (mmm) cc_final: 0.8187 (mmm) REVERT: f 478 ILE cc_start: 0.9033 (mt) cc_final: 0.8818 (mt) REVERT: f 613 MET cc_start: 0.8414 (tmm) cc_final: 0.7985 (tmm) REVERT: g 454 MET cc_start: 0.8458 (mmp) cc_final: 0.7941 (mmp) REVERT: g 577 ASP cc_start: 0.8330 (t0) cc_final: 0.8123 (t0) REVERT: h 407 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8352 (tt) REVERT: h 624 MET cc_start: 0.6974 (mpp) cc_final: 0.6673 (mmp) REVERT: i 478 ILE cc_start: 0.9420 (mt) cc_final: 0.9200 (mp) REVERT: j 450 LEU cc_start: 0.7705 (mt) cc_final: 0.7360 (pp) REVERT: j 499 MET cc_start: 0.8957 (tmm) cc_final: 0.8167 (tmm) REVERT: k 499 MET cc_start: 0.8880 (ttm) cc_final: 0.8636 (ttm) REVERT: k 613 MET cc_start: 0.8591 (tpp) cc_final: 0.8354 (tpp) outliers start: 66 outliers final: 40 residues processed: 420 average time/residue: 0.4685 time to fit residues: 345.4901 Evaluate side-chains 396 residues out of total 5764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 348 time to evaluate : 4.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 354 PHE Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 354 PHE Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 354 PHE Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 88 TRP Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 354 PHE Chi-restraints excluded: chain I residue 20 LYS Chi-restraints excluded: chain I residue 354 PHE Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain a residue 407 LEU Chi-restraints excluded: chain a residue 481 GLN Chi-restraints excluded: chain b residue 407 LEU Chi-restraints excluded: chain b residue 564 ILE Chi-restraints excluded: chain c residue 394 THR Chi-restraints excluded: chain c residue 481 GLN Chi-restraints excluded: chain c residue 510 ILE Chi-restraints excluded: chain c residue 567 ASP Chi-restraints excluded: chain d residue 481 GLN Chi-restraints excluded: chain d residue 485 GLU Chi-restraints excluded: chain d residue 625 LYS Chi-restraints excluded: chain e residue 394 THR Chi-restraints excluded: chain e residue 407 LEU Chi-restraints excluded: chain e residue 442 VAL Chi-restraints excluded: chain e residue 514 GLN Chi-restraints excluded: chain f residue 454 MET Chi-restraints excluded: chain f residue 552 VAL Chi-restraints excluded: chain g residue 407 LEU Chi-restraints excluded: chain g residue 604 LEU Chi-restraints excluded: chain h residue 394 THR Chi-restraints excluded: chain h residue 407 LEU Chi-restraints excluded: chain i residue 481 GLN Chi-restraints excluded: chain j residue 564 ILE Chi-restraints excluded: chain k residue 620 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 671 random chunks: chunk 588 optimal weight: 10.0000 chunk 619 optimal weight: 20.0000 chunk 565 optimal weight: 3.9990 chunk 602 optimal weight: 3.9990 chunk 362 optimal weight: 10.0000 chunk 262 optimal weight: 0.9980 chunk 473 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 544 optimal weight: 6.9990 chunk 570 optimal weight: 8.9990 chunk 600 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 ASN ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 523 ASN ** e 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 484 ASN ** h 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 402 ASN i 469 ASN j 402 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 54120 Z= 0.336 Angle : 0.676 9.727 73337 Z= 0.330 Chirality : 0.044 0.210 8184 Planarity : 0.004 0.048 9405 Dihedral : 5.585 52.060 7403 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.23 % Favored : 93.46 % Rotamer: Outliers : 1.32 % Allowed : 10.29 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.11), residues: 6677 helix: 1.06 (0.10), residues: 3113 sheet: 0.17 (0.20), residues: 759 loop : -1.03 (0.12), residues: 2805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP f 524 HIS 0.006 0.001 HIS I 373 PHE 0.027 0.002 PHE E 354 TYR 0.029 0.002 TYR a 585 ARG 0.006 0.001 ARG i 530 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13354 Ramachandran restraints generated. 6677 Oldfield, 0 Emsley, 6677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13354 Ramachandran restraints generated. 6677 Oldfield, 0 Emsley, 6677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 5764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 344 time to evaluate : 4.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8881 (tpt) cc_final: 0.8594 (tpp) REVERT: C 354 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8408 (m-80) REVERT: D 182 LEU cc_start: 0.8917 (mt) cc_final: 0.8535 (tp) REVERT: E 354 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.7861 (m-80) REVERT: F 354 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7219 (m-80) REVERT: G 229 MET cc_start: 0.8476 (tpp) cc_final: 0.8078 (tpp) REVERT: H 49 MET cc_start: 0.8065 (mmt) cc_final: 0.7482 (ttt) REVERT: H 134 MET cc_start: 0.8762 (tmm) cc_final: 0.8369 (tmm) REVERT: H 229 MET cc_start: 0.8569 (mmm) cc_final: 0.8093 (mmm) REVERT: H 354 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8363 (m-80) REVERT: H 357 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8508 (mmt) REVERT: I 182 LEU cc_start: 0.9077 (mp) cc_final: 0.8592 (tp) REVERT: I 354 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8801 (t80) REVERT: J 125 MET cc_start: 0.9018 (mmm) cc_final: 0.8719 (mmm) REVERT: J 156 ASP cc_start: 0.8218 (t0) cc_final: 0.7942 (t0) REVERT: K 121 MET cc_start: 0.8735 (mtm) cc_final: 0.8414 (mtp) REVERT: K 125 MET cc_start: 0.8433 (mmt) cc_final: 0.7796 (mmp) REVERT: a 613 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8093 (tmm) REVERT: d 624 MET cc_start: 0.6811 (mmm) cc_final: 0.6114 (mmm) REVERT: d 625 LYS cc_start: 0.5972 (OUTLIER) cc_final: 0.5072 (mmmt) REVERT: e 407 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8124 (tt) REVERT: e 488 ARG cc_start: 0.8009 (mtp180) cc_final: 0.7757 (ttm170) REVERT: f 478 ILE cc_start: 0.9007 (mt) cc_final: 0.8699 (tt) REVERT: f 613 MET cc_start: 0.8410 (tmm) cc_final: 0.8006 (tmm) REVERT: g 454 MET cc_start: 0.8574 (mmp) cc_final: 0.8095 (mmp) REVERT: g 577 ASP cc_start: 0.8444 (t0) cc_final: 0.8130 (t0) REVERT: h 407 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8412 (tt) REVERT: h 624 MET cc_start: 0.7055 (mpp) cc_final: 0.6513 (mpp) REVERT: i 624 MET cc_start: 0.5594 (mmp) cc_final: 0.5377 (mmp) REVERT: j 499 MET cc_start: 0.8981 (tmm) cc_final: 0.8211 (tmm) REVERT: k 499 MET cc_start: 0.8953 (ttm) cc_final: 0.8617 (ttm) outliers start: 76 outliers final: 58 residues processed: 403 average time/residue: 0.4676 time to fit residues: 331.3769 Evaluate side-chains 402 residues out of total 5764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 334 time to evaluate : 4.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 354 PHE Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 354 PHE Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 354 PHE Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 88 TRP Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain H residue 354 PHE Chi-restraints excluded: chain H residue 357 MET Chi-restraints excluded: chain I residue 20 LYS Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 354 PHE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 313 ASP Chi-restraints excluded: chain a residue 407 LEU Chi-restraints excluded: chain a residue 481 GLN Chi-restraints excluded: chain a residue 577 ASP Chi-restraints excluded: chain a residue 613 MET Chi-restraints excluded: chain b residue 407 LEU Chi-restraints excluded: chain b residue 564 ILE Chi-restraints excluded: chain b residue 604 LEU Chi-restraints excluded: chain c residue 394 THR Chi-restraints excluded: chain c residue 407 LEU Chi-restraints excluded: chain c residue 481 GLN Chi-restraints excluded: chain c residue 510 ILE Chi-restraints excluded: chain c residue 567 ASP Chi-restraints excluded: chain d residue 481 GLN Chi-restraints excluded: chain d residue 485 GLU Chi-restraints excluded: chain d residue 625 LYS Chi-restraints excluded: chain e residue 394 THR Chi-restraints excluded: chain e residue 407 LEU Chi-restraints excluded: chain e residue 442 VAL Chi-restraints excluded: chain e residue 507 LEU Chi-restraints excluded: chain e residue 510 ILE Chi-restraints excluded: chain f residue 454 MET Chi-restraints excluded: chain f residue 552 VAL Chi-restraints excluded: chain g residue 407 LEU Chi-restraints excluded: chain g residue 571 THR Chi-restraints excluded: chain g residue 604 LEU Chi-restraints excluded: chain h residue 407 LEU Chi-restraints excluded: chain h residue 519 ASP Chi-restraints excluded: chain h residue 571 THR Chi-restraints excluded: chain i residue 394 THR Chi-restraints excluded: chain i residue 481 GLN Chi-restraints excluded: chain i residue 483 LEU Chi-restraints excluded: chain i residue 604 LEU Chi-restraints excluded: chain j residue 494 LEU Chi-restraints excluded: chain j residue 548 THR Chi-restraints excluded: chain j residue 564 ILE Chi-restraints excluded: chain k residue 620 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 671 random chunks: chunk 395 optimal weight: 9.9990 chunk 637 optimal weight: 0.7980 chunk 388 optimal weight: 5.9990 chunk 302 optimal weight: 5.9990 chunk 443 optimal weight: 10.0000 chunk 668 optimal weight: 8.9990 chunk 615 optimal weight: 20.0000 chunk 532 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 411 optimal weight: 3.9990 chunk 326 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 469 ASN ** e 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 54120 Z= 0.246 Angle : 0.629 10.655 73337 Z= 0.304 Chirality : 0.043 0.171 8184 Planarity : 0.004 0.046 9405 Dihedral : 5.523 53.194 7403 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.68 % Favored : 94.02 % Rotamer: Outliers : 1.23 % Allowed : 10.67 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.18 (0.11), residues: 6677 helix: 1.12 (0.10), residues: 3124 sheet: 0.16 (0.19), residues: 759 loop : -1.01 (0.12), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP f 524 HIS 0.005 0.001 HIS I 373 PHE 0.022 0.001 PHE E 354 TYR 0.029 0.001 TYR a 585 ARG 0.005 0.000 ARG i 530 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13354 Ramachandran restraints generated. 6677 Oldfield, 0 Emsley, 6677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13354 Ramachandran restraints generated. 6677 Oldfield, 0 Emsley, 6677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 5764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 340 time to evaluate : 4.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8787 (tpt) cc_final: 0.8531 (tpp) REVERT: C 354 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8345 (m-80) REVERT: D 182 LEU cc_start: 0.8914 (mt) cc_final: 0.8506 (tp) REVERT: E 354 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8048 (m-80) REVERT: F 354 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7302 (m-80) REVERT: G 229 MET cc_start: 0.8479 (tpp) cc_final: 0.8122 (tpp) REVERT: H 49 MET cc_start: 0.8061 (mmt) cc_final: 0.7473 (ttt) REVERT: H 134 MET cc_start: 0.8919 (tmm) cc_final: 0.8564 (tmm) REVERT: H 229 MET cc_start: 0.8567 (mmm) cc_final: 0.8093 (mmm) REVERT: H 354 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8251 (m-80) REVERT: I 354 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8818 (t80) REVERT: J 125 MET cc_start: 0.8991 (mmm) cc_final: 0.8735 (mmm) REVERT: J 156 ASP cc_start: 0.8208 (t0) cc_final: 0.7936 (t0) REVERT: K 125 MET cc_start: 0.8442 (mmt) cc_final: 0.7780 (mmp) REVERT: a 611 MET cc_start: 0.7726 (mmm) cc_final: 0.7240 (tpt) REVERT: a 613 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8065 (tmm) REVERT: b 620 MET cc_start: 0.7203 (mmm) cc_final: 0.6791 (tpt) REVERT: d 499 MET cc_start: 0.8777 (tpt) cc_final: 0.8561 (ttm) REVERT: d 624 MET cc_start: 0.6564 (mmm) cc_final: 0.5667 (mmt) REVERT: d 625 LYS cc_start: 0.6219 (OUTLIER) cc_final: 0.5367 (mmmt) REVERT: e 407 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8082 (tt) REVERT: e 488 ARG cc_start: 0.7990 (mtp180) cc_final: 0.7743 (ttm-80) REVERT: f 478 ILE cc_start: 0.9061 (mt) cc_final: 0.8754 (tt) REVERT: f 613 MET cc_start: 0.8402 (tmm) cc_final: 0.7986 (tmm) REVERT: g 454 MET cc_start: 0.8583 (mmp) cc_final: 0.8095 (mmp) REVERT: g 577 ASP cc_start: 0.8429 (t0) cc_final: 0.8121 (t0) REVERT: g 611 MET cc_start: 0.8296 (mmm) cc_final: 0.7856 (ttm) REVERT: h 407 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8547 (tt) REVERT: h 624 MET cc_start: 0.7067 (mpp) cc_final: 0.6709 (mmp) REVERT: j 499 MET cc_start: 0.8978 (tmm) cc_final: 0.8183 (tmm) REVERT: j 624 MET cc_start: 0.6683 (mpp) cc_final: 0.6472 (mpp) REVERT: k 499 MET cc_start: 0.8855 (ttm) cc_final: 0.8631 (ttm) outliers start: 71 outliers final: 57 residues processed: 393 average time/residue: 0.4811 time to fit residues: 330.8260 Evaluate side-chains 400 residues out of total 5764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 334 time to evaluate : 4.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 354 PHE Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 354 PHE Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 354 PHE Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 88 TRP Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 354 PHE Chi-restraints excluded: chain I residue 20 LYS Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 354 PHE Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 357 MET Chi-restraints excluded: chain a residue 407 LEU Chi-restraints excluded: chain a residue 481 GLN Chi-restraints excluded: chain a residue 577 ASP Chi-restraints excluded: chain a residue 613 MET Chi-restraints excluded: chain b residue 407 LEU Chi-restraints excluded: chain b residue 564 ILE Chi-restraints excluded: chain b residue 604 LEU Chi-restraints excluded: chain c residue 394 THR Chi-restraints excluded: chain c residue 481 GLN Chi-restraints excluded: chain c residue 510 ILE Chi-restraints excluded: chain c residue 567 ASP Chi-restraints excluded: chain d residue 481 GLN Chi-restraints excluded: chain d residue 485 GLU Chi-restraints excluded: chain d residue 625 LYS Chi-restraints excluded: chain e residue 394 THR Chi-restraints excluded: chain e residue 407 LEU Chi-restraints excluded: chain e residue 442 VAL Chi-restraints excluded: chain e residue 507 LEU Chi-restraints excluded: chain e residue 510 ILE Chi-restraints excluded: chain f residue 454 MET Chi-restraints excluded: chain f residue 552 VAL Chi-restraints excluded: chain g residue 407 LEU Chi-restraints excluded: chain g residue 571 THR Chi-restraints excluded: chain g residue 604 LEU Chi-restraints excluded: chain h residue 394 THR Chi-restraints excluded: chain h residue 407 LEU Chi-restraints excluded: chain h residue 519 ASP Chi-restraints excluded: chain h residue 571 THR Chi-restraints excluded: chain i residue 394 THR Chi-restraints excluded: chain i residue 481 GLN Chi-restraints excluded: chain i residue 483 LEU Chi-restraints excluded: chain i residue 604 LEU Chi-restraints excluded: chain j residue 519 ASP Chi-restraints excluded: chain j residue 548 THR Chi-restraints excluded: chain j residue 564 ILE Chi-restraints excluded: chain k residue 620 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 671 random chunks: chunk 422 optimal weight: 6.9990 chunk 567 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 490 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 147 optimal weight: 0.3980 chunk 533 optimal weight: 0.8980 chunk 223 optimal weight: 9.9990 chunk 547 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 ASN ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 560 GLN ** 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 = 0.3244 r_free = 0.3244 target = 0.065155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.048453 restraints weight = 195605.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.049621 restraints weight = 105221.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.050097 restraints weight = 62641.444| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 54120 Z= 0.245 Angle : 0.629 12.047 73337 Z= 0.303 Chirality : 0.043 0.167 8184 Planarity : 0.004 0.047 9405 Dihedral : 5.456 52.050 7403 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.10 % Favored : 93.60 % Rotamer: Outliers : 1.49 % Allowed : 10.62 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.11), residues: 6677 helix: 1.12 (0.10), residues: 3124 sheet: 0.19 (0.19), residues: 759 loop : -1.07 (0.12), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP f 524 HIS 0.005 0.001 HIS I 373 PHE 0.022 0.001 PHE E 354 TYR 0.028 0.001 TYR a 585 ARG 0.004 0.000 ARG i 530 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7909.09 seconds wall clock time: 142 minutes 24.29 seconds (8544.29 seconds total)