Starting phenix.real_space_refine on Tue Apr 16 10:59:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7i_41983/04_2024/8u7i_41983.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7i_41983/04_2024/8u7i_41983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7i_41983/04_2024/8u7i_41983.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7i_41983/04_2024/8u7i_41983.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7i_41983/04_2024/8u7i_41983.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7i_41983/04_2024/8u7i_41983.pdb" } resolution = 2.57 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= 0.009 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: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 24956 2.51 5 N 6452 2.21 5 O 7320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 32": "OD1" <-> "OD2" Residue "A TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A ASP 432": "OD1" <-> "OD2" Residue "A ASP 463": "OD1" <-> "OD2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "B GLU -44": "OE1" <-> "OE2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B GLU 373": "OE1" <-> "OE2" Residue "B ASP 463": "OD1" <-> "OD2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "C ASP 32": "OD1" <-> "OD2" Residue "C TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 373": "OE1" <-> "OE2" Residue "D ASP 32": "OD1" <-> "OD2" Residue "D GLU 231": "OE1" <-> "OE2" Residue "D TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 392": "OD1" <-> "OD2" Residue "D GLU 471": "OE1" <-> "OE2" Residue "D ASP 556": "OD1" <-> "OD2" Residue "E ASP 34": "OD1" <-> "OD2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E ASP 74": "OD1" <-> "OD2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 329": "OE1" <-> "OE2" Residue "F GLU 58": "OE1" <-> "OE2" Residue "F ASP 74": "OD1" <-> "OD2" Residue "F PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G GLU 80": "OE1" <-> "OE2" Residue "G PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 74": "OD1" <-> "OD2" Residue "H PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 146": "OD1" <-> "OD2" Residue "I TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 165": "OE1" <-> "OE2" Residue "I ASP 189": "OD1" <-> "OD2" Residue "I TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 189": "OD1" <-> "OD2" Residue "J PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 234": "OE1" <-> "OE2" Residue "J PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 189": "OD1" <-> "OD2" Residue "K TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 270": "OD1" <-> "OD2" Residue "L TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 165": "OE1" <-> "OE2" Residue "L TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 270": "OD1" <-> "OD2" Residue "M TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 166": "OE1" <-> "OE2" Residue "M ASP 189": "OD1" <-> "OD2" Residue "M TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 256": "OD1" <-> "OD2" Residue "M GLU 258": "OE1" <-> "OE2" Residue "M ASP 269": "OD1" <-> "OD2" Residue "N TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 166": "OE1" <-> "OE2" Residue "N ASP 189": "OD1" <-> "OD2" Residue "N GLU 201": "OE1" <-> "OE2" Residue "N TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 211": "OD1" <-> "OD2" Residue "N GLU 232": "OE1" <-> "OE2" Residue "N GLU 250": "OE1" <-> "OE2" Residue "N ASP 256": "OD1" <-> "OD2" Residue "N GLU 258": "OE1" <-> "OE2" Residue "N ASP 269": "OD1" <-> "OD2" Residue "O TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 165": "OE1" <-> "OE2" Residue "O GLU 166": "OE1" <-> "OE2" Residue "O ASP 189": "OD1" <-> "OD2" Residue "O TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 207": "OE1" <-> "OE2" Residue "O GLU 234": "OE1" <-> "OE2" Residue "O TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 250": "OE1" <-> "OE2" Residue "O ASP 256": "OD1" <-> "OD2" Residue "O GLU 258": "OE1" <-> "OE2" Residue "O ASP 269": "OD1" <-> "OD2" Residue "P GLU 165": "OE1" <-> "OE2" Residue "P GLU 166": "OE1" <-> "OE2" Residue "P ASP 189": "OD1" <-> "OD2" Residue "P ASP 211": "OD1" <-> "OD2" Residue "P GLU 250": "OE1" <-> "OE2" Residue "P ASP 256": "OD1" <-> "OD2" Residue "P GLU 258": "OE1" <-> "OE2" Residue "P ASP 269": "OD1" <-> "OD2" Residue "P GLU 277": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 38864 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5111 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 12, 'TRANS': 613} Chain breaks: 3 Chain: "B" Number of atoms: 5111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5111 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 12, 'TRANS': 613} Chain breaks: 3 Chain: "C" Number of atoms: 5111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5111 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 12, 'TRANS': 613} Chain breaks: 3 Chain: "D" Number of atoms: 5111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5111 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 12, 'TRANS': 613} Chain breaks: 3 Chain: "E" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2326 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 6, 'TRANS': 281} Chain breaks: 5 Chain: "F" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2326 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 6, 'TRANS': 281} Chain breaks: 5 Chain: "G" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2326 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 6, 'TRANS': 281} Chain breaks: 5 Chain: "H" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2326 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 6, 'TRANS': 281} Chain breaks: 5 Chain: "I" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1346 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 9, 'TRANS': 152} Chain: "J" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1346 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 9, 'TRANS': 152} Chain: "K" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1346 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 9, 'TRANS': 152} Chain: "L" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1346 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 9, 'TRANS': 152} Chain: "M" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 933 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Chain: "N" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 933 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Chain: "O" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 933 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Chain: "P" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 933 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Time building chain proxies: 19.32, per 1000 atoms: 0.50 Number of scatterers: 38864 At special positions: 0 Unit cell: (189.57, 167.32, 153.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 136 16.00 O 7320 8.00 N 6452 7.00 C 24956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS I 282 " - pdb=" SG CYS M 285 " distance=2.03 Simple disulfide: pdb=" SG CYS I 284 " - pdb=" SG CYS M 284 " distance=2.03 Simple disulfide: pdb=" SG CYS I 285 " - pdb=" SG CYS M 282 " distance=2.03 Simple disulfide: pdb=" SG CYS J 282 " - pdb=" SG CYS N 285 " distance=2.03 Simple disulfide: pdb=" SG CYS J 284 " - pdb=" SG CYS N 284 " distance=2.04 Simple disulfide: pdb=" SG CYS J 285 " - pdb=" SG CYS N 282 " distance=2.03 Simple disulfide: pdb=" SG CYS K 282 " - pdb=" SG CYS O 285 " distance=2.02 Simple disulfide: pdb=" SG CYS K 284 " - pdb=" SG CYS O 284 " distance=2.03 Simple disulfide: pdb=" SG CYS K 285 " - pdb=" SG CYS O 282 " distance=2.03 Simple disulfide: pdb=" SG CYS L 282 " - pdb=" SG CYS P 285 " distance=2.03 Simple disulfide: pdb=" SG CYS L 284 " - pdb=" SG CYS P 284 " distance=2.03 Simple disulfide: pdb=" SG CYS L 285 " - pdb=" SG CYS P 282 " distance=2.03 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: 15.35 Conformation dependent library (CDL) restraints added in 6.7 seconds 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9048 Finding SS restraints... Secondary structure from input PDB file: 212 helices and 53 sheets defined 51.3% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'A' and resid -53 through -42 Processing helix chain 'A' and resid 31 through 47 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 83 through 94 removed outlier: 3.702A pdb=" N LYS A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.622A pdb=" N ALA A 102 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.960A pdb=" N VAL A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 144 through 148' Processing helix chain 'A' and resid 159 through 175 removed outlier: 3.613A pdb=" N GLN A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 172 " --> pdb=" O LYS A 168 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 201 Processing helix chain 'A' and resid 202 through 220 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 259 through 277 removed outlier: 3.890A pdb=" N TYR A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 353 through 357 removed outlier: 4.352A pdb=" N SER A 357 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 removed outlier: 4.099A pdb=" N SER A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 395 Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 447 through 458 removed outlier: 3.645A pdb=" N CYS A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 493 Processing helix chain 'A' and resid 493 through 503 Processing helix chain 'A' and resid 511 through 520 Processing helix chain 'A' and resid 520 through 529 removed outlier: 3.677A pdb=" N MET A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 540 removed outlier: 4.110A pdb=" N SER A 540 " --> pdb=" O TYR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 552 Processing helix chain 'A' and resid 553 through 563 Processing helix chain 'A' and resid 566 through 574 removed outlier: 4.170A pdb=" N LYS A 570 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing helix chain 'B' and resid -53 through -42 Processing helix chain 'B' and resid 31 through 47 Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 60 through 64 Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.707A pdb=" N LYS B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 144 through 148 removed outlier: 3.937A pdb=" N VAL B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 148' Processing helix chain 'B' and resid 159 through 174 removed outlier: 3.935A pdb=" N GLN B 166 " --> pdb=" O LYS B 162 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LYS B 169 " --> pdb=" O ALA B 165 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR B 170 " --> pdb=" O GLN B 166 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 172 " --> pdb=" O LYS B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 201 Processing helix chain 'B' and resid 202 through 220 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 259 through 277 removed outlier: 3.574A pdb=" N TYR B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 308 Processing helix chain 'B' and resid 321 through 326 Processing helix chain 'B' and resid 353 through 357 removed outlier: 4.361A pdb=" N SER B 357 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 370 removed outlier: 4.100A pdb=" N SER B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA B 369 " --> pdb=" O ALA B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 395 Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 413 through 423 Processing helix chain 'B' and resid 447 through 458 removed outlier: 3.634A pdb=" N CYS B 453 " --> pdb=" O GLY B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 493 Processing helix chain 'B' and resid 493 through 503 Processing helix chain 'B' and resid 511 through 520 Processing helix chain 'B' and resid 521 through 529 Processing helix chain 'B' and resid 532 through 540 removed outlier: 4.095A pdb=" N SER B 540 " --> pdb=" O TYR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 552 Processing helix chain 'B' and resid 553 through 563 Processing helix chain 'B' and resid 566 through 574 removed outlier: 4.156A pdb=" N LYS B 570 " --> pdb=" O PHE B 566 " (cutoff:3.500A) Processing helix chain 'C' and resid -53 through -42 Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 60 through 64 Processing helix chain 'C' and resid 83 through 94 removed outlier: 3.624A pdb=" N LYS C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 144 through 148 removed outlier: 3.922A pdb=" N VAL C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 144 through 148' Processing helix chain 'C' and resid 159 through 175 removed outlier: 3.628A pdb=" N GLN C 166 " --> pdb=" O LYS C 162 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN C 167 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS C 169 " --> pdb=" O ALA C 165 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TYR C 170 " --> pdb=" O GLN C 166 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE C 172 " --> pdb=" O LYS C 168 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER C 175 " --> pdb=" O ILE C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 201 Processing helix chain 'C' and resid 202 through 220 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 259 through 277 removed outlier: 3.618A pdb=" N LYS C 276 " --> pdb=" O TYR C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 308 Processing helix chain 'C' and resid 321 through 326 Processing helix chain 'C' and resid 353 through 357 removed outlier: 4.353A pdb=" N SER C 357 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 removed outlier: 4.100A pdb=" N SER C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C 369 " --> pdb=" O ALA C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 395 Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 413 through 423 Processing helix chain 'C' and resid 447 through 458 removed outlier: 3.682A pdb=" N CYS C 453 " --> pdb=" O GLY C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 493 Processing helix chain 'C' and resid 493 through 503 Processing helix chain 'C' and resid 511 through 529 removed outlier: 7.418A pdb=" N GLU C 522 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 540 removed outlier: 4.154A pdb=" N SER C 540 " --> pdb=" O TYR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 552 Processing helix chain 'C' and resid 553 through 563 Processing helix chain 'C' and resid 566 through 574 removed outlier: 4.221A pdb=" N LYS C 570 " --> pdb=" O PHE C 566 " (cutoff:3.500A) Processing helix chain 'D' and resid -53 through -42 Processing helix chain 'D' and resid 31 through 47 Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'D' and resid 83 through 94 removed outlier: 3.656A pdb=" N LYS D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 97 No H-bonds generated for 'chain 'D' and resid 95 through 97' Processing helix chain 'D' and resid 98 through 102 removed outlier: 3.618A pdb=" N ALA D 102 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 148 removed outlier: 3.951A pdb=" N VAL D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 144 through 148' Processing helix chain 'D' and resid 159 through 175 removed outlier: 3.869A pdb=" N GLN D 166 " --> pdb=" O LYS D 162 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS D 169 " --> pdb=" O ALA D 165 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TYR D 170 " --> pdb=" O GLN D 166 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE D 172 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER D 175 " --> pdb=" O ILE D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 201 Processing helix chain 'D' and resid 202 through 220 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 237 through 239 No H-bonds generated for 'chain 'D' and resid 237 through 239' Processing helix chain 'D' and resid 259 through 277 removed outlier: 3.731A pdb=" N LYS D 276 " --> pdb=" O TYR D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 308 Processing helix chain 'D' and resid 321 through 326 Processing helix chain 'D' and resid 353 through 357 removed outlier: 4.352A pdb=" N SER D 357 " --> pdb=" O ALA D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 370 removed outlier: 4.092A pdb=" N SER D 368 " --> pdb=" O LYS D 364 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA D 369 " --> pdb=" O ALA D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 395 Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 413 through 423 Processing helix chain 'D' and resid 447 through 458 removed outlier: 3.663A pdb=" N CYS D 453 " --> pdb=" O GLY D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 493 Processing helix chain 'D' and resid 493 through 503 Processing helix chain 'D' and resid 511 through 520 Processing helix chain 'D' and resid 520 through 529 removed outlier: 3.771A pdb=" N MET D 524 " --> pdb=" O ILE D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 540 removed outlier: 4.110A pdb=" N SER D 540 " --> pdb=" O TYR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 552 Processing helix chain 'D' and resid 553 through 563 Processing helix chain 'D' and resid 566 through 574 removed outlier: 4.233A pdb=" N LYS D 570 " --> pdb=" O PHE D 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 9 Processing helix chain 'E' and resid 22 through 38 Processing helix chain 'E' and resid 50 through 62 removed outlier: 3.693A pdb=" N ARG E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 81 removed outlier: 3.575A pdb=" N VAL E 77 " --> pdb=" O ASN E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 91 removed outlier: 5.370A pdb=" N LYS E 87 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ASP E 88 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 121 removed outlier: 4.958A pdb=" N GLN E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR E 119 " --> pdb=" O GLN E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 145 Processing helix chain 'E' and resid 145 through 155 Processing helix chain 'E' and resid 163 through 167 Processing helix chain 'E' and resid 168 through 181 removed outlier: 3.688A pdb=" N GLN E 181 " --> pdb=" O TYR E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 214 removed outlier: 4.356A pdb=" N PHE E 207 " --> pdb=" O GLU E 203 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU E 212 " --> pdb=" O ASN E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 326 removed outlier: 3.885A pdb=" N THR E 325 " --> pdb=" O PRO E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 335 Processing helix chain 'E' and resid 342 through 348 Processing helix chain 'E' and resid 353 through 368 removed outlier: 3.626A pdb=" N GLU E 359 " --> pdb=" O ARG E 355 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS E 362 " --> pdb=" O LYS E 358 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE E 363 " --> pdb=" O GLU E 359 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 367 " --> pdb=" O ILE E 363 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU E 368 " --> pdb=" O ILE E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 388 removed outlier: 3.572A pdb=" N VAL E 380 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU E 381 " --> pdb=" O ILE E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 403 removed outlier: 3.651A pdb=" N THR E 398 " --> pdb=" O THR E 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 9 removed outlier: 3.580A pdb=" N LYS F 8 " --> pdb=" O GLU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 38 Processing helix chain 'F' and resid 50 through 62 Processing helix chain 'F' and resid 73 through 81 Processing helix chain 'F' and resid 81 through 91 removed outlier: 5.387A pdb=" N LYS F 87 " --> pdb=" O ARG F 83 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ASP F 88 " --> pdb=" O PRO F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 121 removed outlier: 3.812A pdb=" N LYS F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR F 119 " --> pdb=" O GLN F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 145 removed outlier: 3.549A pdb=" N GLN F 136 " --> pdb=" O ASN F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 164 through 167 Processing helix chain 'F' and resid 168 through 181 Processing helix chain 'F' and resid 203 through 214 removed outlier: 4.335A pdb=" N PHE F 207 " --> pdb=" O GLU F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 335 removed outlier: 4.276A pdb=" N LEU F 327 " --> pdb=" O ASN F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 348 Processing helix chain 'F' and resid 353 through 368 removed outlier: 3.878A pdb=" N LYS F 362 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE F 363 " --> pdb=" O GLU F 359 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU F 368 " --> pdb=" O ILE F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 388 removed outlier: 4.418A pdb=" N ASN F 383 " --> pdb=" O GLN F 379 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 403 Processing helix chain 'G' and resid 3 through 9 Processing helix chain 'G' and resid 22 through 38 Processing helix chain 'G' and resid 50 through 62 Processing helix chain 'G' and resid 73 through 81 removed outlier: 3.620A pdb=" N VAL G 77 " --> pdb=" O ASN G 73 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU G 78 " --> pdb=" O ASP G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 91 removed outlier: 5.449A pdb=" N LYS G 87 " --> pdb=" O ARG G 83 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP G 88 " --> pdb=" O PRO G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 121 removed outlier: 3.807A pdb=" N LYS G 118 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR G 119 " --> pdb=" O GLN G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 145 Processing helix chain 'G' and resid 145 through 155 Processing helix chain 'G' and resid 163 through 167 Processing helix chain 'G' and resid 168 through 181 removed outlier: 3.666A pdb=" N GLN G 181 " --> pdb=" O TYR G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 214 removed outlier: 4.229A pdb=" N PHE G 207 " --> pdb=" O GLU G 203 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE G 211 " --> pdb=" O PHE G 207 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU G 212 " --> pdb=" O ASN G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 335 removed outlier: 3.963A pdb=" N LEU G 327 " --> pdb=" O ASN G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 348 removed outlier: 3.549A pdb=" N GLU G 347 " --> pdb=" O ASP G 343 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE G 348 " --> pdb=" O LEU G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 368 Processing helix chain 'G' and resid 374 through 388 Processing helix chain 'G' and resid 394 through 403 removed outlier: 3.691A pdb=" N THR G 398 " --> pdb=" O THR G 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 9 removed outlier: 3.621A pdb=" N ASP H 9 " --> pdb=" O GLN H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 38 removed outlier: 3.737A pdb=" N THR H 24 " --> pdb=" O GLY H 20 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR H 25 " --> pdb=" O SER H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 59 Processing helix chain 'H' and resid 73 through 81 Processing helix chain 'H' and resid 81 through 91 removed outlier: 5.500A pdb=" N LYS H 87 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ASP H 88 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 121 removed outlier: 3.614A pdb=" N TYR H 119 " --> pdb=" O GLN H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 145 removed outlier: 3.758A pdb=" N GLN H 136 " --> pdb=" O ASN H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 155 Processing helix chain 'H' and resid 163 through 167 Processing helix chain 'H' and resid 168 through 181 Processing helix chain 'H' and resid 204 through 214 removed outlier: 4.054A pdb=" N GLU H 212 " --> pdb=" O ASN H 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 335 removed outlier: 4.073A pdb=" N LEU H 327 " --> pdb=" O ASN H 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 348 removed outlier: 3.751A pdb=" N ILE H 348 " --> pdb=" O LEU H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 353 through 365 Processing helix chain 'H' and resid 374 through 388 Processing helix chain 'H' and resid 394 through 403 removed outlier: 3.522A pdb=" N THR H 398 " --> pdb=" O THR H 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 156 removed outlier: 4.030A pdb=" N GLU I 156 " --> pdb=" O MET I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 179 Processing helix chain 'I' and resid 256 through 277 removed outlier: 3.556A pdb=" N ILE I 275 " --> pdb=" O LEU I 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 286 Processing helix chain 'J' and resid 143 through 150 removed outlier: 3.864A pdb=" N ILE J 148 " --> pdb=" O LEU J 144 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN J 149 " --> pdb=" O LEU J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 158 removed outlier: 4.097A pdb=" N GLU J 156 " --> pdb=" O MET J 153 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR J 157 " --> pdb=" O LEU J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 163 through 179 Processing helix chain 'J' and resid 256 through 276 removed outlier: 3.662A pdb=" N ILE J 275 " --> pdb=" O LEU J 271 " (cutoff:3.500A) Processing helix chain 'J' and resid 283 through 286 Processing helix chain 'K' and resid 143 through 148 removed outlier: 4.365A pdb=" N ILE K 148 " --> pdb=" O LEU K 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 155 Processing helix chain 'K' and resid 163 through 179 Processing helix chain 'K' and resid 256 through 276 Processing helix chain 'L' and resid 151 through 156 Processing helix chain 'L' and resid 163 through 179 Processing helix chain 'L' and resid 256 through 277 Processing helix chain 'L' and resid 283 through 286 removed outlier: 3.515A pdb=" N LYS L 286 " --> pdb=" O LYS L 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 283 through 286' Processing helix chain 'M' and resid 163 through 179 removed outlier: 3.601A pdb=" N ILE M 171 " --> pdb=" O SER M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 207 through 215 removed outlier: 3.649A pdb=" N MET M 215 " --> pdb=" O ASP M 211 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 277 Processing helix chain 'N' and resid 163 through 179 removed outlier: 3.671A pdb=" N ILE N 171 " --> pdb=" O SER N 167 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE N 179 " --> pdb=" O ILE N 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 208 through 215 removed outlier: 3.815A pdb=" N MET N 215 " --> pdb=" O ASP N 211 " (cutoff:3.500A) Processing helix chain 'N' and resid 256 through 277 removed outlier: 3.566A pdb=" N ASP N 270 " --> pdb=" O LYS N 266 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU N 271 " --> pdb=" O PHE N 267 " (cutoff:3.500A) Processing helix chain 'O' and resid 163 through 179 Processing helix chain 'O' and resid 206 through 215 removed outlier: 3.563A pdb=" N VAL O 210 " --> pdb=" O HIS O 206 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP O 211 " --> pdb=" O GLU O 207 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU O 212 " --> pdb=" O TYR O 208 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN O 213 " --> pdb=" O ILE O 209 " (cutoff:3.500A) Processing helix chain 'O' and resid 256 through 276 removed outlier: 3.517A pdb=" N LYS O 274 " --> pdb=" O ASP O 270 " (cutoff:3.500A) Processing helix chain 'O' and resid 282 through 286 removed outlier: 3.996A pdb=" N CYS O 285 " --> pdb=" O CYS O 282 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 179 removed outlier: 3.594A pdb=" N ILE P 171 " --> pdb=" O SER P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 207 through 215 Processing helix chain 'P' and resid 256 through 276 Processing sheet with id=AA1, first strand: chain 'A' and resid -28 through -27 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 20 removed outlier: 6.547A pdb=" N GLU A 15 " --> pdb=" O ASN A 10 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N PHE A 3 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ASP A 76 " --> pdb=" O PHE A 3 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A 5 " --> pdb=" O THR A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 154 removed outlier: 6.507A pdb=" N VAL A 283 " --> pdb=" O TYR A 314 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N PHE A 316 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR A 285 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N SER A 318 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE A 287 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS A 24 " --> pdb=" O ARG A 332 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE A 334 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL A 26 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL A 336 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE A 28 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AA5, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.506A pdb=" N ILE A 142 " --> pdb=" O ARG A 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 224 through 230 Processing sheet with id=AA7, first strand: chain 'A' and resid 241 through 247 Processing sheet with id=AA8, first strand: chain 'A' and resid 403 through 407 removed outlier: 8.185A pdb=" N TYR A 506 " --> pdb=" O HIS A 427 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 429 " --> pdb=" O TYR A 506 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N SER A 508 " --> pdb=" O ILE A 429 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THR A 431 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 436 through 437 Processing sheet with id=AB1, first strand: chain 'B' and resid -28 through -27 Processing sheet with id=AB2, first strand: chain 'B' and resid 14 through 20 removed outlier: 6.619A pdb=" N GLU B 15 " --> pdb=" O ASN B 10 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N PHE B 3 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ASP B 76 " --> pdb=" O PHE B 3 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN B 5 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS B 112 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN B 121 " --> pdb=" O LYS B 112 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 149 through 154 removed outlier: 6.497A pdb=" N VAL B 283 " --> pdb=" O TYR B 314 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N PHE B 316 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TYR B 285 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N SER B 318 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE B 287 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS B 24 " --> pdb=" O ARG B 332 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE B 334 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL B 26 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL B 336 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE B 28 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.517A pdb=" N ILE B 142 " --> pdb=" O ARG B 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 224 through 230 Processing sheet with id=AB6, first strand: chain 'B' and resid 241 through 247 Processing sheet with id=AB7, first strand: chain 'B' and resid 403 through 407 removed outlier: 8.205A pdb=" N TYR B 506 " --> pdb=" O HIS B 427 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE B 429 " --> pdb=" O TYR B 506 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER B 508 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N THR B 431 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 436 through 437 Processing sheet with id=AB9, first strand: chain 'C' and resid -28 through -27 Processing sheet with id=AC1, first strand: chain 'C' and resid 14 through 20 removed outlier: 6.556A pdb=" N GLU C 15 " --> pdb=" O ASN C 10 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N PHE C 3 " --> pdb=" O ASP C 76 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASP C 76 " --> pdb=" O PHE C 3 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN C 5 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS C 112 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN C 121 " --> pdb=" O LYS C 112 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 149 through 154 removed outlier: 3.531A pdb=" N GLU C 288 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL C 283 " --> pdb=" O TYR C 314 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N PHE C 316 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR C 285 " --> pdb=" O PHE C 316 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N SER C 318 " --> pdb=" O TYR C 285 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE C 287 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASN C 25 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS C 24 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE C 334 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL C 26 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL C 336 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE C 28 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.520A pdb=" N ILE C 142 " --> pdb=" O ARG C 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 403 through 407 removed outlier: 8.156A pdb=" N TYR C 506 " --> pdb=" O HIS C 427 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE C 429 " --> pdb=" O TYR C 506 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N SER C 508 " --> pdb=" O ILE C 429 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N THR C 431 " --> pdb=" O SER C 508 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 436 through 437 Processing sheet with id=AC6, first strand: chain 'D' and resid -28 through -27 Processing sheet with id=AC7, first strand: chain 'D' and resid 14 through 20 removed outlier: 6.554A pdb=" N GLU D 15 " --> pdb=" O ASN D 10 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N PHE D 3 " --> pdb=" O ASP D 76 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASP D 76 " --> pdb=" O PHE D 3 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN D 5 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 149 through 154 removed outlier: 6.475A pdb=" N VAL D 283 " --> pdb=" O TYR D 314 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N PHE D 316 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR D 285 " --> pdb=" O PHE D 316 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N SER D 318 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE D 287 " --> pdb=" O SER D 318 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS D 24 " --> pdb=" O ARG D 332 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE D 334 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL D 26 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL D 336 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE D 28 " --> pdb=" O VAL D 336 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 113 through 114 Processing sheet with id=AD1, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.528A pdb=" N ILE D 142 " --> pdb=" O ARG D 139 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 403 through 407 removed outlier: 8.154A pdb=" N TYR D 506 " --> pdb=" O HIS D 427 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE D 429 " --> pdb=" O TYR D 506 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N SER D 508 " --> pdb=" O ILE D 429 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR D 431 " --> pdb=" O SER D 508 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 436 through 437 Processing sheet with id=AD4, first strand: chain 'E' and resid 69 through 72 removed outlier: 6.911A pdb=" N SER E 43 " --> pdb=" O LYS E 158 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N PHE E 160 " --> pdb=" O SER E 43 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA E 45 " --> pdb=" O PHE E 160 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 69 through 72 removed outlier: 6.907A pdb=" N SER F 43 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N PHE F 160 " --> pdb=" O SER F 43 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA F 45 " --> pdb=" O PHE F 160 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ASP F 162 " --> pdb=" O ALA F 45 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL F 47 " --> pdb=" O ASP F 162 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 69 through 72 removed outlier: 6.885A pdb=" N SER G 43 " --> pdb=" O LYS G 158 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N PHE G 160 " --> pdb=" O SER G 43 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA G 45 " --> pdb=" O PHE G 160 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 106 through 107 Processing sheet with id=AD8, first strand: chain 'H' and resid 69 through 72 removed outlier: 6.874A pdb=" N SER H 43 " --> pdb=" O LYS H 158 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N PHE H 160 " --> pdb=" O SER H 43 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA H 45 " --> pdb=" O PHE H 160 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE H 157 " --> pdb=" O LYS H 185 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N PHE H 187 " --> pdb=" O PHE H 157 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE H 159 " --> pdb=" O PHE H 187 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL H 189 " --> pdb=" O ILE H 159 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE H 161 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE H 13 " --> pdb=" O ILE H 188 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 100 through 101 Processing sheet with id=AE1, first strand: chain 'I' and resid 160 through 161 Processing sheet with id=AE2, first strand: chain 'I' and resid 184 through 189 removed outlier: 4.763A pdb=" N ALA I 184 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N VAL I 199 " --> pdb=" O ALA I 184 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILE I 186 " --> pdb=" O VAL I 197 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL I 197 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER I 188 " --> pdb=" O THR I 195 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LYS I 198 " --> pdb=" O GLU I 234 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N GLU I 234 " --> pdb=" O LYS I 198 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU I 200 " --> pdb=" O GLU I 232 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLU I 232 " --> pdb=" O LEU I 200 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU I 202 " --> pdb=" O LYS I 230 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LYS I 230 " --> pdb=" O LEU I 202 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LYS I 204 " --> pdb=" O GLN I 228 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N GLN I 228 " --> pdb=" O LYS I 204 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N HIS I 206 " --> pdb=" O ARG I 226 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG I 226 " --> pdb=" O HIS I 206 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N TYR I 208 " --> pdb=" O GLU I 224 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLU I 224 " --> pdb=" O TYR I 208 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 280 through 281 Processing sheet with id=AE4, first strand: chain 'J' and resid 160 through 161 Processing sheet with id=AE5, first strand: chain 'J' and resid 184 through 189 removed outlier: 6.794A pdb=" N THR J 195 " --> pdb=" O THR J 187 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU J 194 " --> pdb=" O LYS J 237 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS J 237 " --> pdb=" O LEU J 194 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL J 196 " --> pdb=" O ILE J 235 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR J 229 " --> pdb=" O LEU J 202 " (cutoff:3.500A) removed outlier: 11.904A pdb=" N LYS J 204 " --> pdb=" O PHE J 227 " (cutoff:3.500A) removed outlier: 10.330A pdb=" N PHE J 227 " --> pdb=" O LYS J 204 " (cutoff:3.500A) removed outlier: 11.199A pdb=" N HIS J 206 " --> pdb=" O LYS J 225 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N LYS J 225 " --> pdb=" O HIS J 206 " (cutoff:3.500A) removed outlier: 11.157A pdb=" N TYR J 208 " --> pdb=" O LEU J 223 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N LEU J 223 " --> pdb=" O TYR J 208 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 280 through 281 Processing sheet with id=AE7, first strand: chain 'K' and resid 160 through 161 Processing sheet with id=AE8, first strand: chain 'K' and resid 184 through 189 removed outlier: 6.857A pdb=" N THR K 195 " --> pdb=" O THR K 187 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU K 194 " --> pdb=" O LYS K 237 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS K 237 " --> pdb=" O LEU K 194 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL K 196 " --> pdb=" O ILE K 235 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR K 229 " --> pdb=" O LEU K 202 " (cutoff:3.500A) removed outlier: 11.652A pdb=" N LYS K 204 " --> pdb=" O PHE K 227 " (cutoff:3.500A) removed outlier: 9.933A pdb=" N PHE K 227 " --> pdb=" O LYS K 204 " (cutoff:3.500A) removed outlier: 11.422A pdb=" N HIS K 206 " --> pdb=" O LYS K 225 " (cutoff:3.500A) removed outlier: 10.144A pdb=" N LYS K 225 " --> pdb=" O HIS K 206 " (cutoff:3.500A) removed outlier: 11.363A pdb=" N TYR K 208 " --> pdb=" O LEU K 223 " (cutoff:3.500A) removed outlier: 9.873A pdb=" N LEU K 223 " --> pdb=" O TYR K 208 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 280 through 281 removed outlier: 3.783A pdb=" N VAL K 280 " --> pdb=" O ILE K 291 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 160 through 161 Processing sheet with id=AF2, first strand: chain 'L' and resid 184 through 189 removed outlier: 6.781A pdb=" N THR L 195 " --> pdb=" O THR L 187 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS L 198 " --> pdb=" O GLU L 234 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLU L 234 " --> pdb=" O LYS L 198 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LEU L 200 " --> pdb=" O GLU L 232 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLU L 232 " --> pdb=" O LEU L 200 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU L 202 " --> pdb=" O LYS L 230 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LYS L 230 " --> pdb=" O LEU L 202 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LYS L 204 " --> pdb=" O GLN L 228 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLN L 228 " --> pdb=" O LYS L 204 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 210 through 211 removed outlier: 3.566A pdb=" N VAL L 210 " --> pdb=" O GLU L 224 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 279 through 281 Processing sheet with id=AF5, first strand: chain 'M' and resid 184 through 189 removed outlier: 6.493A pdb=" N THR M 195 " --> pdb=" O THR M 187 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS M 198 " --> pdb=" O GLU M 234 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLU M 234 " --> pdb=" O LYS M 198 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 184 through 189 removed outlier: 6.646A pdb=" N THR N 195 " --> pdb=" O THR N 187 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LYS N 198 " --> pdb=" O GLU N 234 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLU N 234 " --> pdb=" O LYS N 198 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 184 through 190 removed outlier: 6.595A pdb=" N THR O 195 " --> pdb=" O THR O 187 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASP O 189 " --> pdb=" O CYS O 193 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N CYS O 193 " --> pdb=" O ASP O 189 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU O 194 " --> pdb=" O LYS O 237 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS O 237 " --> pdb=" O LEU O 194 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL O 196 " --> pdb=" O ILE O 235 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 184 through 190 removed outlier: 6.528A pdb=" N THR P 195 " --> pdb=" O THR P 187 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP P 189 " --> pdb=" O CYS P 193 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N CYS P 193 " --> pdb=" O ASP P 189 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LYS P 198 " --> pdb=" O GLU P 234 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLU P 234 " --> pdb=" O LYS P 198 " (cutoff:3.500A) 1861 hydrogen bonds defined for protein. 5295 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: 17.68 Time building geometry restraints manager: 16.55 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: 12468 1.34 - 1.46: 8857 1.46 - 1.59: 18010 1.59 - 1.71: 1 1.71 - 1.83: 208 Bond restraints: 39544 Sorted by residual: bond pdb=" C LYS N 204 " pdb=" N PRO N 205 " ideal model delta sigma weight residual 1.335 1.358 -0.023 8.70e-03 1.32e+04 6.70e+00 bond pdb=" CB PRO F 129 " pdb=" CG PRO F 129 " ideal model delta sigma weight residual 1.492 1.612 -0.120 5.00e-02 4.00e+02 5.71e+00 bond pdb=" CB GLU N 165 " pdb=" CG GLU N 165 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.21e+00 bond pdb=" CA ASP E 111 " pdb=" C ASP E 111 " ideal model delta sigma weight residual 1.522 1.502 0.020 1.38e-02 5.25e+03 2.10e+00 bond pdb=" CB GLU F 58 " pdb=" CG GLU F 58 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.06e+00 ... (remaining 39539 not shown) Histogram of bond angle deviations from ideal: 97.38 - 104.70: 393 104.70 - 112.02: 19237 112.02 - 119.34: 13075 119.34 - 126.66: 20181 126.66 - 133.98: 218 Bond angle restraints: 53104 Sorted by residual: angle pdb=" CA PRO F 129 " pdb=" N PRO F 129 " pdb=" CD PRO F 129 " ideal model delta sigma weight residual 112.00 102.93 9.07 1.40e+00 5.10e-01 4.20e+01 angle pdb=" CA LYS D 162 " pdb=" CB LYS D 162 " pdb=" CG LYS D 162 " ideal model delta sigma weight residual 114.10 123.07 -8.97 2.00e+00 2.50e-01 2.01e+01 angle pdb=" N LYS O 204 " pdb=" CA LYS O 204 " pdb=" C LYS O 204 " ideal model delta sigma weight residual 109.81 118.95 -9.14 2.21e+00 2.05e-01 1.71e+01 angle pdb=" N LYS M 204 " pdb=" CA LYS M 204 " pdb=" C LYS M 204 " ideal model delta sigma weight residual 109.81 118.68 -8.87 2.21e+00 2.05e-01 1.61e+01 angle pdb=" CA GLN H 115 " pdb=" CB GLN H 115 " pdb=" CG GLN H 115 " ideal model delta sigma weight residual 114.10 122.11 -8.01 2.00e+00 2.50e-01 1.60e+01 ... (remaining 53099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 20534 17.95 - 35.91: 2782 35.91 - 53.86: 758 53.86 - 71.82: 129 71.82 - 89.77: 49 Dihedral angle restraints: 24252 sinusoidal: 10244 harmonic: 14008 Sorted by residual: dihedral pdb=" CB CYS I 282 " pdb=" SG CYS I 282 " pdb=" SG CYS M 285 " pdb=" CB CYS M 285 " ideal model delta sinusoidal sigma weight residual -86.00 -0.39 -85.61 1 1.00e+01 1.00e-02 8.86e+01 dihedral pdb=" CB CYS L 285 " pdb=" SG CYS L 285 " pdb=" SG CYS P 282 " pdb=" CB CYS P 282 " ideal model delta sinusoidal sigma weight residual 93.00 164.40 -71.40 1 1.00e+01 1.00e-02 6.54e+01 dihedral pdb=" CB CYS J 285 " pdb=" SG CYS J 285 " pdb=" SG CYS N 282 " pdb=" CB CYS N 282 " ideal model delta sinusoidal sigma weight residual 93.00 142.71 -49.71 1 1.00e+01 1.00e-02 3.39e+01 ... (remaining 24249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4677 0.048 - 0.096: 908 0.096 - 0.144: 253 0.144 - 0.193: 7 0.193 - 0.241: 3 Chirality restraints: 5848 Sorted by residual: chirality pdb=" CG LEU F 222 " pdb=" CB LEU F 222 " pdb=" CD1 LEU F 222 " pdb=" CD2 LEU F 222 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB ILE N 179 " pdb=" CA ILE N 179 " pdb=" CG1 ILE N 179 " pdb=" CG2 ILE N 179 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA PRO O 205 " pdb=" N PRO O 205 " pdb=" C PRO O 205 " pdb=" CB PRO O 205 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 5845 not shown) Planarity restraints: 6764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN F 128 " -0.085 5.00e-02 4.00e+02 1.23e-01 2.41e+01 pdb=" N PRO F 129 " 0.212 5.00e-02 4.00e+02 pdb=" CA PRO F 129 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO F 129 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS L 204 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO L 205 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO L 205 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO L 205 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 58 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" CD GLU F 58 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU F 58 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU F 58 " 0.014 2.00e-02 2.50e+03 ... (remaining 6761 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 768 2.66 - 3.22: 37559 3.22 - 3.78: 61823 3.78 - 4.34: 85836 4.34 - 4.90: 138219 Nonbonded interactions: 324205 Sorted by model distance: nonbonded pdb=" OH TYR C 170 " pdb=" O LYS C 276 " model vdw 2.101 2.440 nonbonded pdb=" OH TYR I 203 " pdb=" O GLU I 281 " model vdw 2.147 2.440 nonbonded pdb=" OD2 ASP C 250 " pdb=" OH TYR C 254 " model vdw 2.156 2.440 nonbonded pdb=" O GLY H 75 " pdb=" OG SER H 79 " model vdw 2.178 2.440 nonbonded pdb=" O LYS B 162 " pdb=" NZ LYS B 162 " model vdw 2.184 2.520 ... (remaining 324200 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' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.250 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: 0.050 Extract box with map and model: 11.230 Check model and map are aligned: 0.610 Set scattering table: 0.370 Process input model: 102.960 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.350 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:13.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 39544 Z= 0.262 Angle : 0.622 11.122 53104 Z= 0.315 Chirality : 0.041 0.241 5848 Planarity : 0.004 0.123 6764 Dihedral : 17.450 89.772 15168 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.86 % Favored : 97.06 % Rotamer: Outliers : 3.23 % Allowed : 28.69 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.12), residues: 4656 helix: 1.14 (0.12), residues: 2048 sheet: 0.60 (0.20), residues: 716 loop : -0.30 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 199 HIS 0.008 0.001 HIS P 174 PHE 0.012 0.001 PHE F 226 TYR 0.034 0.001 TYR M 203 ARG 0.015 0.000 ARG K 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 386 time to evaluate : 4.863 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: E 102 TYR cc_start: 0.6906 (p90) cc_final: 0.6665 (p90) REVERT: G 176 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8658 (mpp) REVERT: I 144 LEU cc_start: 0.8819 (pp) cc_final: 0.8418 (mm) REVERT: I 270 ASP cc_start: 0.9404 (p0) cc_final: 0.9198 (p0) REVERT: O 166 GLU cc_start: 0.8776 (pm20) cc_final: 0.8575 (pm20) REVERT: P 166 GLU cc_start: 0.9448 (mm-30) cc_final: 0.9206 (tp30) outliers start: 140 outliers final: 119 residues processed: 510 average time/residue: 1.4390 time to fit residues: 902.7869 Evaluate side-chains 496 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 376 time to evaluate : 4.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -71 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue -30 ASP Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain C residue -10 THR Chi-restraints excluded: chain C residue -2 THR Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue -71 VAL Chi-restraints excluded: chain D residue -67 ASP Chi-restraints excluded: chain D residue -10 THR Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 313 LYS Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 73 ASN Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 55 LYS Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 176 MET Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 323 ASN Chi-restraints excluded: chain H residue 352 LEU Chi-restraints excluded: chain H residue 354 SER Chi-restraints excluded: chain I residue 141 ASN Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 215 MET Chi-restraints excluded: chain K residue 141 ASN Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 228 GLN Chi-restraints excluded: chain K residue 229 THR Chi-restraints excluded: chain K residue 253 SER Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain L residue 141 ASN Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 194 LEU Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain L residue 212 LEU Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 279 LEU Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 203 TYR Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain N residue 231 ARG Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 250 GLU Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 253 SER Chi-restraints excluded: chain O residue 282 CYS Chi-restraints excluded: chain P residue 167 SER Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 269 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 395 optimal weight: 9.9990 chunk 354 optimal weight: 0.2980 chunk 196 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 239 optimal weight: 9.9990 chunk 189 optimal weight: 40.0000 chunk 366 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 223 optimal weight: 0.6980 chunk 273 optimal weight: 7.9990 chunk 424 optimal weight: 20.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C -3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 ASN ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 379 GLN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 244 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 GLN M 164 GLN ** N 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 164 GLN O 213 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 39544 Z= 0.254 Angle : 0.569 9.070 53104 Z= 0.296 Chirality : 0.043 0.258 5848 Planarity : 0.003 0.069 6764 Dihedral : 6.926 164.775 5334 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.77 % Favored : 97.14 % Rotamer: Outliers : 4.57 % Allowed : 25.60 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.12), residues: 4656 helix: 1.64 (0.11), residues: 2072 sheet: 0.68 (0.20), residues: 688 loop : -0.26 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 199 HIS 0.006 0.001 HIS P 174 PHE 0.011 0.001 PHE A 315 TYR 0.022 0.001 TYR M 203 ARG 0.008 0.000 ARG K 226 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 391 time to evaluate : 4.364 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: A 221 LYS cc_start: 0.9147 (tppt) cc_final: 0.8936 (mppt) REVERT: A 261 ARG cc_start: 0.8594 (ttm110) cc_final: 0.8154 (tpp80) REVERT: A 288 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8480 (tt0) REVERT: B 288 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8440 (tt0) REVERT: B 455 ASN cc_start: 0.9249 (OUTLIER) cc_final: 0.8768 (t0) REVERT: C 221 LYS cc_start: 0.9185 (tppt) cc_final: 0.8952 (mppt) REVERT: C 288 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8534 (tt0) REVERT: C 452 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7332 (mtp180) REVERT: D 261 ARG cc_start: 0.8637 (tpp80) cc_final: 0.8399 (tpp80) REVERT: D 288 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8562 (tt0) REVERT: D 395 GLU cc_start: 0.8909 (tp30) cc_final: 0.8255 (tp30) REVERT: E 102 TYR cc_start: 0.6972 (p90) cc_final: 0.6751 (p90) REVERT: F 60 ARG cc_start: 0.8744 (mtp180) cc_final: 0.8495 (mtp180) REVERT: G 60 ARG cc_start: 0.8805 (mtp180) cc_final: 0.8522 (mtm-85) REVERT: G 176 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8585 (mpp) REVERT: H 83 ARG cc_start: 0.9107 (ttm170) cc_final: 0.8777 (ttm170) REVERT: H 217 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.7079 (t80) REVERT: H 222 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7882 (tm) REVERT: I 218 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8323 (mtp85) REVERT: I 228 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8581 (pp30) REVERT: I 270 ASP cc_start: 0.9285 (p0) cc_final: 0.9055 (p0) REVERT: J 226 ARG cc_start: 0.8818 (ttm170) cc_final: 0.8316 (ttm170) REVERT: J 272 MET cc_start: 0.8880 (mmm) cc_final: 0.8523 (tpp) REVERT: M 165 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8238 (tm-30) REVERT: M 169 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9043 (ttmm) REVERT: M 211 ASP cc_start: 0.9112 (m-30) cc_final: 0.8700 (m-30) REVERT: N 166 GLU cc_start: 0.9377 (mm-30) cc_final: 0.9048 (tp30) REVERT: N 189 ASP cc_start: 0.8887 (t0) cc_final: 0.8617 (t0) REVERT: P 165 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8872 (tm-30) REVERT: P 166 GLU cc_start: 0.9430 (mm-30) cc_final: 0.9055 (tp30) REVERT: P 169 LYS cc_start: 0.9432 (OUTLIER) cc_final: 0.9170 (ttpp) REVERT: P 211 ASP cc_start: 0.9304 (t0) cc_final: 0.9034 (t0) REVERT: P 269 ASP cc_start: 0.8732 (m-30) cc_final: 0.8526 (m-30) outliers start: 198 outliers final: 77 residues processed: 549 average time/residue: 1.0195 time to fit residues: 693.0618 Evaluate side-chains 453 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 363 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue -30 ASP Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue -67 ASP Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue -71 VAL Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 73 ASN Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 176 MET Chi-restraints excluded: chain G residue 323 ASN Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 217 PHE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 323 ASN Chi-restraints excluded: chain H residue 343 ASP Chi-restraints excluded: chain I residue 191 ASP Chi-restraints excluded: chain I residue 203 TYR Chi-restraints excluded: chain I residue 215 MET Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 228 GLN Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 146 ASP Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain L residue 141 ASN Chi-restraints excluded: chain L residue 189 ASP Chi-restraints excluded: chain L residue 216 TYR Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain M residue 164 GLN Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 279 LEU Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain N residue 248 ILE Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain P residue 233 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 236 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 353 optimal weight: 0.9980 chunk 289 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 425 optimal weight: 0.9990 chunk 459 optimal weight: 6.9990 chunk 379 optimal weight: 8.9990 chunk 422 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 chunk 341 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 GLN ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 GLN ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 244 GLN L 164 GLN M 164 GLN ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 213 ASN ** O 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 276 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39544 Z= 0.203 Angle : 0.543 9.297 53104 Z= 0.279 Chirality : 0.041 0.213 5848 Planarity : 0.003 0.061 6764 Dihedral : 5.104 48.988 5198 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.79 % Favored : 97.12 % Rotamer: Outliers : 4.48 % Allowed : 25.81 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.13), residues: 4656 helix: 1.78 (0.11), residues: 2108 sheet: 0.77 (0.20), residues: 664 loop : -0.21 (0.15), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 199 HIS 0.004 0.001 HIS K 174 PHE 0.010 0.001 PHE B 315 TYR 0.024 0.001 TYR I 161 ARG 0.008 0.000 ARG K 226 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 398 time to evaluate : 5.055 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: A 281 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8985 (ptpp) REVERT: A 288 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: B 288 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8413 (tt0) REVERT: B 455 ASN cc_start: 0.9250 (OUTLIER) cc_final: 0.8760 (t0) REVERT: C 162 LYS cc_start: 0.9561 (tptp) cc_final: 0.9325 (tppt) REVERT: C 221 LYS cc_start: 0.9181 (tppt) cc_final: 0.8948 (mppt) REVERT: C 247 LYS cc_start: 0.8428 (tppp) cc_final: 0.8200 (tptp) REVERT: C 281 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8975 (ptpp) REVERT: C 452 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7434 (mtp180) REVERT: D 173 GLU cc_start: 0.8683 (pp20) cc_final: 0.8440 (pp20) REVERT: D 261 ARG cc_start: 0.8638 (tpp80) cc_final: 0.8315 (tpp80) REVERT: D 281 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8979 (ptpp) REVERT: D 288 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8518 (tt0) REVERT: D 395 GLU cc_start: 0.8890 (tp30) cc_final: 0.8420 (tp30) REVERT: E 55 LYS cc_start: 0.8874 (mtmm) cc_final: 0.8581 (pttm) REVERT: F 115 GLN cc_start: 0.9010 (pp30) cc_final: 0.8732 (pp30) REVERT: F 136 GLN cc_start: 0.8709 (pt0) cc_final: 0.8156 (pm20) REVERT: G 60 ARG cc_start: 0.8783 (mtp180) cc_final: 0.8561 (mtm-85) REVERT: G 176 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8535 (mpp) REVERT: H 217 PHE cc_start: 0.7350 (OUTLIER) cc_final: 0.7035 (t80) REVERT: H 222 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7890 (tm) REVERT: I 218 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8299 (mtp85) REVERT: I 228 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8593 (pp30) REVERT: I 270 ASP cc_start: 0.9287 (p0) cc_final: 0.9060 (p0) REVERT: J 136 HIS cc_start: 0.8828 (p90) cc_final: 0.8620 (p90) REVERT: J 226 ARG cc_start: 0.8897 (ttm170) cc_final: 0.8594 (ttm170) REVERT: J 272 MET cc_start: 0.8845 (mmm) cc_final: 0.8473 (tpp) REVERT: K 218 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8320 (mtp85) REVERT: L 270 ASP cc_start: 0.9335 (p0) cc_final: 0.9109 (p0) REVERT: M 165 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8223 (tm-30) REVERT: M 169 LYS cc_start: 0.9455 (OUTLIER) cc_final: 0.9088 (ttmm) REVERT: M 211 ASP cc_start: 0.9085 (m-30) cc_final: 0.8671 (m-30) REVERT: O 270 ASP cc_start: 0.9353 (OUTLIER) cc_final: 0.9022 (p0) REVERT: P 165 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8840 (tm-30) REVERT: P 166 GLU cc_start: 0.9396 (mm-30) cc_final: 0.8685 (tp30) REVERT: P 169 LYS cc_start: 0.9418 (OUTLIER) cc_final: 0.8925 (tmmm) REVERT: P 269 ASP cc_start: 0.8815 (m-30) cc_final: 0.8569 (m-30) REVERT: P 270 ASP cc_start: 0.9287 (OUTLIER) cc_final: 0.8971 (p0) outliers start: 194 outliers final: 81 residues processed: 547 average time/residue: 1.4556 time to fit residues: 979.7048 Evaluate side-chains 478 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 379 time to evaluate : 5.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue -67 ASP Chi-restraints excluded: chain C residue -10 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue -10 THR Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 73 ASN Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 176 MET Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 217 PHE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 215 MET Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 228 GLN Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 233 VAL Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 218 ARG Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain L residue 141 ASN Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain L residue 216 TYR Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain M residue 162 LEU Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 279 LEU Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 279 LEU Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 248 ILE Chi-restraints excluded: chain O residue 270 ASP Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain P residue 212 LEU Chi-restraints excluded: chain P residue 232 GLU Chi-restraints excluded: chain P residue 270 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 420 optimal weight: 7.9990 chunk 320 optimal weight: 20.0000 chunk 220 optimal weight: 2.9990 chunk 47 optimal weight: 0.0970 chunk 203 optimal weight: 4.9990 chunk 285 optimal weight: 9.9990 chunk 427 optimal weight: 9.9990 chunk 452 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 404 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 GLN ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 GLN L 293 ASN ** M 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 39544 Z= 0.190 Angle : 0.543 9.302 53104 Z= 0.276 Chirality : 0.041 0.202 5848 Planarity : 0.003 0.056 6764 Dihedral : 4.845 51.202 5185 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.75 % Favored : 97.16 % Rotamer: Outliers : 4.62 % Allowed : 25.74 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.13), residues: 4656 helix: 1.86 (0.11), residues: 2080 sheet: 0.76 (0.20), residues: 664 loop : -0.20 (0.15), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 199 HIS 0.004 0.001 HIS K 174 PHE 0.011 0.001 PHE E 207 TYR 0.024 0.001 TYR M 203 ARG 0.008 0.000 ARG K 226 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 401 time to evaluate : 5.097 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: A 162 LYS cc_start: 0.9527 (tptp) cc_final: 0.9312 (tppt) REVERT: A 170 TYR cc_start: 0.8076 (t80) cc_final: 0.7713 (t80) REVERT: A 173 GLU cc_start: 0.8690 (pp20) cc_final: 0.8464 (pp20) REVERT: A 281 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8976 (ptpp) REVERT: A 288 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8425 (tt0) REVERT: B 30 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.9003 (tpp) REVERT: B 288 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: B 395 GLU cc_start: 0.8756 (tp30) cc_final: 0.8212 (tp30) REVERT: B 455 ASN cc_start: 0.9241 (OUTLIER) cc_final: 0.8835 (t0) REVERT: C 173 GLU cc_start: 0.8757 (pp20) cc_final: 0.8555 (pp20) REVERT: C 221 LYS cc_start: 0.9179 (tppt) cc_final: 0.8957 (mppt) REVERT: C 247 LYS cc_start: 0.8494 (tppp) cc_final: 0.8260 (tptp) REVERT: C 281 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8966 (ptpp) REVERT: C 397 GLU cc_start: 0.8580 (pm20) cc_final: 0.8357 (pm20) REVERT: C 452 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7538 (mtp180) REVERT: D 173 GLU cc_start: 0.8703 (pp20) cc_final: 0.8496 (pp20) REVERT: D 261 ARG cc_start: 0.8632 (tpp80) cc_final: 0.8393 (tpp80) REVERT: D 281 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8977 (ptpp) REVERT: D 288 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8480 (tt0) REVERT: D 395 GLU cc_start: 0.8877 (tp30) cc_final: 0.8460 (tp30) REVERT: E 55 LYS cc_start: 0.8912 (mtmm) cc_final: 0.8630 (pttm) REVERT: E 102 TYR cc_start: 0.7059 (p90) cc_final: 0.6783 (p90) REVERT: F 115 GLN cc_start: 0.9027 (pp30) cc_final: 0.8817 (pp30) REVERT: F 136 GLN cc_start: 0.8737 (pt0) cc_final: 0.8158 (pm20) REVERT: G 55 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8829 (mppt) REVERT: H 83 ARG cc_start: 0.9062 (ttm170) cc_final: 0.8722 (ttm-80) REVERT: H 217 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.7103 (t80) REVERT: H 222 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7468 (tm) REVERT: I 218 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8277 (mtp85) REVERT: I 228 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8502 (pp30) REVERT: I 270 ASP cc_start: 0.9286 (p0) cc_final: 0.9065 (p0) REVERT: J 136 HIS cc_start: 0.8832 (p90) cc_final: 0.8596 (p90) REVERT: J 226 ARG cc_start: 0.8904 (ttm170) cc_final: 0.8580 (ttm170) REVERT: J 241 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.9199 (ttpp) REVERT: J 270 ASP cc_start: 0.9435 (OUTLIER) cc_final: 0.9150 (p0) REVERT: J 272 MET cc_start: 0.8880 (mmm) cc_final: 0.8480 (tpp) REVERT: K 218 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8391 (mtp85) REVERT: K 228 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8046 (tm-30) REVERT: L 270 ASP cc_start: 0.9311 (p0) cc_final: 0.9108 (p0) REVERT: M 165 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8246 (tm-30) REVERT: M 169 LYS cc_start: 0.9439 (OUTLIER) cc_final: 0.9056 (ttmm) REVERT: M 211 ASP cc_start: 0.9052 (m-30) cc_final: 0.8676 (m-30) REVERT: O 270 ASP cc_start: 0.9356 (OUTLIER) cc_final: 0.8960 (p0) REVERT: P 165 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8834 (tm-30) REVERT: P 166 GLU cc_start: 0.9352 (mm-30) cc_final: 0.8583 (tp30) REVERT: P 169 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.8942 (tmmm) REVERT: P 269 ASP cc_start: 0.8815 (m-30) cc_final: 0.8550 (m-30) REVERT: P 270 ASP cc_start: 0.9357 (OUTLIER) cc_final: 0.8967 (p0) outliers start: 200 outliers final: 78 residues processed: 546 average time/residue: 1.4667 time to fit residues: 981.3320 Evaluate side-chains 480 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 380 time to evaluate : 4.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain B residue -55 THR Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain C residue -67 ASP Chi-restraints excluded: chain C residue -10 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 73 ASN Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain G residue 55 LYS Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 217 PHE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 228 GLN Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 241 LYS Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 146 ASP Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 218 ARG Chi-restraints excluded: chain K residue 228 GLN Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain L residue 141 ASN Chi-restraints excluded: chain L residue 194 LEU Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain L residue 212 LEU Chi-restraints excluded: chain L residue 216 TYR Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 279 LEU Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain O residue 248 ILE Chi-restraints excluded: chain O residue 270 ASP Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 208 TYR Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain P residue 270 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 376 optimal weight: 3.9990 chunk 256 optimal weight: 0.3980 chunk 6 optimal weight: 4.9990 chunk 336 optimal weight: 10.0000 chunk 186 optimal weight: 50.0000 chunk 386 optimal weight: 6.9990 chunk 312 optimal weight: 0.0670 chunk 0 optimal weight: 60.0000 chunk 230 optimal weight: 5.9990 chunk 406 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 overall best weight: 3.0924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 305 GLN ** E 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 GLN ** M 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 39544 Z= 0.327 Angle : 0.580 10.085 53104 Z= 0.295 Chirality : 0.043 0.281 5848 Planarity : 0.003 0.053 6764 Dihedral : 4.654 52.897 5171 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.84 % Favored : 97.08 % Rotamer: Outliers : 4.50 % Allowed : 26.43 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.13), residues: 4656 helix: 1.88 (0.12), residues: 2080 sheet: 0.65 (0.20), residues: 688 loop : -0.22 (0.15), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 199 HIS 0.007 0.001 HIS L 151 PHE 0.013 0.001 PHE C 315 TYR 0.024 0.001 TYR I 161 ARG 0.010 0.000 ARG K 226 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 393 time to evaluate : 4.860 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: A 15 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8604 (tt0) REVERT: A 170 TYR cc_start: 0.8119 (t80) cc_final: 0.7707 (t80) REVERT: A 281 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.9044 (ptpt) REVERT: A 288 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8489 (tt0) REVERT: B 30 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.9006 (tpp) REVERT: B 157 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9163 (pp) REVERT: B 288 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8388 (tt0) REVERT: B 395 GLU cc_start: 0.8792 (tp30) cc_final: 0.8531 (tp30) REVERT: C 157 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9009 (pp) REVERT: C 221 LYS cc_start: 0.9185 (tppt) cc_final: 0.8957 (mppt) REVERT: C 247 LYS cc_start: 0.8480 (tppp) cc_final: 0.8217 (tptp) REVERT: C 281 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.9029 (ptpt) REVERT: C 288 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8533 (tt0) REVERT: C 397 GLU cc_start: 0.8601 (pm20) cc_final: 0.8351 (pm20) REVERT: C 452 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7482 (mtp180) REVERT: D 15 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8604 (tt0) REVERT: D 173 GLU cc_start: 0.8730 (pp20) cc_final: 0.8519 (pp20) REVERT: D 206 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8733 (mtmm) REVERT: D 288 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8547 (tt0) REVERT: D 395 GLU cc_start: 0.8884 (tp30) cc_final: 0.8485 (tp30) REVERT: E 55 LYS cc_start: 0.8897 (mtmm) cc_final: 0.8634 (pttm) REVERT: F 136 GLN cc_start: 0.8721 (pt0) cc_final: 0.8121 (pm20) REVERT: G 55 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8752 (mppt) REVERT: H 83 ARG cc_start: 0.9058 (ttm170) cc_final: 0.8847 (ttm170) REVERT: H 217 PHE cc_start: 0.7375 (OUTLIER) cc_final: 0.7073 (t80) REVERT: I 222 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8445 (ptmm) REVERT: I 228 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8463 (pp30) REVERT: I 270 ASP cc_start: 0.9310 (p0) cc_final: 0.9085 (p0) REVERT: J 136 HIS cc_start: 0.8871 (p90) cc_final: 0.8622 (p90) REVERT: J 226 ARG cc_start: 0.8905 (ttm170) cc_final: 0.8525 (ttm170) REVERT: J 241 LYS cc_start: 0.9467 (OUTLIER) cc_final: 0.9216 (ttpp) REVERT: J 270 ASP cc_start: 0.9449 (OUTLIER) cc_final: 0.9165 (p0) REVERT: K 164 GLN cc_start: 0.9235 (tp-100) cc_final: 0.8695 (tp-100) REVERT: K 218 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8346 (mtp85) REVERT: K 228 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8060 (tm-30) REVERT: M 165 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8379 (tm-30) REVERT: M 169 LYS cc_start: 0.9436 (OUTLIER) cc_final: 0.9059 (ttmm) REVERT: O 270 ASP cc_start: 0.9360 (OUTLIER) cc_final: 0.8935 (p0) REVERT: P 165 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8850 (tm-30) REVERT: P 166 GLU cc_start: 0.9348 (mm-30) cc_final: 0.8587 (tp30) REVERT: P 169 LYS cc_start: 0.9430 (OUTLIER) cc_final: 0.8922 (tmmm) REVERT: P 269 ASP cc_start: 0.8935 (m-30) cc_final: 0.8662 (m-30) REVERT: P 270 ASP cc_start: 0.9383 (OUTLIER) cc_final: 0.9021 (p0) outliers start: 195 outliers final: 91 residues processed: 543 average time/residue: 1.4885 time to fit residues: 987.4623 Evaluate side-chains 493 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 377 time to evaluate : 4.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue -55 THR Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue -10 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 73 ASN Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 359 GLU Chi-restraints excluded: chain G residue 55 LYS Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 217 PHE Chi-restraints excluded: chain H residue 323 ASN Chi-restraints excluded: chain H residue 343 ASP Chi-restraints excluded: chain I residue 191 ASP Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 222 LYS Chi-restraints excluded: chain I residue 228 GLN Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 241 LYS Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 146 ASP Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 218 ARG Chi-restraints excluded: chain K residue 228 GLN Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 194 LEU Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain L residue 212 LEU Chi-restraints excluded: chain L residue 216 TYR Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 248 ILE Chi-restraints excluded: chain O residue 258 GLU Chi-restraints excluded: chain O residue 270 ASP Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 208 TYR Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain P residue 212 LEU Chi-restraints excluded: chain P residue 270 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 152 optimal weight: 3.9990 chunk 407 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 452 optimal weight: 0.8980 chunk 375 optimal weight: 4.9990 chunk 209 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 237 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 GLN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 HIS I 141 ASN ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 GLN ** M 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 164 GLN ** P 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 39544 Z= 0.250 Angle : 0.580 8.946 53104 Z= 0.293 Chirality : 0.042 0.255 5848 Planarity : 0.003 0.051 6764 Dihedral : 4.523 53.074 5161 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.94 % Favored : 96.97 % Rotamer: Outliers : 4.27 % Allowed : 26.62 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.13), residues: 4656 helix: 1.89 (0.11), residues: 2108 sheet: 0.62 (0.20), residues: 688 loop : -0.20 (0.15), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 199 HIS 0.004 0.001 HIS K 174 PHE 0.011 0.001 PHE D 315 TYR 0.026 0.001 TYR M 203 ARG 0.012 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 403 time to evaluate : 6.508 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: A 15 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8589 (tt0) REVERT: A 281 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8995 (ptpt) REVERT: A 288 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8442 (tt0) REVERT: B 157 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9143 (pp) REVERT: B 288 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: B 395 GLU cc_start: 0.8796 (tp30) cc_final: 0.8259 (tp30) REVERT: C 221 LYS cc_start: 0.9179 (tppt) cc_final: 0.8956 (mppt) REVERT: C 247 LYS cc_start: 0.8482 (tppp) cc_final: 0.8217 (tptp) REVERT: C 266 SER cc_start: 0.9318 (OUTLIER) cc_final: 0.9063 (p) REVERT: C 281 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.9018 (ptpt) REVERT: C 288 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8508 (tt0) REVERT: C 395 GLU cc_start: 0.8919 (tp30) cc_final: 0.8505 (tp30) REVERT: C 397 GLU cc_start: 0.8549 (pm20) cc_final: 0.8311 (pm20) REVERT: C 452 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7527 (mtp180) REVERT: D 15 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8591 (tt0) REVERT: D 173 GLU cc_start: 0.8724 (pp20) cc_final: 0.8505 (pp20) REVERT: D 206 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8738 (mtmm) REVERT: D 288 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8477 (tt0) REVERT: D 395 GLU cc_start: 0.8879 (tp30) cc_final: 0.8490 (tp30) REVERT: F 136 GLN cc_start: 0.8720 (pt0) cc_final: 0.8119 (pm20) REVERT: G 8 LYS cc_start: 0.8874 (mtmm) cc_final: 0.8635 (mttt) REVERT: H 83 ARG cc_start: 0.9061 (ttm170) cc_final: 0.8837 (ttm170) REVERT: H 217 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.7010 (t80) REVERT: H 222 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7272 (tm) REVERT: I 222 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8503 (ptmm) REVERT: I 228 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8461 (pp30) REVERT: I 270 ASP cc_start: 0.9292 (p0) cc_final: 0.9074 (p0) REVERT: J 136 HIS cc_start: 0.8874 (p90) cc_final: 0.8617 (p90) REVERT: J 226 ARG cc_start: 0.8867 (ttm170) cc_final: 0.8460 (ttm170) REVERT: J 241 LYS cc_start: 0.9448 (OUTLIER) cc_final: 0.9199 (ttpp) REVERT: J 270 ASP cc_start: 0.9444 (OUTLIER) cc_final: 0.9153 (p0) REVERT: K 218 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8342 (mtp85) REVERT: M 165 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8332 (tm-30) REVERT: M 169 LYS cc_start: 0.9429 (OUTLIER) cc_final: 0.9058 (ttmm) REVERT: N 277 GLU cc_start: 0.9177 (pp20) cc_final: 0.8627 (pp20) REVERT: O 164 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8366 (mt0) REVERT: O 270 ASP cc_start: 0.9365 (OUTLIER) cc_final: 0.8945 (p0) REVERT: P 165 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8832 (tm-30) REVERT: P 166 GLU cc_start: 0.9328 (mm-30) cc_final: 0.8577 (tp30) REVERT: P 169 LYS cc_start: 0.9417 (OUTLIER) cc_final: 0.8932 (tmmm) REVERT: P 269 ASP cc_start: 0.8949 (m-30) cc_final: 0.8675 (m-30) REVERT: P 270 ASP cc_start: 0.9376 (p0) cc_final: 0.9011 (p0) outliers start: 185 outliers final: 97 residues processed: 539 average time/residue: 1.5305 time to fit residues: 1014.7275 Evaluate side-chains 506 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 386 time to evaluate : 4.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue -55 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain C residue -67 ASP Chi-restraints excluded: chain C residue -10 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue -10 THR Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 73 ASN Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 359 GLU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 171 MET Chi-restraints excluded: chain G residue 221 HIS Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 217 PHE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 343 ASP Chi-restraints excluded: chain I residue 141 ASN Chi-restraints excluded: chain I residue 191 ASP Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 215 MET Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 222 LYS Chi-restraints excluded: chain I residue 228 GLN Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 241 LYS Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 218 ARG Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain L residue 141 ASN Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 164 GLN Chi-restraints excluded: chain L residue 194 LEU Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain L residue 212 LEU Chi-restraints excluded: chain L residue 216 TYR Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 279 LEU Chi-restraints excluded: chain N residue 163 SER Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 279 LEU Chi-restraints excluded: chain O residue 164 GLN Chi-restraints excluded: chain O residue 248 ILE Chi-restraints excluded: chain O residue 270 ASP Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 208 TYR Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain P residue 212 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 436 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 257 optimal weight: 10.0000 chunk 330 optimal weight: 30.0000 chunk 256 optimal weight: 2.9990 chunk 381 optimal weight: 9.9990 chunk 252 optimal weight: 10.0000 chunk 451 optimal weight: 6.9990 chunk 282 optimal weight: 10.0000 chunk 275 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 174 HIS J 244 GLN L 164 GLN ** M 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 164 GLN ** P 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 39544 Z= 0.336 Angle : 0.604 10.434 53104 Z= 0.305 Chirality : 0.043 0.274 5848 Planarity : 0.003 0.057 6764 Dihedral : 4.566 54.537 5161 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.77 % Favored : 97.14 % Rotamer: Outliers : 4.11 % Allowed : 26.94 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.13), residues: 4656 helix: 1.85 (0.11), residues: 2108 sheet: 0.59 (0.20), residues: 688 loop : -0.21 (0.15), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 199 HIS 0.004 0.001 HIS K 174 PHE 0.014 0.001 PHE I 138 TYR 0.029 0.001 TYR I 161 ARG 0.012 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 398 time to evaluate : 4.820 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 15 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8594 (tt0) REVERT: B 157 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9175 (pp) REVERT: B 288 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8368 (tt0) REVERT: B 395 GLU cc_start: 0.8783 (tp30) cc_final: 0.8503 (tp30) REVERT: C 15 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8568 (tt0) REVERT: C 221 LYS cc_start: 0.9168 (tppt) cc_final: 0.8909 (mppt) REVERT: C 266 SER cc_start: 0.9336 (OUTLIER) cc_final: 0.9068 (p) REVERT: C 288 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8528 (tt0) REVERT: C 395 GLU cc_start: 0.8917 (tp30) cc_final: 0.8498 (tp30) REVERT: C 397 GLU cc_start: 0.8578 (pm20) cc_final: 0.8327 (pm20) REVERT: C 452 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7500 (mtp180) REVERT: C 463 ASP cc_start: 0.9001 (p0) cc_final: 0.8796 (p0) REVERT: D 15 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8601 (tt0) REVERT: D 206 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8752 (mtmm) REVERT: D 288 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8512 (tt0) REVERT: D 395 GLU cc_start: 0.8884 (tp30) cc_final: 0.8501 (tp30) REVERT: E 111 ASP cc_start: 0.8831 (t0) cc_final: 0.8150 (p0) REVERT: F 115 GLN cc_start: 0.9034 (pp30) cc_final: 0.8775 (pp30) REVERT: F 136 GLN cc_start: 0.8709 (pt0) cc_final: 0.8114 (pm20) REVERT: F 359 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7022 (pp20) REVERT: G 8 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8717 (mttt) REVERT: H 83 ARG cc_start: 0.9059 (ttm170) cc_final: 0.8834 (ttm170) REVERT: H 181 GLN cc_start: 0.9051 (tm-30) cc_final: 0.8535 (tm-30) REVERT: H 217 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.7040 (t80) REVERT: H 222 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7161 (tm) REVERT: I 222 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8546 (ptmm) REVERT: I 228 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8454 (pp30) REVERT: I 270 ASP cc_start: 0.9295 (p0) cc_final: 0.9082 (p0) REVERT: J 136 HIS cc_start: 0.8867 (p90) cc_final: 0.8594 (p90) REVERT: J 141 ASN cc_start: 0.9434 (OUTLIER) cc_final: 0.9137 (p0) REVERT: J 228 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7683 (pp30) REVERT: J 241 LYS cc_start: 0.9465 (OUTLIER) cc_final: 0.9212 (ttpp) REVERT: J 270 ASP cc_start: 0.9442 (OUTLIER) cc_final: 0.9161 (p0) REVERT: K 164 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.8782 (tp-100) REVERT: K 218 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8343 (mtp85) REVERT: L 164 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8416 (mm-40) REVERT: L 270 ASP cc_start: 0.9370 (p0) cc_final: 0.9162 (p0) REVERT: M 165 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8317 (tm-30) REVERT: M 169 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9038 (ttmm) REVERT: M 236 TYR cc_start: 0.9016 (t80) cc_final: 0.8771 (t80) REVERT: N 201 GLU cc_start: 0.8797 (tp30) cc_final: 0.8377 (mm-30) REVERT: N 202 LEU cc_start: 0.8813 (mm) cc_final: 0.8574 (tp) REVERT: N 203 TYR cc_start: 0.8909 (p90) cc_final: 0.8320 (p90) REVERT: N 207 GLU cc_start: 0.8471 (tt0) cc_final: 0.8234 (tp30) REVERT: N 277 GLU cc_start: 0.9189 (pp20) cc_final: 0.8632 (pp20) REVERT: O 270 ASP cc_start: 0.9366 (OUTLIER) cc_final: 0.8937 (p0) REVERT: P 165 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8476 (tm-30) REVERT: P 166 GLU cc_start: 0.9339 (mm-30) cc_final: 0.8846 (tp30) REVERT: P 169 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.9036 (ttmm) REVERT: P 269 ASP cc_start: 0.8996 (m-30) cc_final: 0.8727 (m-30) REVERT: P 270 ASP cc_start: 0.9399 (OUTLIER) cc_final: 0.9033 (p0) outliers start: 178 outliers final: 106 residues processed: 528 average time/residue: 1.4773 time to fit residues: 951.5911 Evaluate side-chains 513 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 381 time to evaluate : 4.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue -55 THR Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue -67 ASP Chi-restraints excluded: chain C residue -10 THR Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue -10 THR Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 73 ASN Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 359 GLU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 171 MET Chi-restraints excluded: chain G residue 221 HIS Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 217 PHE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 343 ASP Chi-restraints excluded: chain I residue 141 ASN Chi-restraints excluded: chain I residue 162 LEU Chi-restraints excluded: chain I residue 191 ASP Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 215 MET Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 222 LYS Chi-restraints excluded: chain I residue 228 GLN Chi-restraints excluded: chain J residue 141 ASN Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 228 GLN Chi-restraints excluded: chain J residue 241 LYS Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 164 GLN Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 218 ARG Chi-restraints excluded: chain K residue 228 GLN Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain L residue 141 ASN Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 164 GLN Chi-restraints excluded: chain L residue 194 LEU Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain L residue 212 LEU Chi-restraints excluded: chain L residue 216 TYR Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 279 LEU Chi-restraints excluded: chain N residue 163 SER Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 279 LEU Chi-restraints excluded: chain O residue 162 LEU Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 248 ILE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 258 GLU Chi-restraints excluded: chain O residue 270 ASP Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 208 TYR Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain P residue 212 LEU Chi-restraints excluded: chain P residue 270 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 279 optimal weight: 8.9990 chunk 180 optimal weight: 2.9990 chunk 269 optimal weight: 8.9990 chunk 135 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 286 optimal weight: 6.9990 chunk 307 optimal weight: 6.9990 chunk 223 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 354 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN B 305 GLN ** E 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN F 181 GLN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 GLN ** M 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 164 GLN ** P 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 39544 Z= 0.174 Angle : 0.595 11.561 53104 Z= 0.297 Chirality : 0.042 0.287 5848 Planarity : 0.003 0.060 6764 Dihedral : 4.511 57.699 5161 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.64 % Favored : 97.27 % Rotamer: Outliers : 3.44 % Allowed : 27.95 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.13), residues: 4656 helix: 1.88 (0.11), residues: 2116 sheet: 0.59 (0.20), residues: 688 loop : -0.15 (0.15), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 199 HIS 0.005 0.001 HIS K 174 PHE 0.013 0.001 PHE L 227 TYR 0.029 0.001 TYR O 168 ARG 0.013 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 401 time to evaluate : 4.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8397 (tt0) REVERT: A 397 GLU cc_start: 0.8500 (pm20) cc_final: 0.8229 (pm20) REVERT: B 288 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: B 395 GLU cc_start: 0.8782 (tp30) cc_final: 0.8262 (tp30) REVERT: C 15 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8540 (tt0) REVERT: C 206 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8674 (mtmm) REVERT: C 221 LYS cc_start: 0.9157 (tppt) cc_final: 0.8907 (mppt) REVERT: C 247 LYS cc_start: 0.8558 (tppp) cc_final: 0.8286 (tptp) REVERT: C 266 SER cc_start: 0.9267 (OUTLIER) cc_final: 0.8997 (p) REVERT: C 395 GLU cc_start: 0.8895 (tp30) cc_final: 0.8469 (tp30) REVERT: C 397 GLU cc_start: 0.8532 (pm20) cc_final: 0.8279 (pm20) REVERT: C 452 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7568 (mtp180) REVERT: C 463 ASP cc_start: 0.9026 (p0) cc_final: 0.8797 (p0) REVERT: D 206 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8640 (mtmm) REVERT: D 288 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8409 (tt0) REVERT: D 395 GLU cc_start: 0.8866 (tp30) cc_final: 0.8482 (tp30) REVERT: D 452 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7502 (mtp180) REVERT: E 102 TYR cc_start: 0.7175 (p90) cc_final: 0.6921 (p90) REVERT: E 111 ASP cc_start: 0.8805 (t0) cc_final: 0.8143 (p0) REVERT: F 58 GLU cc_start: 0.9194 (tm-30) cc_final: 0.8975 (tm-30) REVERT: F 60 ARG cc_start: 0.8417 (mtp180) cc_final: 0.8142 (mtp180) REVERT: F 115 GLN cc_start: 0.9017 (pp30) cc_final: 0.8755 (pp30) REVERT: F 136 GLN cc_start: 0.8704 (pt0) cc_final: 0.8099 (pm20) REVERT: F 359 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6999 (pp20) REVERT: G 8 LYS cc_start: 0.8957 (mtmm) cc_final: 0.8685 (mttt) REVERT: G 58 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8934 (tm-30) REVERT: H 83 ARG cc_start: 0.9071 (ttm170) cc_final: 0.8836 (ttm170) REVERT: H 181 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8523 (tm-30) REVERT: H 217 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.7044 (t80) REVERT: H 222 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7119 (tm) REVERT: I 222 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8511 (ptmm) REVERT: I 228 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8473 (pp30) REVERT: I 270 ASP cc_start: 0.9281 (p0) cc_final: 0.9054 (p0) REVERT: J 136 HIS cc_start: 0.8865 (p90) cc_final: 0.8635 (p90) REVERT: J 141 ASN cc_start: 0.9451 (OUTLIER) cc_final: 0.9146 (p0) REVERT: J 241 LYS cc_start: 0.9440 (OUTLIER) cc_final: 0.9191 (ttpp) REVERT: J 270 ASP cc_start: 0.9437 (OUTLIER) cc_final: 0.9154 (p0) REVERT: K 164 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.8795 (tp-100) REVERT: K 218 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8400 (mtp85) REVERT: K 228 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7971 (tm-30) REVERT: L 164 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8454 (mm-40) REVERT: M 165 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8350 (tm-30) REVERT: M 169 LYS cc_start: 0.9435 (OUTLIER) cc_final: 0.9060 (ttmm) REVERT: N 201 GLU cc_start: 0.8796 (tp30) cc_final: 0.8369 (mm-30) REVERT: N 203 TYR cc_start: 0.8857 (p90) cc_final: 0.8347 (p90) REVERT: N 277 GLU cc_start: 0.9189 (pp20) cc_final: 0.8631 (pp20) REVERT: O 270 ASP cc_start: 0.9345 (OUTLIER) cc_final: 0.8927 (p0) REVERT: P 165 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8532 (tm-30) REVERT: P 166 GLU cc_start: 0.9322 (mm-30) cc_final: 0.8826 (tp30) REVERT: P 169 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.9081 (ttmm) REVERT: P 269 ASP cc_start: 0.8990 (m-30) cc_final: 0.8719 (m-30) REVERT: P 270 ASP cc_start: 0.9374 (OUTLIER) cc_final: 0.9002 (p0) outliers start: 149 outliers final: 82 residues processed: 510 average time/residue: 1.5048 time to fit residues: 937.3279 Evaluate side-chains 498 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 391 time to evaluate : 4.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue -55 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue -10 THR Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue -10 THR Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 73 ASN Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 359 GLU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 171 MET Chi-restraints excluded: chain G residue 221 HIS Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 217 PHE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 343 ASP Chi-restraints excluded: chain I residue 162 LEU Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 222 LYS Chi-restraints excluded: chain I residue 228 GLN Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain J residue 141 ASN Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 241 LYS Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 164 GLN Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 218 ARG Chi-restraints excluded: chain K residue 228 GLN Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain L residue 141 ASN Chi-restraints excluded: chain L residue 164 GLN Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain L residue 212 LEU Chi-restraints excluded: chain L residue 216 TYR Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 279 LEU Chi-restraints excluded: chain N residue 164 GLN Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 279 LEU Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 270 ASP Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 208 TYR Chi-restraints excluded: chain P residue 212 LEU Chi-restraints excluded: chain P residue 270 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 410 optimal weight: 10.0000 chunk 432 optimal weight: 10.0000 chunk 394 optimal weight: 0.0040 chunk 420 optimal weight: 7.9990 chunk 253 optimal weight: 0.0050 chunk 183 optimal weight: 6.9990 chunk 330 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 chunk 379 optimal weight: 10.0000 chunk 397 optimal weight: 9.9990 chunk 418 optimal weight: 6.9990 overall best weight: 4.0012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 GLN ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 GLN ** M 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 39544 Z= 0.408 Angle : 0.643 11.456 53104 Z= 0.323 Chirality : 0.044 0.261 5848 Planarity : 0.003 0.070 6764 Dihedral : 4.545 56.451 5159 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.84 % Favored : 97.06 % Rotamer: Outliers : 3.55 % Allowed : 27.79 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.13), residues: 4656 helix: 1.82 (0.11), residues: 2116 sheet: 0.52 (0.20), residues: 692 loop : -0.19 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 199 HIS 0.005 0.001 HIS K 174 PHE 0.014 0.001 PHE C 315 TYR 0.027 0.001 TYR O 168 ARG 0.014 0.001 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 384 time to evaluate : 4.923 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: A 288 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8494 (tt0) REVERT: B 288 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8378 (tt0) REVERT: B 395 GLU cc_start: 0.8832 (tp30) cc_final: 0.8559 (tp30) REVERT: C 15 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8564 (tt0) REVERT: C 206 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8702 (mtmm) REVERT: C 221 LYS cc_start: 0.9168 (tppt) cc_final: 0.8896 (mppt) REVERT: C 247 LYS cc_start: 0.8549 (tppp) cc_final: 0.8262 (tptp) REVERT: C 288 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8580 (tt0) REVERT: C 395 GLU cc_start: 0.8923 (tp30) cc_final: 0.8495 (tp30) REVERT: C 397 GLU cc_start: 0.8576 (pm20) cc_final: 0.8306 (pm20) REVERT: C 452 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7527 (mtp180) REVERT: C 463 ASP cc_start: 0.9020 (p0) cc_final: 0.8782 (p0) REVERT: D 206 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8750 (mtmm) REVERT: D 288 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8541 (tt0) REVERT: D 395 GLU cc_start: 0.8881 (tp30) cc_final: 0.8498 (tp30) REVERT: E 102 TYR cc_start: 0.7163 (p90) cc_final: 0.6897 (p90) REVERT: E 111 ASP cc_start: 0.8865 (t0) cc_final: 0.8175 (p0) REVERT: F 58 GLU cc_start: 0.9202 (tm-30) cc_final: 0.8982 (tm-30) REVERT: F 60 ARG cc_start: 0.8451 (mtp180) cc_final: 0.8232 (mtp180) REVERT: F 115 GLN cc_start: 0.9026 (pp30) cc_final: 0.8773 (pp30) REVERT: F 136 GLN cc_start: 0.8686 (pt0) cc_final: 0.8097 (pm20) REVERT: F 222 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8022 (tm) REVERT: G 8 LYS cc_start: 0.8959 (mtmm) cc_final: 0.8722 (mttt) REVERT: G 58 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8958 (tm-30) REVERT: H 181 GLN cc_start: 0.9054 (tm-30) cc_final: 0.8521 (tm-30) REVERT: H 217 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.7018 (t80) REVERT: H 222 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7179 (tm) REVERT: I 222 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8672 (ptmm) REVERT: I 228 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8270 (tm130) REVERT: I 270 ASP cc_start: 0.9308 (p0) cc_final: 0.9095 (p0) REVERT: J 136 HIS cc_start: 0.8895 (p90) cc_final: 0.8666 (p90) REVERT: J 141 ASN cc_start: 0.9413 (OUTLIER) cc_final: 0.9110 (p0) REVERT: J 241 LYS cc_start: 0.9468 (OUTLIER) cc_final: 0.9217 (ttpp) REVERT: J 270 ASP cc_start: 0.9435 (OUTLIER) cc_final: 0.9157 (p0) REVERT: K 164 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.8801 (tp-100) REVERT: K 218 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8361 (mtp85) REVERT: L 164 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.8569 (mm-40) REVERT: L 228 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8330 (pp30) REVERT: M 165 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8312 (tm-30) REVERT: M 169 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9026 (ttmm) REVERT: N 201 GLU cc_start: 0.8729 (tp30) cc_final: 0.8501 (tm-30) REVERT: N 277 GLU cc_start: 0.9185 (pp20) cc_final: 0.8605 (pp20) REVERT: O 270 ASP cc_start: 0.9351 (OUTLIER) cc_final: 0.8936 (p0) REVERT: P 165 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8479 (tm-30) REVERT: P 166 GLU cc_start: 0.9330 (mm-30) cc_final: 0.8840 (tp30) REVERT: P 169 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.9040 (ttmm) REVERT: P 269 ASP cc_start: 0.9058 (m-30) cc_final: 0.8781 (m-30) REVERT: P 270 ASP cc_start: 0.9396 (OUTLIER) cc_final: 0.9036 (p0) outliers start: 154 outliers final: 96 residues processed: 496 average time/residue: 1.4976 time to fit residues: 907.9486 Evaluate side-chains 490 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 370 time to evaluate : 4.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue -55 THR Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue -10 THR Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue -10 THR Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 73 ASN Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 359 GLU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 171 MET Chi-restraints excluded: chain G residue 221 HIS Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 217 PHE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 343 ASP Chi-restraints excluded: chain I residue 141 ASN Chi-restraints excluded: chain I residue 162 LEU Chi-restraints excluded: chain I residue 191 ASP Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 222 LYS Chi-restraints excluded: chain I residue 228 GLN Chi-restraints excluded: chain J residue 141 ASN Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 241 LYS Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 164 GLN Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 218 ARG Chi-restraints excluded: chain K residue 228 GLN Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 164 GLN Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain L residue 212 LEU Chi-restraints excluded: chain L residue 216 TYR Chi-restraints excluded: chain L residue 228 GLN Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 279 LEU Chi-restraints excluded: chain N residue 163 SER Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 248 ILE Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 270 ASP Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 208 TYR Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain P residue 212 LEU Chi-restraints excluded: chain P residue 270 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 276 optimal weight: 0.0770 chunk 444 optimal weight: 6.9990 chunk 271 optimal weight: 10.0000 chunk 210 optimal weight: 3.9990 chunk 308 optimal weight: 10.0000 chunk 466 optimal weight: 8.9990 chunk 429 optimal weight: 6.9990 chunk 371 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 286 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 39544 Z= 0.277 Angle : 0.633 15.441 53104 Z= 0.315 Chirality : 0.043 0.288 5848 Planarity : 0.003 0.063 6764 Dihedral : 4.497 57.455 5158 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.81 % Favored : 97.10 % Rotamer: Outliers : 3.05 % Allowed : 28.55 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.13), residues: 4656 helix: 1.83 (0.11), residues: 2116 sheet: 0.51 (0.20), residues: 692 loop : -0.18 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 199 HIS 0.005 0.001 HIS K 174 PHE 0.012 0.001 PHE G 103 TYR 0.030 0.001 TYR M 203 ARG 0.014 0.000 ARG K 226 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 380 time to evaluate : 4.958 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: A 162 LYS cc_start: 0.9526 (tptp) cc_final: 0.9314 (tppt) REVERT: A 288 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8454 (tt0) REVERT: B 288 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: B 395 GLU cc_start: 0.8815 (tp30) cc_final: 0.8541 (tp30) REVERT: C 15 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8549 (tt0) REVERT: C 206 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8676 (mtmm) REVERT: C 221 LYS cc_start: 0.9162 (tppt) cc_final: 0.8893 (mppt) REVERT: C 266 SER cc_start: 0.9310 (OUTLIER) cc_final: 0.9020 (p) REVERT: C 395 GLU cc_start: 0.8909 (tp30) cc_final: 0.8419 (tp30) REVERT: C 397 GLU cc_start: 0.8557 (pm20) cc_final: 0.8262 (pm20) REVERT: C 452 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7508 (mtp180) REVERT: C 463 ASP cc_start: 0.9005 (p0) cc_final: 0.8748 (p0) REVERT: D 206 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8742 (mtmm) REVERT: D 288 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: D 395 GLU cc_start: 0.8873 (tp30) cc_final: 0.8491 (tp30) REVERT: E 102 TYR cc_start: 0.7167 (p90) cc_final: 0.6897 (p90) REVERT: E 111 ASP cc_start: 0.8840 (t0) cc_final: 0.8132 (p0) REVERT: F 58 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8971 (tm-30) REVERT: F 60 ARG cc_start: 0.8498 (mtp180) cc_final: 0.8275 (mtp180) REVERT: F 115 GLN cc_start: 0.9011 (pp30) cc_final: 0.8766 (pp30) REVERT: F 136 GLN cc_start: 0.8690 (pt0) cc_final: 0.8089 (pm20) REVERT: F 222 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8023 (tm) REVERT: G 8 LYS cc_start: 0.8992 (mtmm) cc_final: 0.8662 (mppt) REVERT: G 58 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8948 (tm-30) REVERT: H 83 ARG cc_start: 0.9065 (ttm170) cc_final: 0.8818 (ttm170) REVERT: H 181 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8525 (tm-30) REVERT: H 217 PHE cc_start: 0.7341 (OUTLIER) cc_final: 0.7015 (t80) REVERT: H 222 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7177 (tm) REVERT: I 222 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8699 (ptmm) REVERT: I 228 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8262 (tm130) REVERT: I 270 ASP cc_start: 0.9285 (p0) cc_final: 0.9075 (p0) REVERT: J 136 HIS cc_start: 0.8888 (p90) cc_final: 0.8660 (p90) REVERT: J 141 ASN cc_start: 0.9448 (OUTLIER) cc_final: 0.9170 (p0) REVERT: J 241 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.9197 (ttpp) REVERT: J 270 ASP cc_start: 0.9430 (OUTLIER) cc_final: 0.9153 (p0) REVERT: K 164 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.8798 (tp-100) REVERT: K 218 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8422 (mtp85) REVERT: L 161 TYR cc_start: 0.9072 (p90) cc_final: 0.8800 (p90) REVERT: L 164 GLN cc_start: 0.9253 (tp40) cc_final: 0.8422 (mm-40) REVERT: L 228 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8264 (pp30) REVERT: M 165 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8353 (tm-30) REVERT: M 169 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.9083 (ttmm) REVERT: N 201 GLU cc_start: 0.8729 (tp30) cc_final: 0.8357 (tm-30) REVERT: N 277 GLU cc_start: 0.9183 (pp20) cc_final: 0.8643 (pp20) REVERT: O 270 ASP cc_start: 0.9354 (OUTLIER) cc_final: 0.8937 (p0) REVERT: P 165 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8456 (tm-30) REVERT: P 166 GLU cc_start: 0.9327 (mm-30) cc_final: 0.8830 (tp30) REVERT: P 169 LYS cc_start: 0.9431 (OUTLIER) cc_final: 0.9038 (ttmm) REVERT: P 269 ASP cc_start: 0.9083 (m-30) cc_final: 0.8816 (m-30) REVERT: P 270 ASP cc_start: 0.9393 (OUTLIER) cc_final: 0.9042 (p0) outliers start: 132 outliers final: 93 residues processed: 476 average time/residue: 1.5098 time to fit residues: 877.4688 Evaluate side-chains 491 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 375 time to evaluate : 4.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue -55 THR Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue -10 THR Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue -10 THR Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 73 ASN Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 359 GLU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 171 MET Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 217 PHE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 343 ASP Chi-restraints excluded: chain I residue 141 ASN Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 222 LYS Chi-restraints excluded: chain I residue 228 GLN Chi-restraints excluded: chain J residue 141 ASN Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 241 LYS Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 164 GLN Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 218 ARG Chi-restraints excluded: chain K residue 228 GLN Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain L residue 212 LEU Chi-restraints excluded: chain L residue 216 TYR Chi-restraints excluded: chain L residue 228 GLN Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 279 LEU Chi-restraints excluded: chain N residue 164 GLN Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 248 ILE Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 270 ASP Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 208 TYR Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain P residue 212 LEU Chi-restraints excluded: chain P residue 270 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 294 optimal weight: 5.9990 chunk 395 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 342 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 371 optimal weight: 0.2980 chunk 155 optimal weight: 0.8980 chunk 381 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 GLN ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.121562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.073564 restraints weight = 83966.341| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.21 r_work: 0.2903 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39544 Z= 0.180 Angle : 0.614 10.931 53104 Z= 0.305 Chirality : 0.042 0.325 5848 Planarity : 0.003 0.049 6764 Dihedral : 4.424 57.487 5158 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.75 % Favored : 97.16 % Rotamer: Outliers : 2.79 % Allowed : 28.88 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.13), residues: 4656 helix: 1.92 (0.11), residues: 2116 sheet: 0.67 (0.21), residues: 632 loop : -0.21 (0.15), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 199 HIS 0.006 0.001 HIS K 174 PHE 0.011 0.001 PHE E 207 TYR 0.028 0.001 TYR O 168 ARG 0.016 0.000 ARG K 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15019.05 seconds wall clock time: 286 minutes 15.51 seconds (17175.51 seconds total)