Starting phenix.real_space_refine on Wed May 15 19:56:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuw_37862/05_2024/8wuw_37862_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuw_37862/05_2024/8wuw_37862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuw_37862/05_2024/8wuw_37862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuw_37862/05_2024/8wuw_37862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuw_37862/05_2024/8wuw_37862_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuw_37862/05_2024/8wuw_37862_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 7 8.98 5 P 42 5.49 5 Mg 14 5.21 5 S 168 5.16 5 C 40705 2.51 5 N 11172 2.21 5 O 12733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 328": "OD1" <-> "OD2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "H TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 530": "OE1" <-> "OE2" Residue "a TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 76": "OE1" <-> "OE2" Residue "a ASP 80": "OD1" <-> "OD2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B ASP 328": "OD1" <-> "OD2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B ASP 499": "OD1" <-> "OD2" Residue "I TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 441": "OD1" <-> "OD2" Residue "b TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 41": "OE1" <-> "OE2" Residue "i PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 328": "OD1" <-> "OD2" Residue "C GLU 391": "OE1" <-> "OE2" Residue "J TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 59": "OE1" <-> "OE2" Residue "J GLU 391": "OE1" <-> "OE2" Residue "J ASP 398": "OD1" <-> "OD2" Residue "J ASP 441": "OD1" <-> "OD2" Residue "J GLU 530": "OE1" <-> "OE2" Residue "c GLU 17": "OE1" <-> "OE2" Residue "c GLU 20": "OE1" <-> "OE2" Residue "c TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 10": "OE1" <-> "OE2" Residue "D PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 252": "OE1" <-> "OE2" Residue "D ASP 328": "OD1" <-> "OD2" Residue "K TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 179": "OE1" <-> "OE2" Residue "K GLU 530": "OE1" <-> "OE2" Residue "d GLU 20": "OE1" <-> "OE2" Residue "k TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 76": "OE1" <-> "OE2" Residue "E TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 252": "OE1" <-> "OE2" Residue "E GLU 391": "OE1" <-> "OE2" Residue "E ASP 499": "OD1" <-> "OD2" Residue "L TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 291": "OD1" <-> "OD2" Residue "L ASP 441": "OD1" <-> "OD2" Residue "e ASP 80": "OD1" <-> "OD2" Residue "e TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 90": "OD1" <-> "OD2" Residue "e GLU 91": "OE1" <-> "OE2" Residue "l GLU 78": "OE1" <-> "OE2" Residue "F TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 252": "OE1" <-> "OE2" Residue "F TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 328": "OD1" <-> "OD2" Residue "F GLU 386": "OE1" <-> "OE2" Residue "F GLU 391": "OE1" <-> "OE2" Residue "M TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 391": "OE1" <-> "OE2" Residue "M ASP 441": "OD1" <-> "OD2" Residue "f GLU 17": "OE1" <-> "OE2" Residue "f GLU 20": "OE1" <-> "OE2" Residue "f TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 328": "OD1" <-> "OD2" Residue "G GLU 391": "OE1" <-> "OE2" Residue "N PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 291": "OD1" <-> "OD2" Residue "N GLU 391": "OE1" <-> "OE2" Residue "N ASP 398": "OD1" <-> "OD2" Residue "N GLU 494": "OE1" <-> "OE2" Residue "N GLU 530": "OE1" <-> "OE2" Residue "g GLU 20": "OE1" <-> "OE2" Residue "g TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 89": "OE1" <-> "OE2" Residue "g ASP 90": "OD1" <-> "OD2" Residue "g GLU 91": "OE1" <-> "OE2" Residue "n PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 64841 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "H" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "a" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "h" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 545 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Chain: "B" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "I" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "b" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "i" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 545 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Chain: "C" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "J" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "c" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "j" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 545 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Chain: "D" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "K" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "d" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "k" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 545 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Chain: "E" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "L" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "e" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "l" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 545 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Chain: "F" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "M" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "f" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "m" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 545 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Chain: "G" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "N" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "g" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "n" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 545 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 24.50, per 1000 atoms: 0.38 Number of scatterers: 64841 At special positions: 0 Unit cell: (159.424, 160.176, 259.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 7 19.00 S 168 16.00 P 42 15.00 Mg 14 11.99 O 12733 8.00 N 11172 7.00 C 40705 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 21.18 Conformation dependent library (CDL) restraints added in 8.7 seconds 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15582 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 290 helices and 113 sheets defined 46.5% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.12 Creating SS restraints... Processing helix chain 'A' and resid 9 through 30 removed outlier: 3.787A pdb=" N VAL A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N THR A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 removed outlier: 3.840A pdb=" N GLU A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 84 removed outlier: 3.517A pdb=" N GLU A 76 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 109 Processing helix chain 'A' and resid 113 through 134 Processing helix chain 'A' and resid 141 through 151 Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 230 through 243 Proline residue: A 235 - end of helix removed outlier: 3.653A pdb=" N ARG A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 282 through 294 removed outlier: 3.748A pdb=" N ARG A 285 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR A 288 " --> pdb=" O ARG A 285 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A 289 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN A 290 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 294 " --> pdb=" O ASP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 358 removed outlier: 3.766A pdb=" N GLN A 343 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU A 354 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU A 355 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 373 removed outlier: 3.895A pdb=" N ARG A 368 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 372 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 373 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 409 removed outlier: 3.646A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 428 removed outlier: 3.945A pdb=" N ALA A 425 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASN A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 447 Processing helix chain 'A' and resid 449 through 457 Processing helix chain 'A' and resid 462 through 475 removed outlier: 4.193A pdb=" N LYS A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 495 No H-bonds generated for 'chain 'A' and resid 492 through 495' Processing helix chain 'A' and resid 501 through 520 removed outlier: 3.767A pdb=" N THR A 520 " --> pdb=" O GLY A 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 30 removed outlier: 3.652A pdb=" N ALA H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL H 29 " --> pdb=" O ASN H 25 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 59 removed outlier: 3.530A pdb=" N GLU H 59 " --> pdb=" O THR H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 85 removed outlier: 3.697A pdb=" N GLY H 70 " --> pdb=" O TYR H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 108 Processing helix chain 'H' and resid 113 through 134 Processing helix chain 'H' and resid 141 through 151 Processing helix chain 'H' and resid 156 through 169 Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'H' and resid 230 through 243 Proline residue: H 235 - end of helix Processing helix chain 'H' and resid 256 through 268 Processing helix chain 'H' and resid 282 through 295 removed outlier: 3.876A pdb=" N ILE H 292 " --> pdb=" O LEU H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 309 No H-bonds generated for 'chain 'H' and resid 307 through 309' Processing helix chain 'H' and resid 339 through 351 removed outlier: 4.304A pdb=" N ALA H 344 " --> pdb=" O GLU H 340 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ARG H 345 " --> pdb=" O ALA H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 359 No H-bonds generated for 'chain 'H' and resid 357 through 359' Processing helix chain 'H' and resid 362 through 372 removed outlier: 4.351A pdb=" N LYS H 371 " --> pdb=" O GLU H 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 386 through 409 removed outlier: 3.584A pdb=" N GLU H 391 " --> pdb=" O ALA H 387 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS H 392 " --> pdb=" O GLU H 388 " (cutoff:3.500A) Processing helix chain 'H' and resid 417 through 426 removed outlier: 4.163A pdb=" N ALA H 425 " --> pdb=" O ARG H 421 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU H 426 " --> pdb=" O ALA H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 434 through 447 Processing helix chain 'H' and resid 449 through 458 Processing helix chain 'H' and resid 462 through 475 removed outlier: 4.022A pdb=" N LYS H 474 " --> pdb=" O LEU H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 492 through 495 No H-bonds generated for 'chain 'H' and resid 492 through 495' Processing helix chain 'H' and resid 501 through 519 Processing helix chain 'B' and resid 9 through 30 removed outlier: 3.796A pdb=" N VAL B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N THR B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 59 removed outlier: 3.870A pdb=" N GLU B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 84 removed outlier: 3.540A pdb=" N GLU B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 109 Processing helix chain 'B' and resid 113 through 134 Processing helix chain 'B' and resid 141 through 151 Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 230 through 243 Proline residue: B 235 - end of helix removed outlier: 4.190A pdb=" N ARG B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 268 Processing helix chain 'B' and resid 282 through 294 removed outlier: 3.807A pdb=" N ARG B 285 " --> pdb=" O GLY B 282 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU B 289 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN B 290 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE B 294 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 358 removed outlier: 4.158A pdb=" N LEU B 354 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU B 355 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 373 removed outlier: 3.752A pdb=" N ARG B 368 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 372 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 373 " --> pdb=" O ALA B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 409 removed outlier: 3.665A pdb=" N GLU B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 428 removed outlier: 3.948A pdb=" N ALA B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP B 427 " --> pdb=" O SER B 423 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASN B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 447 Processing helix chain 'B' and resid 449 through 457 Processing helix chain 'B' and resid 462 through 475 removed outlier: 4.194A pdb=" N LYS B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 495 No H-bonds generated for 'chain 'B' and resid 492 through 495' Processing helix chain 'B' and resid 501 through 520 removed outlier: 3.757A pdb=" N THR B 520 " --> pdb=" O GLY B 516 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 30 removed outlier: 3.653A pdb=" N ALA I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL I 29 " --> pdb=" O ASN I 25 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N THR I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 59 removed outlier: 3.535A pdb=" N GLU I 59 " --> pdb=" O THR I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 85 removed outlier: 3.607A pdb=" N GLY I 70 " --> pdb=" O TYR I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 108 Processing helix chain 'I' and resid 113 through 134 Processing helix chain 'I' and resid 141 through 151 Processing helix chain 'I' and resid 156 through 169 Processing helix chain 'I' and resid 202 through 204 No H-bonds generated for 'chain 'I' and resid 202 through 204' Processing helix chain 'I' and resid 230 through 243 Proline residue: I 235 - end of helix Processing helix chain 'I' and resid 256 through 268 Processing helix chain 'I' and resid 282 through 295 removed outlier: 3.537A pdb=" N ASP I 287 " --> pdb=" O ARG I 284 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP I 291 " --> pdb=" O TYR I 288 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE I 292 " --> pdb=" O LEU I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 343 through 351 Processing helix chain 'I' and resid 357 through 359 No H-bonds generated for 'chain 'I' and resid 357 through 359' Processing helix chain 'I' and resid 362 through 372 removed outlier: 4.052A pdb=" N LYS I 371 " --> pdb=" O GLU I 367 " (cutoff:3.500A) Processing helix chain 'I' and resid 386 through 409 Processing helix chain 'I' and resid 417 through 426 removed outlier: 4.130A pdb=" N ALA I 425 " --> pdb=" O ARG I 421 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU I 426 " --> pdb=" O ALA I 422 " (cutoff:3.500A) Processing helix chain 'I' and resid 434 through 447 Processing helix chain 'I' and resid 449 through 458 Processing helix chain 'I' and resid 462 through 475 removed outlier: 4.009A pdb=" N LYS I 474 " --> pdb=" O LEU I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 492 through 495 No H-bonds generated for 'chain 'I' and resid 492 through 495' Processing helix chain 'I' and resid 501 through 519 Processing helix chain 'b' and resid 31 through 33 No H-bonds generated for 'chain 'b' and resid 31 through 33' Processing helix chain 'b' and resid 89 through 91 No H-bonds generated for 'chain 'b' and resid 89 through 91' Processing helix chain 'C' and resid 9 through 30 removed outlier: 3.774A pdb=" N VAL C 29 " --> pdb=" O ASN C 25 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N THR C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 59 removed outlier: 3.866A pdb=" N GLU C 59 " --> pdb=" O THR C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 84 removed outlier: 3.555A pdb=" N GLU C 76 " --> pdb=" O GLN C 72 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 109 Processing helix chain 'C' and resid 113 through 134 Processing helix chain 'C' and resid 141 through 151 Processing helix chain 'C' and resid 156 through 169 Processing helix chain 'C' and resid 230 through 243 Proline residue: C 235 - end of helix removed outlier: 3.973A pdb=" N ARG C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 268 Processing helix chain 'C' and resid 282 through 294 removed outlier: 3.698A pdb=" N ARG C 285 " --> pdb=" O GLY C 282 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR C 288 " --> pdb=" O ARG C 285 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU C 289 " --> pdb=" O LYS C 286 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN C 290 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE C 294 " --> pdb=" O ASP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 339 through 358 removed outlier: 4.402A pdb=" N LEU C 354 " --> pdb=" O LYS C 350 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU C 355 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER C 358 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 373 removed outlier: 3.854A pdb=" N ARG C 368 " --> pdb=" O LEU C 365 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU C 372 " --> pdb=" O LEU C 369 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER C 373 " --> pdb=" O ALA C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 409 removed outlier: 3.646A pdb=" N GLU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 426 removed outlier: 3.952A pdb=" N ALA C 425 " --> pdb=" O ARG C 421 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 447 Processing helix chain 'C' and resid 449 through 457 Processing helix chain 'C' and resid 462 through 475 removed outlier: 4.226A pdb=" N LYS C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 495 No H-bonds generated for 'chain 'C' and resid 492 through 495' Processing helix chain 'C' and resid 501 through 520 removed outlier: 3.775A pdb=" N THR C 520 " --> pdb=" O GLY C 516 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 30 removed outlier: 3.627A pdb=" N ALA J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL J 29 " --> pdb=" O ASN J 25 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N THR J 30 " --> pdb=" O ALA J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 59 removed outlier: 3.602A pdb=" N GLU J 59 " --> pdb=" O THR J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 85 removed outlier: 3.681A pdb=" N GLY J 70 " --> pdb=" O TYR J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 108 Processing helix chain 'J' and resid 113 through 134 Processing helix chain 'J' and resid 141 through 151 Processing helix chain 'J' and resid 156 through 169 Processing helix chain 'J' and resid 202 through 204 No H-bonds generated for 'chain 'J' and resid 202 through 204' Processing helix chain 'J' and resid 230 through 243 Proline residue: J 235 - end of helix Processing helix chain 'J' and resid 256 through 268 Processing helix chain 'J' and resid 282 through 296 removed outlier: 3.656A pdb=" N ILE J 292 " --> pdb=" O LEU J 289 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR J 296 " --> pdb=" O ALA J 293 " (cutoff:3.500A) Processing helix chain 'J' and resid 339 through 351 removed outlier: 4.408A pdb=" N ALA J 344 " --> pdb=" O GLU J 340 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ARG J 345 " --> pdb=" O ALA J 341 " (cutoff:3.500A) Processing helix chain 'J' and resid 357 through 359 No H-bonds generated for 'chain 'J' and resid 357 through 359' Processing helix chain 'J' and resid 362 through 372 removed outlier: 4.291A pdb=" N LYS J 371 " --> pdb=" O GLU J 367 " (cutoff:3.500A) Processing helix chain 'J' and resid 386 through 409 Processing helix chain 'J' and resid 417 through 426 removed outlier: 4.136A pdb=" N ALA J 425 " --> pdb=" O ARG J 421 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU J 426 " --> pdb=" O ALA J 422 " (cutoff:3.500A) Processing helix chain 'J' and resid 434 through 447 Processing helix chain 'J' and resid 449 through 458 Processing helix chain 'J' and resid 462 through 475 removed outlier: 4.027A pdb=" N LYS J 474 " --> pdb=" O LEU J 470 " (cutoff:3.500A) Processing helix chain 'J' and resid 492 through 495 No H-bonds generated for 'chain 'J' and resid 492 through 495' Processing helix chain 'J' and resid 501 through 519 Processing helix chain 'c' and resid 89 through 91 No H-bonds generated for 'chain 'c' and resid 89 through 91' Processing helix chain 'D' and resid 9 through 30 removed outlier: 3.777A pdb=" N VAL D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N THR D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 59 removed outlier: 3.850A pdb=" N GLU D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 84 removed outlier: 3.516A pdb=" N GLU D 76 " --> pdb=" O GLN D 72 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 109 Processing helix chain 'D' and resid 113 through 134 Processing helix chain 'D' and resid 141 through 151 Processing helix chain 'D' and resid 156 through 169 Processing helix chain 'D' and resid 230 through 243 Proline residue: D 235 - end of helix removed outlier: 3.580A pdb=" N ARG D 242 " --> pdb=" O GLU D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 268 Processing helix chain 'D' and resid 282 through 296 removed outlier: 3.636A pdb=" N ARG D 285 " --> pdb=" O GLY D 282 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU D 289 " --> pdb=" O LYS D 286 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN D 290 " --> pdb=" O ASP D 287 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE D 294 " --> pdb=" O ASP D 291 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU D 295 " --> pdb=" O ILE D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 358 removed outlier: 4.382A pdb=" N LEU D 354 " --> pdb=" O LYS D 350 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU D 355 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 373 removed outlier: 3.888A pdb=" N ARG D 368 " --> pdb=" O LEU D 365 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU D 372 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER D 373 " --> pdb=" O ALA D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 409 removed outlier: 3.656A pdb=" N GLU D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 428 removed outlier: 3.948A pdb=" N ALA D 425 " --> pdb=" O ARG D 421 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASP D 427 " --> pdb=" O SER D 423 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASN D 428 " --> pdb=" O GLU D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 447 Processing helix chain 'D' and resid 449 through 457 Processing helix chain 'D' and resid 462 through 475 removed outlier: 4.191A pdb=" N LYS D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 495 No H-bonds generated for 'chain 'D' and resid 492 through 495' Processing helix chain 'D' and resid 501 through 520 removed outlier: 3.806A pdb=" N THR D 520 " --> pdb=" O GLY D 516 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 30 removed outlier: 3.661A pdb=" N ALA K 26 " --> pdb=" O LYS K 22 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL K 29 " --> pdb=" O ASN K 25 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N THR K 30 " --> pdb=" O ALA K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 59 removed outlier: 3.506A pdb=" N GLU K 59 " --> pdb=" O THR K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 85 removed outlier: 3.560A pdb=" N GLY K 70 " --> pdb=" O TYR K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 108 Processing helix chain 'K' and resid 113 through 134 Processing helix chain 'K' and resid 141 through 151 Processing helix chain 'K' and resid 156 through 169 Processing helix chain 'K' and resid 202 through 204 No H-bonds generated for 'chain 'K' and resid 202 through 204' Processing helix chain 'K' and resid 230 through 243 Proline residue: K 235 - end of helix Processing helix chain 'K' and resid 256 through 268 Processing helix chain 'K' and resid 282 through 295 removed outlier: 3.520A pdb=" N ASP K 287 " --> pdb=" O ARG K 284 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 351 removed outlier: 4.590A pdb=" N ALA K 344 " --> pdb=" O GLU K 340 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ARG K 345 " --> pdb=" O ALA K 341 " (cutoff:3.500A) Processing helix chain 'K' and resid 357 through 359 No H-bonds generated for 'chain 'K' and resid 357 through 359' Processing helix chain 'K' and resid 362 through 372 removed outlier: 4.082A pdb=" N LYS K 371 " --> pdb=" O GLU K 367 " (cutoff:3.500A) Processing helix chain 'K' and resid 386 through 409 Processing helix chain 'K' and resid 417 through 426 removed outlier: 4.168A pdb=" N ALA K 425 " --> pdb=" O ARG K 421 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU K 426 " --> pdb=" O ALA K 422 " (cutoff:3.500A) Processing helix chain 'K' and resid 434 through 447 Processing helix chain 'K' and resid 449 through 458 Processing helix chain 'K' and resid 462 through 475 removed outlier: 4.016A pdb=" N LYS K 474 " --> pdb=" O LEU K 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 492 through 495 No H-bonds generated for 'chain 'K' and resid 492 through 495' Processing helix chain 'K' and resid 501 through 519 Processing helix chain 'd' and resid 89 through 91 No H-bonds generated for 'chain 'd' and resid 89 through 91' Processing helix chain 'E' and resid 9 through 30 removed outlier: 3.786A pdb=" N VAL E 29 " --> pdb=" O ASN E 25 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N THR E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 59 removed outlier: 3.880A pdb=" N GLU E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 84 removed outlier: 3.531A pdb=" N GLU E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 109 Processing helix chain 'E' and resid 113 through 134 Processing helix chain 'E' and resid 141 through 151 Processing helix chain 'E' and resid 156 through 169 Processing helix chain 'E' and resid 230 through 243 Proline residue: E 235 - end of helix removed outlier: 4.306A pdb=" N ARG E 242 " --> pdb=" O GLU E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 268 Processing helix chain 'E' and resid 283 through 294 removed outlier: 3.830A pdb=" N GLN E 290 " --> pdb=" O LYS E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 358 removed outlier: 3.574A pdb=" N GLN E 343 " --> pdb=" O LYS E 339 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU E 354 " --> pdb=" O LYS E 350 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU E 355 " --> pdb=" O ARG E 351 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER E 358 " --> pdb=" O LEU E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 373 removed outlier: 3.786A pdb=" N ARG E 368 " --> pdb=" O LEU E 365 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU E 372 " --> pdb=" O LEU E 369 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER E 373 " --> pdb=" O ALA E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 409 removed outlier: 3.669A pdb=" N GLU E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 428 removed outlier: 3.935A pdb=" N ALA E 425 " --> pdb=" O ARG E 421 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP E 427 " --> pdb=" O SER E 423 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ASN E 428 " --> pdb=" O GLU E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 447 Processing helix chain 'E' and resid 449 through 457 Processing helix chain 'E' and resid 462 through 475 removed outlier: 4.179A pdb=" N LYS E 474 " --> pdb=" O LEU E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 495 No H-bonds generated for 'chain 'E' and resid 492 through 495' Processing helix chain 'E' and resid 501 through 520 removed outlier: 3.759A pdb=" N THR E 520 " --> pdb=" O GLY E 516 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 30 removed outlier: 3.652A pdb=" N ALA L 26 " --> pdb=" O LYS L 22 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL L 29 " --> pdb=" O ASN L 25 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N THR L 30 " --> pdb=" O ALA L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 59 removed outlier: 3.601A pdb=" N GLU L 59 " --> pdb=" O THR L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 85 removed outlier: 3.678A pdb=" N GLY L 70 " --> pdb=" O TYR L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 108 Processing helix chain 'L' and resid 113 through 134 Processing helix chain 'L' and resid 141 through 151 Processing helix chain 'L' and resid 156 through 169 Processing helix chain 'L' and resid 202 through 204 No H-bonds generated for 'chain 'L' and resid 202 through 204' Processing helix chain 'L' and resid 230 through 243 Proline residue: L 235 - end of helix Processing helix chain 'L' and resid 256 through 268 Processing helix chain 'L' and resid 282 through 293 removed outlier: 3.784A pdb=" N ILE L 292 " --> pdb=" O LEU L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 343 through 351 Processing helix chain 'L' and resid 357 through 359 No H-bonds generated for 'chain 'L' and resid 357 through 359' Processing helix chain 'L' and resid 362 through 372 removed outlier: 4.122A pdb=" N LYS L 371 " --> pdb=" O GLU L 367 " (cutoff:3.500A) Processing helix chain 'L' and resid 386 through 409 Processing helix chain 'L' and resid 417 through 426 removed outlier: 4.142A pdb=" N ALA L 425 " --> pdb=" O ARG L 421 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU L 426 " --> pdb=" O ALA L 422 " (cutoff:3.500A) Processing helix chain 'L' and resid 434 through 447 Processing helix chain 'L' and resid 449 through 458 Processing helix chain 'L' and resid 462 through 475 removed outlier: 4.034A pdb=" N LYS L 474 " --> pdb=" O LEU L 470 " (cutoff:3.500A) Processing helix chain 'L' and resid 492 through 495 No H-bonds generated for 'chain 'L' and resid 492 through 495' Processing helix chain 'L' and resid 501 through 519 Processing helix chain 'e' and resid 31 through 33 No H-bonds generated for 'chain 'e' and resid 31 through 33' Processing helix chain 'F' and resid 9 through 30 removed outlier: 3.793A pdb=" N VAL F 29 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N THR F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 59 removed outlier: 3.884A pdb=" N GLU F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 84 removed outlier: 3.507A pdb=" N GLU F 76 " --> pdb=" O GLN F 72 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA F 78 " --> pdb=" O VAL F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 109 Processing helix chain 'F' and resid 113 through 134 Processing helix chain 'F' and resid 141 through 151 Processing helix chain 'F' and resid 156 through 169 Processing helix chain 'F' and resid 230 through 243 Proline residue: F 235 - end of helix removed outlier: 3.702A pdb=" N ARG F 242 " --> pdb=" O GLU F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 268 Processing helix chain 'F' and resid 282 through 294 removed outlier: 3.510A pdb=" N ARG F 285 " --> pdb=" O GLY F 282 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP F 287 " --> pdb=" O ARG F 284 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR F 288 " --> pdb=" O ARG F 285 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU F 289 " --> pdb=" O LYS F 286 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN F 290 " --> pdb=" O ASP F 287 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE F 294 " --> pdb=" O ASP F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 339 through 358 removed outlier: 3.780A pdb=" N GLN F 343 " --> pdb=" O LYS F 339 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG F 351 " --> pdb=" O GLU F 347 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU F 354 " --> pdb=" O LYS F 350 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU F 355 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER F 358 " --> pdb=" O LEU F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 371 removed outlier: 3.737A pdb=" N ARG F 368 " --> pdb=" O LEU F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 409 removed outlier: 3.628A pdb=" N GLU F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 426 removed outlier: 3.951A pdb=" N ALA F 425 " --> pdb=" O ARG F 421 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 447 Processing helix chain 'F' and resid 449 through 457 Processing helix chain 'F' and resid 462 through 475 removed outlier: 4.230A pdb=" N LYS F 474 " --> pdb=" O LEU F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 495 No H-bonds generated for 'chain 'F' and resid 492 through 495' Processing helix chain 'F' and resid 501 through 520 removed outlier: 3.772A pdb=" N THR F 520 " --> pdb=" O GLY F 516 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 30 removed outlier: 3.676A pdb=" N ALA M 26 " --> pdb=" O LYS M 22 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL M 29 " --> pdb=" O ASN M 25 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N THR M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 59 removed outlier: 3.652A pdb=" N GLU M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 85 removed outlier: 3.611A pdb=" N GLY M 70 " --> pdb=" O TYR M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 108 Processing helix chain 'M' and resid 113 through 134 Processing helix chain 'M' and resid 141 through 151 Processing helix chain 'M' and resid 156 through 169 Processing helix chain 'M' and resid 202 through 204 No H-bonds generated for 'chain 'M' and resid 202 through 204' Processing helix chain 'M' and resid 230 through 243 Proline residue: M 235 - end of helix Processing helix chain 'M' and resid 256 through 268 Processing helix chain 'M' and resid 282 through 296 removed outlier: 3.834A pdb=" N ILE M 292 " --> pdb=" O LEU M 289 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR M 296 " --> pdb=" O ALA M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 307 through 309 No H-bonds generated for 'chain 'M' and resid 307 through 309' Processing helix chain 'M' and resid 343 through 351 Processing helix chain 'M' and resid 357 through 359 No H-bonds generated for 'chain 'M' and resid 357 through 359' Processing helix chain 'M' and resid 362 through 372 removed outlier: 4.118A pdb=" N LYS M 371 " --> pdb=" O GLU M 367 " (cutoff:3.500A) Processing helix chain 'M' and resid 386 through 409 removed outlier: 3.577A pdb=" N GLU M 391 " --> pdb=" O ALA M 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 417 through 426 removed outlier: 4.152A pdb=" N ALA M 425 " --> pdb=" O ARG M 421 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU M 426 " --> pdb=" O ALA M 422 " (cutoff:3.500A) Processing helix chain 'M' and resid 434 through 447 Processing helix chain 'M' and resid 449 through 458 Processing helix chain 'M' and resid 462 through 475 removed outlier: 4.067A pdb=" N LYS M 474 " --> pdb=" O LEU M 470 " (cutoff:3.500A) Processing helix chain 'M' and resid 492 through 495 No H-bonds generated for 'chain 'M' and resid 492 through 495' Processing helix chain 'M' and resid 501 through 519 Processing helix chain 'f' and resid 89 through 91 No H-bonds generated for 'chain 'f' and resid 89 through 91' Processing helix chain 'G' and resid 9 through 30 removed outlier: 3.796A pdb=" N VAL G 29 " --> pdb=" O ASN G 25 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 59 removed outlier: 3.878A pdb=" N GLU G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 84 removed outlier: 3.513A pdb=" N GLU G 76 " --> pdb=" O GLN G 72 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA G 78 " --> pdb=" O VAL G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 109 Processing helix chain 'G' and resid 113 through 134 Processing helix chain 'G' and resid 141 through 151 Processing helix chain 'G' and resid 156 through 169 Processing helix chain 'G' and resid 230 through 243 Proline residue: G 235 - end of helix removed outlier: 4.008A pdb=" N ARG G 242 " --> pdb=" O GLU G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 268 Processing helix chain 'G' and resid 282 through 294 removed outlier: 3.849A pdb=" N ARG G 285 " --> pdb=" O GLY G 282 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU G 289 " --> pdb=" O LYS G 286 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN G 290 " --> pdb=" O ASP G 287 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE G 294 " --> pdb=" O ASP G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 358 removed outlier: 3.596A pdb=" N GLN G 343 " --> pdb=" O LYS G 339 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU G 354 " --> pdb=" O LYS G 350 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU G 355 " --> pdb=" O ARG G 351 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER G 358 " --> pdb=" O LEU G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 363 through 373 removed outlier: 3.903A pdb=" N ARG G 368 " --> pdb=" O LEU G 365 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU G 372 " --> pdb=" O LEU G 369 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER G 373 " --> pdb=" O ALA G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 409 removed outlier: 3.679A pdb=" N GLU G 391 " --> pdb=" O ALA G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 427 removed outlier: 3.952A pdb=" N ALA G 425 " --> pdb=" O ARG G 421 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU G 426 " --> pdb=" O ALA G 422 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP G 427 " --> pdb=" O SER G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 434 through 447 Processing helix chain 'G' and resid 449 through 457 Processing helix chain 'G' and resid 462 through 475 removed outlier: 4.192A pdb=" N LYS G 474 " --> pdb=" O LEU G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 492 through 495 No H-bonds generated for 'chain 'G' and resid 492 through 495' Processing helix chain 'G' and resid 501 through 520 removed outlier: 3.796A pdb=" N THR G 520 " --> pdb=" O GLY G 516 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 30 removed outlier: 3.679A pdb=" N ALA N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL N 29 " --> pdb=" O ASN N 25 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N THR N 30 " --> pdb=" O ALA N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 54 through 59 removed outlier: 3.502A pdb=" N GLU N 59 " --> pdb=" O THR N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 85 removed outlier: 3.688A pdb=" N GLY N 70 " --> pdb=" O TYR N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 108 Processing helix chain 'N' and resid 113 through 134 Processing helix chain 'N' and resid 141 through 151 Processing helix chain 'N' and resid 156 through 169 Processing helix chain 'N' and resid 202 through 204 No H-bonds generated for 'chain 'N' and resid 202 through 204' Processing helix chain 'N' and resid 230 through 243 Proline residue: N 235 - end of helix Processing helix chain 'N' and resid 256 through 268 Processing helix chain 'N' and resid 282 through 295 removed outlier: 3.644A pdb=" N ASP N 291 " --> pdb=" O TYR N 288 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE N 292 " --> pdb=" O LEU N 289 " (cutoff:3.500A) Processing helix chain 'N' and resid 341 through 351 removed outlier: 4.170A pdb=" N ALA N 344 " --> pdb=" O ALA N 341 " (cutoff:3.500A) Processing helix chain 'N' and resid 357 through 359 No H-bonds generated for 'chain 'N' and resid 357 through 359' Processing helix chain 'N' and resid 362 through 372 removed outlier: 4.089A pdb=" N LYS N 371 " --> pdb=" O GLU N 367 " (cutoff:3.500A) Processing helix chain 'N' and resid 386 through 409 Processing helix chain 'N' and resid 417 through 426 removed outlier: 4.150A pdb=" N ALA N 425 " --> pdb=" O ARG N 421 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU N 426 " --> pdb=" O ALA N 422 " (cutoff:3.500A) Processing helix chain 'N' and resid 434 through 447 Processing helix chain 'N' and resid 449 through 458 Processing helix chain 'N' and resid 462 through 475 removed outlier: 4.023A pdb=" N LYS N 474 " --> pdb=" O LEU N 470 " (cutoff:3.500A) Processing helix chain 'N' and resid 492 through 495 No H-bonds generated for 'chain 'N' and resid 492 through 495' Processing helix chain 'N' and resid 501 through 519 Processing sheet with id= A, first strand: chain 'A' and resid 4 through 8 Processing sheet with id= B, first strand: chain 'A' and resid 38 through 40 Processing sheet with id= C, first strand: chain 'A' and resid 174 through 179 removed outlier: 3.571A pdb=" N VAL A 174 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 193 through 195 removed outlier: 3.865A pdb=" N MET A 193 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 332 " --> pdb=" O MET A 193 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 219 through 222 removed outlier: 3.599A pdb=" N ALA A 251 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 411 through 413 Processing sheet with id= G, first strand: chain 'A' and resid 480 through 483 Processing sheet with id= H, first strand: chain 'H' and resid 4 through 8 Processing sheet with id= I, first strand: chain 'H' and resid 38 through 40 Processing sheet with id= J, first strand: chain 'H' and resid 175 through 178 removed outlier: 9.044A pdb=" N THR H 176 " --> pdb=" O GLY H 375 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA H 377 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N GLU H 178 " --> pdb=" O ALA H 377 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE H 379 " --> pdb=" O GLU H 178 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 193 through 195 Processing sheet with id= L, first strand: chain 'H' and resid 218 through 222 removed outlier: 6.676A pdb=" N LEU H 221 " --> pdb=" O PRO H 246 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU H 248 " --> pdb=" O LEU H 221 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 411 through 413 Processing sheet with id= N, first strand: chain 'H' and resid 480 through 483 removed outlier: 3.883A pdb=" N ASP H 488 " --> pdb=" O ASP H 483 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'a' and resid 75 through 79 removed outlier: 9.764A pdb=" N LYS a 83 " --> pdb=" O ARG a 15 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG a 15 " --> pdb=" O LYS a 83 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA a 44 " --> pdb=" O VAL a 12 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LYS a 14 " --> pdb=" O VAL a 42 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL a 42 " --> pdb=" O LYS a 14 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'a' and resid 48 through 50 Processing sheet with id= Q, first strand: chain 'h' and resid 85 through 88 removed outlier: 3.659A pdb=" N ALA h 44 " --> pdb=" O VAL h 12 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 4 through 8 Processing sheet with id= S, first strand: chain 'B' and resid 38 through 40 Processing sheet with id= T, first strand: chain 'B' and resid 174 through 179 removed outlier: 3.629A pdb=" N VAL B 174 " --> pdb=" O GLY B 375 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 193 through 195 removed outlier: 3.922A pdb=" N MET B 193 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 332 " --> pdb=" O MET B 193 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 219 through 222 removed outlier: 3.567A pdb=" N ALA B 251 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 411 through 413 Processing sheet with id= X, first strand: chain 'B' and resid 480 through 483 Processing sheet with id= Y, first strand: chain 'I' and resid 4 through 8 Processing sheet with id= Z, first strand: chain 'I' and resid 38 through 40 Processing sheet with id= AA, first strand: chain 'I' and resid 175 through 178 removed outlier: 9.155A pdb=" N THR I 176 " --> pdb=" O GLY I 375 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA I 377 " --> pdb=" O THR I 176 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLU I 178 " --> pdb=" O ALA I 377 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE I 379 " --> pdb=" O GLU I 178 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'I' and resid 218 through 222 removed outlier: 6.319A pdb=" N LEU I 221 " --> pdb=" O PRO I 246 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LEU I 248 " --> pdb=" O LEU I 221 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'I' and resid 323 through 325 Processing sheet with id= AD, first strand: chain 'I' and resid 411 through 413 Processing sheet with id= AE, first strand: chain 'I' and resid 480 through 483 removed outlier: 3.891A pdb=" N ASP I 488 " --> pdb=" O ASP I 483 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'b' and resid 75 through 79 removed outlier: 9.202A pdb=" N LYS b 83 " --> pdb=" O ARG b 15 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ARG b 15 " --> pdb=" O LYS b 83 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS b 14 " --> pdb=" O VAL b 42 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N VAL b 42 " --> pdb=" O LYS b 14 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'i' and resid 85 through 88 removed outlier: 3.569A pdb=" N ALA i 44 " --> pdb=" O VAL i 12 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 4 through 8 Processing sheet with id= AI, first strand: chain 'C' and resid 38 through 40 Processing sheet with id= AJ, first strand: chain 'C' and resid 174 through 179 removed outlier: 3.619A pdb=" N VAL C 174 " --> pdb=" O GLY C 375 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 213 through 216 Processing sheet with id= AL, first strand: chain 'C' and resid 219 through 222 removed outlier: 3.503A pdb=" N ALA C 251 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 411 through 413 Processing sheet with id= AN, first strand: chain 'C' and resid 480 through 483 Processing sheet with id= AO, first strand: chain 'J' and resid 4 through 8 Processing sheet with id= AP, first strand: chain 'J' and resid 38 through 40 Processing sheet with id= AQ, first strand: chain 'J' and resid 175 through 178 removed outlier: 8.995A pdb=" N THR J 176 " --> pdb=" O GLY J 375 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA J 377 " --> pdb=" O THR J 176 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLU J 178 " --> pdb=" O ALA J 377 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE J 379 " --> pdb=" O GLU J 178 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'J' and resid 193 through 195 Processing sheet with id= AS, first strand: chain 'J' and resid 218 through 222 removed outlier: 6.791A pdb=" N LEU J 221 " --> pdb=" O PRO J 246 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU J 248 " --> pdb=" O LEU J 221 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'J' and resid 411 through 413 Processing sheet with id= AU, first strand: chain 'J' and resid 480 through 483 removed outlier: 3.850A pdb=" N ASP J 488 " --> pdb=" O ASP J 483 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'c' and resid 75 through 79 removed outlier: 10.005A pdb=" N LYS c 83 " --> pdb=" O ARG c 15 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ARG c 15 " --> pdb=" O LYS c 83 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LYS c 14 " --> pdb=" O VAL c 42 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N VAL c 42 " --> pdb=" O LYS c 14 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'j' and resid 85 through 88 removed outlier: 3.698A pdb=" N ALA j 44 " --> pdb=" O VAL j 12 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'D' and resid 4 through 8 Processing sheet with id= AY, first strand: chain 'D' and resid 38 through 40 Processing sheet with id= AZ, first strand: chain 'D' and resid 174 through 179 removed outlier: 3.512A pdb=" N VAL D 174 " --> pdb=" O GLY D 375 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'D' and resid 213 through 216 Processing sheet with id= BB, first strand: chain 'D' and resid 219 through 222 removed outlier: 3.883A pdb=" N ALA D 251 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'D' and resid 411 through 413 Processing sheet with id= BD, first strand: chain 'D' and resid 480 through 483 Processing sheet with id= BE, first strand: chain 'K' and resid 4 through 8 Processing sheet with id= BF, first strand: chain 'K' and resid 38 through 40 Processing sheet with id= BG, first strand: chain 'K' and resid 175 through 178 removed outlier: 9.336A pdb=" N THR K 176 " --> pdb=" O GLY K 375 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA K 377 " --> pdb=" O THR K 176 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N GLU K 178 " --> pdb=" O ALA K 377 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE K 379 " --> pdb=" O GLU K 178 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'K' and resid 218 through 222 removed outlier: 7.079A pdb=" N LEU K 221 " --> pdb=" O PRO K 246 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU K 248 " --> pdb=" O LEU K 221 " (cutoff:3.500A) No H-bonds generated for sheet with id= BH Processing sheet with id= BI, first strand: chain 'K' and resid 323 through 325 Processing sheet with id= BJ, first strand: chain 'K' and resid 411 through 413 Processing sheet with id= BK, first strand: chain 'K' and resid 480 through 483 removed outlier: 3.875A pdb=" N ASP K 488 " --> pdb=" O ASP K 483 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'd' and resid 75 through 79 removed outlier: 9.854A pdb=" N LYS d 83 " --> pdb=" O ARG d 15 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ARG d 15 " --> pdb=" O LYS d 83 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA d 44 " --> pdb=" O VAL d 12 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N LYS d 14 " --> pdb=" O VAL d 42 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N VAL d 42 " --> pdb=" O LYS d 14 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'k' and resid 85 through 88 removed outlier: 3.773A pdb=" N LEU k 85 " --> pdb=" O VAL k 13 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA k 44 " --> pdb=" O VAL k 12 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'E' and resid 4 through 8 Processing sheet with id= BO, first strand: chain 'E' and resid 38 through 40 Processing sheet with id= BP, first strand: chain 'E' and resid 174 through 179 removed outlier: 3.596A pdb=" N VAL E 174 " --> pdb=" O GLY E 375 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'E' and resid 213 through 216 removed outlier: 3.519A pdb=" N VAL E 323 " --> pdb=" O LEU E 215 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'E' and resid 219 through 222 Processing sheet with id= BS, first strand: chain 'E' and resid 411 through 413 Processing sheet with id= BT, first strand: chain 'E' and resid 480 through 483 Processing sheet with id= BU, first strand: chain 'L' and resid 4 through 8 Processing sheet with id= BV, first strand: chain 'L' and resid 38 through 40 Processing sheet with id= BW, first strand: chain 'L' and resid 175 through 178 removed outlier: 9.004A pdb=" N THR L 176 " --> pdb=" O GLY L 375 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA L 377 " --> pdb=" O THR L 176 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLU L 178 " --> pdb=" O ALA L 377 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE L 379 " --> pdb=" O GLU L 178 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'L' and resid 193 through 195 removed outlier: 3.507A pdb=" N MET L 193 " --> pdb=" O ILE L 332 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LYS L 322 " --> pdb=" O VAL L 333 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'L' and resid 218 through 222 removed outlier: 6.792A pdb=" N LEU L 221 " --> pdb=" O PRO L 246 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU L 248 " --> pdb=" O LEU L 221 " (cutoff:3.500A) No H-bonds generated for sheet with id= BY Processing sheet with id= BZ, first strand: chain 'L' and resid 411 through 413 Processing sheet with id= CA, first strand: chain 'L' and resid 480 through 483 removed outlier: 3.855A pdb=" N ASP L 488 " --> pdb=" O ASP L 483 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'e' and resid 75 through 79 removed outlier: 10.025A pdb=" N LYS e 83 " --> pdb=" O ARG e 15 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ARG e 15 " --> pdb=" O LYS e 83 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA e 44 " --> pdb=" O VAL e 12 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYS e 14 " --> pdb=" O VAL e 42 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL e 42 " --> pdb=" O LYS e 14 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'l' and resid 85 through 88 removed outlier: 4.022A pdb=" N ALA l 44 " --> pdb=" O VAL l 12 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'F' and resid 4 through 8 Processing sheet with id= CE, first strand: chain 'F' and resid 38 through 40 Processing sheet with id= CF, first strand: chain 'F' and resid 174 through 179 removed outlier: 3.509A pdb=" N VAL F 174 " --> pdb=" O GLY F 375 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'F' and resid 213 through 216 Processing sheet with id= CH, first strand: chain 'F' and resid 219 through 222 removed outlier: 3.631A pdb=" N ALA F 251 " --> pdb=" O VAL F 276 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'F' and resid 411 through 413 Processing sheet with id= CJ, first strand: chain 'F' and resid 480 through 483 Processing sheet with id= CK, first strand: chain 'M' and resid 4 through 8 Processing sheet with id= CL, first strand: chain 'M' and resid 38 through 40 Processing sheet with id= CM, first strand: chain 'M' and resid 175 through 178 removed outlier: 9.053A pdb=" N THR M 176 " --> pdb=" O GLY M 375 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA M 377 " --> pdb=" O THR M 176 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N GLU M 178 " --> pdb=" O ALA M 377 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ILE M 379 " --> pdb=" O GLU M 178 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'M' and resid 193 through 195 Processing sheet with id= CO, first strand: chain 'M' and resid 218 through 222 removed outlier: 6.286A pdb=" N LEU M 221 " --> pdb=" O PRO M 246 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU M 248 " --> pdb=" O LEU M 221 " (cutoff:3.500A) No H-bonds generated for sheet with id= CO Processing sheet with id= CP, first strand: chain 'M' and resid 411 through 413 Processing sheet with id= CQ, first strand: chain 'M' and resid 480 through 483 removed outlier: 3.896A pdb=" N ASP M 488 " --> pdb=" O ASP M 483 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'f' and resid 75 through 79 removed outlier: 9.895A pdb=" N LYS f 83 " --> pdb=" O ARG f 15 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG f 15 " --> pdb=" O LYS f 83 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA f 44 " --> pdb=" O VAL f 12 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LYS f 14 " --> pdb=" O VAL f 42 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N VAL f 42 " --> pdb=" O LYS f 14 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain 'm' and resid 85 through 88 removed outlier: 3.870A pdb=" N ALA m 44 " --> pdb=" O VAL m 12 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain 'G' and resid 4 through 8 Processing sheet with id= CU, first strand: chain 'G' and resid 38 through 40 Processing sheet with id= CV, first strand: chain 'G' and resid 174 through 179 removed outlier: 3.543A pdb=" N VAL G 174 " --> pdb=" O GLY G 375 " (cutoff:3.500A) Processing sheet with id= CW, first strand: chain 'G' and resid 213 through 216 removed outlier: 3.504A pdb=" N VAL G 323 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'G' and resid 219 through 222 Processing sheet with id= CY, first strand: chain 'G' and resid 411 through 413 Processing sheet with id= CZ, first strand: chain 'G' and resid 480 through 483 Processing sheet with id= DA, first strand: chain 'N' and resid 4 through 8 Processing sheet with id= DB, first strand: chain 'N' and resid 38 through 40 Processing sheet with id= DC, first strand: chain 'N' and resid 175 through 178 removed outlier: 9.255A pdb=" N THR N 176 " --> pdb=" O GLY N 375 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA N 377 " --> pdb=" O THR N 176 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N GLU N 178 " --> pdb=" O ALA N 377 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE N 379 " --> pdb=" O GLU N 178 " (cutoff:3.500A) Processing sheet with id= DD, first strand: chain 'N' and resid 218 through 222 removed outlier: 6.995A pdb=" N LEU N 221 " --> pdb=" O PRO N 246 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU N 248 " --> pdb=" O LEU N 221 " (cutoff:3.500A) No H-bonds generated for sheet with id= DD Processing sheet with id= DE, first strand: chain 'N' and resid 323 through 325 Processing sheet with id= DF, first strand: chain 'N' and resid 411 through 413 Processing sheet with id= DG, first strand: chain 'N' and resid 480 through 483 removed outlier: 3.894A pdb=" N ASP N 488 " --> pdb=" O ASP N 483 " (cutoff:3.500A) Processing sheet with id= DH, first strand: chain 'g' and resid 75 through 79 removed outlier: 9.394A pdb=" N LYS g 83 " --> pdb=" O ARG g 15 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ARG g 15 " --> pdb=" O LYS g 83 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA g 44 " --> pdb=" O VAL g 12 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LYS g 14 " --> pdb=" O VAL g 42 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL g 42 " --> pdb=" O LYS g 14 " (cutoff:3.500A) Processing sheet with id= DI, first strand: chain 'n' and resid 85 through 88 removed outlier: 3.872A pdb=" N ALA n 44 " --> pdb=" O VAL n 12 " (cutoff:3.500A) 3132 hydrogen bonds defined for protein. 8718 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: 29.01 Time building geometry restraints manager: 23.31 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: 21897 1.34 - 1.46: 11690 1.46 - 1.58: 31492 1.58 - 1.70: 56 1.70 - 1.82: 322 Bond restraints: 65457 Sorted by residual: bond pdb=" CB LYS B 327 " pdb=" CG LYS B 327 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.76e+00 bond pdb=" CB LYS G 327 " pdb=" CG LYS G 327 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.71e+00 bond pdb=" CB LYS A 327 " pdb=" CG LYS A 327 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.65e+00 bond pdb=" CB LYS D 327 " pdb=" CG LYS D 327 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.65e+00 bond pdb=" CB LYS C 327 " pdb=" CG LYS C 327 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.65e+00 ... (remaining 65452 not shown) Histogram of bond angle deviations from ideal: 97.20 - 104.62: 889 104.62 - 112.05: 33964 112.05 - 119.47: 22705 119.47 - 126.90: 30404 126.90 - 134.32: 434 Bond angle restraints: 88396 Sorted by residual: angle pdb=" CB MET L 211 " pdb=" CG MET L 211 " pdb=" SD MET L 211 " ideal model delta sigma weight residual 112.70 129.59 -16.89 3.00e+00 1.11e-01 3.17e+01 angle pdb=" C TYR f 8 " pdb=" CA TYR f 8 " pdb=" CB TYR f 8 " ideal model delta sigma weight residual 117.23 110.11 7.12 1.36e+00 5.41e-01 2.74e+01 angle pdb=" N MET L 211 " pdb=" CA MET L 211 " pdb=" C MET L 211 " ideal model delta sigma weight residual 110.91 105.53 5.38 1.17e+00 7.31e-01 2.11e+01 angle pdb=" CB LYS G 327 " pdb=" CG LYS G 327 " pdb=" CD LYS G 327 " ideal model delta sigma weight residual 111.30 121.36 -10.06 2.30e+00 1.89e-01 1.91e+01 angle pdb=" CB LYS A 327 " pdb=" CG LYS A 327 " pdb=" CD LYS A 327 " ideal model delta sigma weight residual 111.30 121.32 -10.02 2.30e+00 1.89e-01 1.90e+01 ... (remaining 88391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 36077 17.99 - 35.98: 3415 35.98 - 53.97: 881 53.97 - 71.96: 280 71.96 - 89.95: 199 Dihedral angle restraints: 40852 sinusoidal: 16597 harmonic: 24255 Sorted by residual: dihedral pdb=" CA MET d 16 " pdb=" C MET d 16 " pdb=" N GLU d 17 " pdb=" CA GLU d 17 " ideal model delta harmonic sigma weight residual -180.00 -156.58 -23.42 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA MET e 16 " pdb=" C MET e 16 " pdb=" N GLU e 17 " pdb=" CA GLU e 17 " ideal model delta harmonic sigma weight residual -180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA TYR G 223 " pdb=" C TYR G 223 " pdb=" N GLU G 224 " pdb=" CA GLU G 224 " ideal model delta harmonic sigma weight residual -180.00 -159.82 -20.18 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 40849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 6865 0.031 - 0.062: 2310 0.062 - 0.094: 815 0.094 - 0.125: 541 0.125 - 0.156: 67 Chirality restraints: 10598 Sorted by residual: chirality pdb=" CA ASP e 80 " pdb=" N ASP e 80 " pdb=" C ASP e 80 " pdb=" CB ASP e 80 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.07e-01 chirality pdb=" CG LEU C 314 " pdb=" CB LEU C 314 " pdb=" CD1 LEU C 314 " pdb=" CD2 LEU C 314 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA ILE J 250 " pdb=" N ILE J 250 " pdb=" C ILE J 250 " pdb=" CB ILE J 250 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.77e-01 ... (remaining 10595 not shown) Planarity restraints: 11312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 44 " 0.016 2.00e-02 2.50e+03 1.62e-02 6.59e+00 pdb=" CG TRP E 44 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP E 44 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP E 44 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 44 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 44 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 44 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 44 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 44 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 44 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 44 " -0.013 2.00e-02 2.50e+03 1.38e-02 4.79e+00 pdb=" CG TRP A 44 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP A 44 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 44 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 44 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 44 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 44 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 44 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 44 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 44 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET L 211 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.18e+00 pdb=" C MET L 211 " 0.035 2.00e-02 2.50e+03 pdb=" O MET L 211 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU L 212 " -0.012 2.00e-02 2.50e+03 ... (remaining 11309 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.63: 723 2.63 - 3.26: 68982 3.26 - 3.89: 128625 3.89 - 4.51: 171453 4.51 - 5.14: 263680 Nonbonded interactions: 633463 Sorted by model distance: nonbonded pdb=" OD1 ASP H 87 " pdb="MG MG H 601 " model vdw 2.007 2.170 nonbonded pdb=" OD1 ASP J 87 " pdb="MG MG J 601 " model vdw 2.009 2.170 nonbonded pdb=" OD1 ASP N 87 " pdb="MG MG N 601 " model vdw 2.009 2.170 nonbonded pdb=" OD1 ASP L 87 " pdb="MG MG L 601 " model vdw 2.010 2.170 nonbonded pdb=" OD1 ASP M 87 " pdb="MG MG M 601 " model vdw 2.016 2.170 ... (remaining 633458 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 529 or resid 602)) selection = (chain 'B' and (resid 3 through 529 or resid 602)) selection = (chain 'C' and (resid 3 through 529 or resid 602)) selection = (chain 'D' and (resid 3 through 529 or resid 602)) selection = (chain 'E' and (resid 3 through 529 or resid 602)) selection = (chain 'F' and (resid 3 through 529 or resid 602)) selection = (chain 'G' and (resid 3 through 529 or resid 602)) selection = (chain 'H' and (resid 3 through 529 or resid 603)) selection = (chain 'I' and (resid 3 through 529 or resid 603)) selection = (chain 'J' and (resid 3 through 529 or resid 603)) selection = (chain 'K' and (resid 3 through 529 or resid 603)) selection = (chain 'L' and (resid 3 through 529 or resid 603)) selection = (chain 'M' and (resid 3 through 529 or resid 603)) selection = (chain 'N' and (resid 3 through 529 or resid 603)) } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' } 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: 6.200 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: 0.060 Extract box with map and model: 27.530 Check model and map are aligned: 0.360 Set scattering table: 0.440 Process input model: 142.410 Find NCS groups from input model: 4.440 Set up NCS constraints: 0.780 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: 0.020 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 194.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.002 0.040 65457 Z= 0.141 Angle : 0.580 16.886 88396 Z= 0.294 Chirality : 0.042 0.156 10598 Planarity : 0.003 0.053 11312 Dihedral : 17.053 89.948 25270 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.18 % Allowed : 18.19 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.09), residues: 8470 helix: 1.75 (0.08), residues: 3892 sheet: 1.21 (0.16), residues: 1085 loop : -0.10 (0.10), residues: 3493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP E 44 HIS 0.002 0.000 HIS F 266 PHE 0.024 0.001 PHE m 69 TYR 0.023 0.001 TYR D 223 ARG 0.014 0.000 ARG E 285 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 554 time to evaluate : 5.400 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 38 GLN cc_start: 0.7779 (mt0) cc_final: 0.7443 (mm-40) REVERT: a 70 ASN cc_start: 0.8036 (t0) cc_final: 0.7607 (t0) REVERT: b 38 GLN cc_start: 0.7399 (mt0) cc_final: 0.7119 (mm-40) REVERT: b 41 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8165 (tp30) REVERT: i 8 TYR cc_start: 0.4607 (p90) cc_final: 0.4368 (p90) REVERT: i 11 ILE cc_start: 0.2931 (mm) cc_final: 0.2703 (mt) REVERT: c 41 GLU cc_start: 0.8411 (tp30) cc_final: 0.8097 (tp30) REVERT: D 288 TYR cc_start: 0.9146 (m-80) cc_final: 0.8700 (m-10) REVERT: E 316 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.6910 (pmm) REVERT: l 8 TYR cc_start: 0.4859 (p90) cc_final: 0.4579 (p90) REVERT: F 265 ASN cc_start: 0.9219 (t0) cc_final: 0.8868 (t0) REVERT: F 277 LYS cc_start: 0.7717 (mtmm) cc_final: 0.7218 (mppt) REVERT: G 199 TYR cc_start: 0.7104 (OUTLIER) cc_final: 0.6159 (t80) REVERT: G 219 PHE cc_start: 0.8558 (m-80) cc_final: 0.8329 (m-80) REVERT: G 265 ASN cc_start: 0.9219 (t0) cc_final: 0.8815 (t0) outliers start: 81 outliers final: 65 residues processed: 623 average time/residue: 1.1957 time to fit residues: 1003.3036 Evaluate side-chains 560 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 493 time to evaluate : 5.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain b residue 29 ILE Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 195 PHE Chi-restraints excluded: chain d residue 95 VAL Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 378 ILE Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain l residue 67 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 285 ARG Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 486 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 207 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 709 optimal weight: 10.0000 chunk 636 optimal weight: 0.9980 chunk 353 optimal weight: 0.1980 chunk 217 optimal weight: 5.9990 chunk 429 optimal weight: 0.0670 chunk 340 optimal weight: 1.9990 chunk 658 optimal weight: 0.1980 chunk 254 optimal weight: 1.9990 chunk 400 optimal weight: 5.9990 chunk 490 optimal weight: 0.5980 chunk 762 optimal weight: 4.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 55 GLN I 510 ASN i 55 GLN J 510 ASN ** j 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 510 ASN d 38 GLN L 510 ASN e 70 ASN M 510 ASN f 55 GLN m 55 GLN N 510 ASN g 55 GLN g 70 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 65457 Z= 0.148 Angle : 0.546 10.250 88396 Z= 0.278 Chirality : 0.043 0.169 10598 Planarity : 0.003 0.041 11312 Dihedral : 9.612 63.416 9577 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.10 % Allowed : 17.72 % Favored : 79.18 % 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: 1.43 (0.09), residues: 8470 helix: 1.84 (0.08), residues: 4011 sheet: 1.12 (0.16), residues: 1071 loop : -0.13 (0.11), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 44 HIS 0.001 0.000 HIS B 266 PHE 0.011 0.001 PHE A 195 TYR 0.021 0.001 TYR B 223 ARG 0.012 0.000 ARG n 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 523 time to evaluate : 5.367 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: A 114 MET cc_start: 0.9141 (tpt) cc_final: 0.8935 (tpp) REVERT: A 199 TYR cc_start: 0.7025 (OUTLIER) cc_final: 0.6229 (t80) REVERT: A 327 LYS cc_start: 0.8841 (tppt) cc_final: 0.8588 (tppt) REVERT: H 316 MET cc_start: -0.0980 (tpt) cc_final: -0.2088 (tpp) REVERT: a 38 GLN cc_start: 0.7867 (mt0) cc_final: 0.7454 (mm-40) REVERT: a 70 ASN cc_start: 0.7949 (t0) cc_final: 0.7646 (t0) REVERT: B 193 MET cc_start: 0.8469 (tpt) cc_final: 0.8063 (tpt) REVERT: B 219 PHE cc_start: 0.8907 (m-80) cc_final: 0.8616 (m-80) REVERT: b 38 GLN cc_start: 0.7475 (mt0) cc_final: 0.7213 (mt0) REVERT: i 50 LEU cc_start: 0.5053 (OUTLIER) cc_final: 0.4799 (tp) REVERT: C 199 TYR cc_start: 0.7110 (OUTLIER) cc_final: 0.6079 (t80) REVERT: C 327 LYS cc_start: 0.8795 (tppt) cc_final: 0.8425 (tppt) REVERT: J 301 ILE cc_start: 0.0780 (OUTLIER) cc_final: 0.0571 (mt) REVERT: J 345 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8226 (tmt-80) REVERT: c 41 GLU cc_start: 0.8423 (tp30) cc_final: 0.8055 (tp30) REVERT: D 199 TYR cc_start: 0.6901 (OUTLIER) cc_final: 0.5786 (t80) REVERT: D 288 TYR cc_start: 0.9166 (m-80) cc_final: 0.8734 (m-10) REVERT: D 327 LYS cc_start: 0.8840 (tppt) cc_final: 0.8464 (tppt) REVERT: K 494 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8195 (mp0) REVERT: d 5 ARG cc_start: 0.7246 (ttp80) cc_final: 0.7039 (ttp80) REVERT: k 5 ARG cc_start: 0.2009 (OUTLIER) cc_final: 0.1333 (mtm180) REVERT: E 199 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.6446 (t80) REVERT: E 327 LYS cc_start: 0.8826 (tppt) cc_final: 0.8618 (tppt) REVERT: L 211 MET cc_start: 0.5927 (tpt) cc_final: 0.5247 (tmt) REVERT: L 349 ILE cc_start: 0.6796 (OUTLIER) cc_final: 0.6574 (tt) REVERT: F 199 TYR cc_start: 0.6794 (OUTLIER) cc_final: 0.5683 (t80) REVERT: F 265 ASN cc_start: 0.9139 (t0) cc_final: 0.8812 (t0) REVERT: F 350 LYS cc_start: 0.8152 (pptt) cc_final: 0.7784 (pptt) REVERT: F 391 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7278 (tm-30) REVERT: M 314 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6675 (pp) REVERT: f 12 VAL cc_start: 0.7991 (OUTLIER) cc_final: 0.7777 (t) REVERT: G 219 PHE cc_start: 0.8809 (m-80) cc_final: 0.8525 (m-80) REVERT: G 265 ASN cc_start: 0.9179 (t0) cc_final: 0.8740 (t0) REVERT: N 59 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8633 (mm-30) REVERT: N 314 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.6098 (pp) REVERT: n 51 LEU cc_start: 0.1914 (OUTLIER) cc_final: 0.1452 (tp) outliers start: 212 outliers final: 73 residues processed: 686 average time/residue: 1.2080 time to fit residues: 1126.0190 Evaluate side-chains 578 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 489 time to evaluate : 5.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 211 MET Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain h residue 85 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain b residue 29 ILE Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain J residue 301 ILE Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain J residue 345 ARG Chi-restraints excluded: chain c residue 16 MET Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 211 MET Chi-restraints excluded: chain K residue 494 GLU Chi-restraints excluded: chain d residue 9 ASP Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 29 ILE Chi-restraints excluded: chain k residue 5 ARG Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 349 ILE Chi-restraints excluded: chain e residue 9 ASP Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 67 VAL Chi-restraints excluded: chain l residue 77 VAL Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 211 MET Chi-restraints excluded: chain M residue 301 ILE Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 207 ASN Chi-restraints excluded: chain N residue 314 LEU Chi-restraints excluded: chain g residue 16 MET Chi-restraints excluded: chain n residue 51 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 423 optimal weight: 5.9990 chunk 236 optimal weight: 0.0970 chunk 634 optimal weight: 7.9990 chunk 519 optimal weight: 0.8980 chunk 210 optimal weight: 3.9990 chunk 764 optimal weight: 7.9990 chunk 825 optimal weight: 8.9990 chunk 680 optimal weight: 9.9990 chunk 757 optimal weight: 8.9990 chunk 260 optimal weight: 7.9990 chunk 613 optimal weight: 6.9990 overall best weight: 3.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN H 510 ASN B 283 GLN I 510 ASN C 283 GLN J 510 ASN ** j 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 510 ASN d 38 GLN E 265 ASN L 510 ASN l 38 GLN M 510 ASN f 38 GLN N 510 ASN g 70 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 65457 Z= 0.371 Angle : 0.587 9.446 88396 Z= 0.298 Chirality : 0.045 0.190 10598 Planarity : 0.004 0.039 11312 Dihedral : 9.299 57.997 9528 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.68 % Allowed : 18.25 % Favored : 78.07 % 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: 1.21 (0.09), residues: 8470 helix: 1.68 (0.08), residues: 4018 sheet: 0.79 (0.15), residues: 1099 loop : -0.19 (0.10), residues: 3353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 44 HIS 0.002 0.001 HIS K 401 PHE 0.014 0.001 PHE m 69 TYR 0.012 0.001 TYR l 8 ARG 0.008 0.000 ARG f 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 498 time to evaluate : 5.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.9194 (tpt) cc_final: 0.8987 (tpp) REVERT: A 199 TYR cc_start: 0.7046 (OUTLIER) cc_final: 0.6015 (t80) REVERT: A 252 GLU cc_start: 0.8389 (tt0) cc_final: 0.7958 (tt0) REVERT: A 316 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7171 (pmm) REVERT: A 327 LYS cc_start: 0.8899 (tppt) cc_final: 0.8522 (tppt) REVERT: A 391 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7319 (tm-30) REVERT: H 316 MET cc_start: -0.0848 (tpt) cc_final: -0.1742 (tpp) REVERT: a 38 GLN cc_start: 0.7917 (mt0) cc_final: 0.7469 (mm-40) REVERT: B 193 MET cc_start: 0.8532 (tpt) cc_final: 0.8002 (tpt) REVERT: B 219 PHE cc_start: 0.8987 (m-80) cc_final: 0.8680 (m-80) REVERT: b 38 GLN cc_start: 0.7434 (mt0) cc_final: 0.7130 (mm-40) REVERT: b 47 ASP cc_start: 0.8733 (p0) cc_final: 0.8481 (p0) REVERT: i 50 LEU cc_start: 0.5146 (OUTLIER) cc_final: 0.4890 (tp) REVERT: C 199 TYR cc_start: 0.7021 (OUTLIER) cc_final: 0.5900 (t80) REVERT: C 265 ASN cc_start: 0.9128 (OUTLIER) cc_final: 0.8848 (t0) REVERT: C 316 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7325 (pmm) REVERT: C 327 LYS cc_start: 0.8813 (tppt) cc_final: 0.8338 (tppt) REVERT: c 41 GLU cc_start: 0.8430 (tp30) cc_final: 0.8004 (tp30) REVERT: j 51 LEU cc_start: 0.1496 (OUTLIER) cc_final: 0.1159 (tp) REVERT: D 37 GLU cc_start: 0.9354 (OUTLIER) cc_final: 0.8971 (mt-10) REVERT: D 193 MET cc_start: 0.8223 (tpt) cc_final: 0.7917 (tpt) REVERT: D 199 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.5834 (t80) REVERT: D 288 TYR cc_start: 0.9149 (m-80) cc_final: 0.8686 (m-10) REVERT: D 327 LYS cc_start: 0.8872 (tppt) cc_final: 0.8453 (tppt) REVERT: D 391 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: k 5 ARG cc_start: 0.1957 (OUTLIER) cc_final: 0.1274 (mtm180) REVERT: E 37 GLU cc_start: 0.9379 (OUTLIER) cc_final: 0.8920 (mt-10) REVERT: E 199 TYR cc_start: 0.7098 (OUTLIER) cc_final: 0.6362 (t80) REVERT: E 219 PHE cc_start: 0.8643 (m-80) cc_final: 0.8421 (m-80) REVERT: E 287 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8496 (p0) REVERT: E 316 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7298 (pmm) REVERT: E 327 LYS cc_start: 0.8903 (tppt) cc_final: 0.8667 (tppt) REVERT: F 43 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8271 (mmtt) REVERT: F 199 TYR cc_start: 0.6788 (OUTLIER) cc_final: 0.5994 (t80) REVERT: F 265 ASN cc_start: 0.9137 (t0) cc_final: 0.8751 (t0) REVERT: F 316 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.6963 (pmm) REVERT: F 319 ARG cc_start: 0.8639 (mmm-85) cc_final: 0.7445 (ttp-110) REVERT: F 327 LYS cc_start: 0.8876 (tppt) cc_final: 0.8588 (tppt) REVERT: F 351 ARG cc_start: 0.6951 (ptt90) cc_final: 0.6469 (ptt-90) REVERT: F 391 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: M 314 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6664 (pp) REVERT: f 12 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7733 (t) REVERT: G 219 PHE cc_start: 0.8958 (m-80) cc_final: 0.8654 (m-80) REVERT: G 265 ASN cc_start: 0.9196 (t0) cc_final: 0.8736 (t0) REVERT: G 285 ARG cc_start: 0.8588 (mmm-85) cc_final: 0.8006 (mmm-85) REVERT: N 314 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.5856 (pp) REVERT: N 389 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8211 (tm) REVERT: n 51 LEU cc_start: 0.2085 (OUTLIER) cc_final: 0.1696 (tp) outliers start: 252 outliers final: 99 residues processed: 690 average time/residue: 1.1872 time to fit residues: 1103.8451 Evaluate side-chains 602 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 478 time to evaluate : 5.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain a residue 50 LEU Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain a residue 88 SER Chi-restraints excluded: chain h residue 67 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 85 LEU Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain c residue 9 ASP Chi-restraints excluded: chain c residue 16 MET Chi-restraints excluded: chain c residue 52 SER Chi-restraints excluded: chain j residue 12 VAL Chi-restraints excluded: chain j residue 51 LEU Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 211 MET Chi-restraints excluded: chain d residue 29 ILE Chi-restraints excluded: chain k residue 5 ARG Chi-restraints excluded: chain E residue 37 GLU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain e residue 9 ASP Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 39 ILE Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 67 VAL Chi-restraints excluded: chain l residue 77 VAL Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 211 MET Chi-restraints excluded: chain M residue 301 ILE Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 52 SER Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 296 THR Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 386 GLU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 486 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain N residue 314 LEU Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain g residue 9 ASP Chi-restraints excluded: chain g residue 16 MET Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 51 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 755 optimal weight: 9.9990 chunk 574 optimal weight: 0.9980 chunk 396 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 364 optimal weight: 1.9990 chunk 513 optimal weight: 6.9990 chunk 766 optimal weight: 3.9990 chunk 811 optimal weight: 4.9990 chunk 400 optimal weight: 3.9990 chunk 726 optimal weight: 0.6980 chunk 218 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 510 ASN h 55 GLN I 510 ASN J 510 ASN ** c 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 510 ASN ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 510 ASN g 70 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 65457 Z= 0.208 Angle : 0.548 9.875 88396 Z= 0.275 Chirality : 0.044 0.241 10598 Planarity : 0.003 0.041 11312 Dihedral : 8.533 57.695 9523 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.25 % Allowed : 19.42 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.09), residues: 8470 helix: 1.78 (0.08), residues: 4011 sheet: 0.65 (0.15), residues: 1134 loop : -0.20 (0.11), residues: 3325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 44 HIS 0.001 0.000 HIS N 266 PHE 0.013 0.001 PHE N 219 TYR 0.016 0.001 TYR H 288 ARG 0.008 0.000 ARG a 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 477 time to evaluate : 5.326 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: A 199 TYR cc_start: 0.6990 (OUTLIER) cc_final: 0.5964 (t80) REVERT: A 252 GLU cc_start: 0.8392 (tt0) cc_final: 0.7973 (tt0) REVERT: A 327 LYS cc_start: 0.8894 (tppt) cc_final: 0.8540 (tppt) REVERT: H 316 MET cc_start: -0.0846 (tpt) cc_final: -0.1388 (tpp) REVERT: a 5 ARG cc_start: 0.7922 (ttp80) cc_final: 0.7560 (ttp80) REVERT: a 38 GLN cc_start: 0.7910 (mt0) cc_final: 0.7544 (mm-40) REVERT: B 193 MET cc_start: 0.8589 (tpt) cc_final: 0.8113 (tpt) REVERT: B 219 PHE cc_start: 0.8980 (m-80) cc_final: 0.8679 (m-80) REVERT: B 285 ARG cc_start: 0.8228 (mmm-85) cc_final: 0.7595 (mmm-85) REVERT: b 38 GLN cc_start: 0.7462 (mt0) cc_final: 0.7178 (mm-40) REVERT: b 47 ASP cc_start: 0.8787 (p0) cc_final: 0.8536 (p0) REVERT: C 199 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.5961 (t80) REVERT: C 265 ASN cc_start: 0.9112 (OUTLIER) cc_final: 0.8854 (t0) REVERT: C 285 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7388 (mmm-85) REVERT: C 327 LYS cc_start: 0.8807 (tppt) cc_final: 0.8358 (tppt) REVERT: c 41 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7925 (tp30) REVERT: j 51 LEU cc_start: 0.1448 (OUTLIER) cc_final: 0.1110 (tp) REVERT: D 193 MET cc_start: 0.8223 (tpt) cc_final: 0.7929 (tpt) REVERT: D 199 TYR cc_start: 0.6944 (OUTLIER) cc_final: 0.5609 (t80) REVERT: D 288 TYR cc_start: 0.9164 (m-80) cc_final: 0.8715 (m-10) REVERT: D 327 LYS cc_start: 0.8877 (tppt) cc_final: 0.8425 (tppt) REVERT: D 391 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7372 (tm-30) REVERT: E 199 TYR cc_start: 0.7133 (OUTLIER) cc_final: 0.6374 (t80) REVERT: E 219 PHE cc_start: 0.8652 (m-80) cc_final: 0.8429 (m-80) REVERT: E 265 ASN cc_start: 0.9165 (OUTLIER) cc_final: 0.8766 (t0) REVERT: E 287 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8500 (p0) REVERT: E 316 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7096 (pmm) REVERT: E 327 LYS cc_start: 0.8841 (tppt) cc_final: 0.8615 (tppt) REVERT: L 211 MET cc_start: 0.5542 (tpt) cc_final: 0.4833 (tmt) REVERT: F 199 TYR cc_start: 0.6821 (OUTLIER) cc_final: 0.6115 (t80) REVERT: F 265 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8725 (t0) REVERT: F 391 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7129 (tm-30) REVERT: f 12 VAL cc_start: 0.7933 (OUTLIER) cc_final: 0.7700 (t) REVERT: G 219 PHE cc_start: 0.8942 (m-80) cc_final: 0.8618 (m-80) REVERT: G 265 ASN cc_start: 0.9191 (t0) cc_final: 0.8761 (t0) REVERT: G 285 ARG cc_start: 0.8603 (mmm-85) cc_final: 0.8014 (mmm-85) REVERT: G 369 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8129 (mt) REVERT: N 314 LEU cc_start: 0.6083 (OUTLIER) cc_final: 0.5627 (pp) REVERT: N 349 ILE cc_start: 0.7187 (OUTLIER) cc_final: 0.6966 (pp) REVERT: N 389 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8173 (tm) REVERT: n 51 LEU cc_start: 0.1715 (OUTLIER) cc_final: 0.1307 (tp) outliers start: 222 outliers final: 101 residues processed: 659 average time/residue: 1.1444 time to fit residues: 1027.5106 Evaluate side-chains 587 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 465 time to evaluate : 5.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain a residue 50 LEU Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain h residue 67 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain b residue 52 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain c residue 9 ASP Chi-restraints excluded: chain c residue 39 ILE Chi-restraints excluded: chain c residue 41 GLU Chi-restraints excluded: chain j residue 12 VAL Chi-restraints excluded: chain j residue 51 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain d residue 9 ASP Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 441 ASP Chi-restraints excluded: chain e residue 9 ASP Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 39 ILE Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 67 VAL Chi-restraints excluded: chain l residue 77 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 305 LEU Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 52 SER Chi-restraints excluded: chain m residue 15 ARG Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 296 THR Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 386 GLU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 207 ASN Chi-restraints excluded: chain N residue 211 MET Chi-restraints excluded: chain N residue 314 LEU Chi-restraints excluded: chain N residue 349 ILE Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 9 ASP Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 51 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 676 optimal weight: 8.9990 chunk 460 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 604 optimal weight: 0.8980 chunk 335 optimal weight: 1.9990 chunk 692 optimal weight: 9.9990 chunk 561 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 414 optimal weight: 1.9990 chunk 728 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 510 ASN I 510 ASN J 510 ASN ** c 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 510 ASN L 510 ASN F 283 GLN m 55 GLN g 70 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 65457 Z= 0.253 Angle : 0.558 14.907 88396 Z= 0.279 Chirality : 0.044 0.290 10598 Planarity : 0.003 0.049 11312 Dihedral : 7.961 58.154 9522 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.57 % Allowed : 19.73 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.09), residues: 8470 helix: 1.80 (0.08), residues: 4004 sheet: 0.63 (0.16), residues: 1092 loop : -0.21 (0.10), residues: 3374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 44 HIS 0.001 0.000 HIS K 401 PHE 0.020 0.001 PHE H 195 TYR 0.015 0.001 TYR D 223 ARG 0.009 0.000 ARG E 285 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 482 time to evaluate : 5.502 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: A 199 TYR cc_start: 0.7027 (OUTLIER) cc_final: 0.5925 (t80) REVERT: A 219 PHE cc_start: 0.8533 (m-80) cc_final: 0.8325 (m-80) REVERT: A 252 GLU cc_start: 0.8406 (tt0) cc_final: 0.7987 (tt0) REVERT: A 327 LYS cc_start: 0.8886 (tppt) cc_final: 0.8501 (tppt) REVERT: A 391 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7187 (tm-30) REVERT: H 316 MET cc_start: 0.0184 (tpt) cc_final: -0.1085 (tpp) REVERT: a 5 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7563 (ttp80) REVERT: a 38 GLN cc_start: 0.7966 (mt0) cc_final: 0.7586 (mm-40) REVERT: B 193 MET cc_start: 0.8626 (tpt) cc_final: 0.8136 (tpt) REVERT: B 219 PHE cc_start: 0.8998 (m-80) cc_final: 0.8721 (m-80) REVERT: b 38 GLN cc_start: 0.7447 (mt0) cc_final: 0.7158 (mm-40) REVERT: b 47 ASP cc_start: 0.8818 (p0) cc_final: 0.8574 (p0) REVERT: i 8 TYR cc_start: 0.4640 (p90) cc_final: 0.4197 (p90) REVERT: C 199 TYR cc_start: 0.7076 (OUTLIER) cc_final: 0.6555 (t80) REVERT: C 265 ASN cc_start: 0.9119 (OUTLIER) cc_final: 0.8828 (t0) REVERT: J 345 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8188 (tmt-80) REVERT: c 5 ARG cc_start: 0.8131 (ttp80) cc_final: 0.7884 (ttp80) REVERT: c 41 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7876 (tp30) REVERT: j 51 LEU cc_start: 0.1450 (OUTLIER) cc_final: 0.1085 (tp) REVERT: D 193 MET cc_start: 0.8231 (tpt) cc_final: 0.7910 (tpt) REVERT: D 199 TYR cc_start: 0.6829 (OUTLIER) cc_final: 0.5628 (t80) REVERT: D 288 TYR cc_start: 0.9161 (m-80) cc_final: 0.8677 (m-10) REVERT: D 327 LYS cc_start: 0.8887 (tppt) cc_final: 0.8537 (tppt) REVERT: D 391 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: K 314 LEU cc_start: 0.6132 (OUTLIER) cc_final: 0.5782 (OUTLIER) REVERT: E 37 GLU cc_start: 0.9377 (OUTLIER) cc_final: 0.8914 (mt-10) REVERT: E 199 TYR cc_start: 0.7077 (OUTLIER) cc_final: 0.6211 (t80) REVERT: E 219 PHE cc_start: 0.8704 (m-80) cc_final: 0.8427 (m-80) REVERT: E 265 ASN cc_start: 0.9149 (OUTLIER) cc_final: 0.8726 (t0) REVERT: E 316 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7147 (pmm) REVERT: E 327 LYS cc_start: 0.8827 (tppt) cc_final: 0.8522 (tppt) REVERT: L 211 MET cc_start: 0.5675 (tpt) cc_final: 0.4844 (tmt) REVERT: l 7 LEU cc_start: 0.2241 (pp) cc_final: 0.1959 (tp) REVERT: l 51 LEU cc_start: 0.2086 (OUTLIER) cc_final: 0.1689 (tp) REVERT: F 43 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8266 (mmtt) REVERT: F 199 TYR cc_start: 0.6914 (OUTLIER) cc_final: 0.6017 (t80) REVERT: F 265 ASN cc_start: 0.9098 (OUTLIER) cc_final: 0.8717 (t0) REVERT: F 391 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7126 (tm-30) REVERT: M 59 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8786 (mm-30) REVERT: G 219 PHE cc_start: 0.8963 (m-80) cc_final: 0.8575 (m-80) REVERT: G 265 ASN cc_start: 0.9198 (OUTLIER) cc_final: 0.8751 (t0) REVERT: G 285 ARG cc_start: 0.8651 (mmm-85) cc_final: 0.8064 (mmm-85) REVERT: N 314 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5580 (pp) REVERT: N 389 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8148 (tm) REVERT: n 51 LEU cc_start: 0.1721 (OUTLIER) cc_final: 0.0353 (mm) REVERT: n 69 PHE cc_start: 0.4271 (OUTLIER) cc_final: 0.3950 (p90) outliers start: 244 outliers final: 125 residues processed: 677 average time/residue: 1.1483 time to fit residues: 1059.1773 Evaluate side-chains 615 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 466 time to evaluate : 5.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 16 MET Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain a residue 50 LEU Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain a residue 88 SER Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 67 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain J residue 345 ARG Chi-restraints excluded: chain c residue 9 ASP Chi-restraints excluded: chain c residue 16 MET Chi-restraints excluded: chain c residue 39 ILE Chi-restraints excluded: chain c residue 41 GLU Chi-restraints excluded: chain j residue 51 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 314 LEU Chi-restraints excluded: chain d residue 9 ASP Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 16 MET Chi-restraints excluded: chain d residue 29 ILE Chi-restraints excluded: chain E residue 37 GLU Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 441 ASP Chi-restraints excluded: chain e residue 9 ASP Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 39 ILE Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 51 LEU Chi-restraints excluded: chain l residue 67 VAL Chi-restraints excluded: chain l residue 77 VAL Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 52 SER Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 265 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 296 THR Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 386 GLU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 486 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 207 ASN Chi-restraints excluded: chain N residue 211 MET Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 314 LEU Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 9 ASP Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 29 ILE Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 69 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 273 optimal weight: 30.0000 chunk 731 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 476 optimal weight: 0.7980 chunk 200 optimal weight: 7.9990 chunk 812 optimal weight: 0.9980 chunk 674 optimal weight: 20.0000 chunk 376 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 268 optimal weight: 10.0000 chunk 426 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN H 510 ASN I 510 ASN b 38 GLN J 510 ASN c 38 GLN ** j 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 510 ASN L 510 ASN M 510 ASN N 510 ASN g 70 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 65457 Z= 0.152 Angle : 0.536 12.445 88396 Z= 0.268 Chirality : 0.043 0.250 10598 Planarity : 0.003 0.046 11312 Dihedral : 6.863 58.373 9522 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.07 % Allowed : 20.28 % Favored : 76.65 % 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: 1.36 (0.09), residues: 8470 helix: 1.95 (0.08), residues: 3976 sheet: 0.58 (0.16), residues: 1113 loop : -0.20 (0.10), residues: 3381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 44 HIS 0.001 0.000 HIS N 266 PHE 0.016 0.001 PHE H 195 TYR 0.012 0.001 TYR c 8 ARG 0.009 0.000 ARG E 285 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 486 time to evaluate : 5.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 TYR cc_start: 0.7020 (OUTLIER) cc_final: 0.5907 (t80) REVERT: A 219 PHE cc_start: 0.8502 (m-80) cc_final: 0.8301 (m-80) REVERT: A 252 GLU cc_start: 0.8385 (tt0) cc_final: 0.7989 (tt0) REVERT: A 327 LYS cc_start: 0.8882 (tppt) cc_final: 0.8507 (tppt) REVERT: A 391 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7019 (tm-30) REVERT: H 316 MET cc_start: -0.0113 (tpt) cc_final: -0.1176 (tpp) REVERT: H 363 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7238 (pm20) REVERT: a 5 ARG cc_start: 0.7809 (ttp80) cc_final: 0.7514 (ttp80) REVERT: a 38 GLN cc_start: 0.7903 (mt0) cc_final: 0.7556 (mm-40) REVERT: h 51 LEU cc_start: 0.0936 (OUTLIER) cc_final: 0.0513 (tp) REVERT: B 193 MET cc_start: 0.8642 (tpt) cc_final: 0.8178 (tpt) REVERT: B 219 PHE cc_start: 0.9011 (m-80) cc_final: 0.8694 (m-80) REVERT: b 38 GLN cc_start: 0.7512 (mt0) cc_final: 0.7257 (mm-40) REVERT: b 47 ASP cc_start: 0.8785 (p0) cc_final: 0.8536 (p0) REVERT: i 8 TYR cc_start: 0.4497 (p90) cc_final: 0.4123 (p90) REVERT: C 199 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.5995 (t80) REVERT: C 265 ASN cc_start: 0.9100 (OUTLIER) cc_final: 0.8813 (t0) REVERT: C 445 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8970 (tttm) REVERT: J 105 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8825 (mtp85) REVERT: c 5 ARG cc_start: 0.8109 (ttp80) cc_final: 0.7872 (ttt90) REVERT: c 41 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7848 (tp30) REVERT: j 51 LEU cc_start: 0.1427 (OUTLIER) cc_final: 0.1039 (tp) REVERT: D 193 MET cc_start: 0.8197 (tpt) cc_final: 0.7991 (tpt) REVERT: D 199 TYR cc_start: 0.6765 (OUTLIER) cc_final: 0.5466 (t80) REVERT: D 327 LYS cc_start: 0.8854 (tppt) cc_final: 0.8504 (tppt) REVERT: D 391 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7098 (tm-30) REVERT: E 199 TYR cc_start: 0.7029 (OUTLIER) cc_final: 0.6143 (t80) REVERT: E 219 PHE cc_start: 0.8734 (m-80) cc_final: 0.8447 (m-80) REVERT: E 265 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8726 (t0) REVERT: E 327 LYS cc_start: 0.8823 (tppt) cc_final: 0.8551 (tppt) REVERT: L 441 ASP cc_start: 0.9113 (OUTLIER) cc_final: 0.8696 (m-30) REVERT: l 51 LEU cc_start: 0.2111 (OUTLIER) cc_final: 0.1710 (tp) REVERT: l 69 PHE cc_start: 0.3875 (OUTLIER) cc_final: 0.3228 (p90) REVERT: F 193 MET cc_start: 0.8453 (tpt) cc_final: 0.8166 (tpt) REVERT: F 199 TYR cc_start: 0.6800 (OUTLIER) cc_final: 0.5760 (t80) REVERT: F 265 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8712 (t0) REVERT: F 327 LYS cc_start: 0.8853 (tppt) cc_final: 0.8525 (tppt) REVERT: F 391 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.6888 (tm-30) REVERT: M 59 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8754 (mm-30) REVERT: G 219 PHE cc_start: 0.8983 (m-80) cc_final: 0.8607 (m-80) REVERT: G 265 ASN cc_start: 0.9169 (OUTLIER) cc_final: 0.8744 (t0) REVERT: G 285 ARG cc_start: 0.8647 (mmm-85) cc_final: 0.8011 (mmm-85) REVERT: N 59 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8666 (mm-30) REVERT: N 314 LEU cc_start: 0.6059 (OUTLIER) cc_final: 0.5596 (pp) REVERT: N 389 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8131 (tm) REVERT: n 51 LEU cc_start: 0.1488 (OUTLIER) cc_final: 0.0248 (mm) outliers start: 210 outliers final: 108 residues processed: 646 average time/residue: 1.1885 time to fit residues: 1043.2484 Evaluate side-chains 601 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 468 time to evaluate : 5.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 363 GLU Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 16 MET Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain a residue 50 LEU Chi-restraints excluded: chain a residue 88 SER Chi-restraints excluded: chain h residue 51 LEU Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 67 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain b residue 16 MET Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 52 SER Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 445 LYS Chi-restraints excluded: chain J residue 105 ARG Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain c residue 16 MET Chi-restraints excluded: chain c residue 29 ILE Chi-restraints excluded: chain c residue 39 ILE Chi-restraints excluded: chain c residue 41 GLU Chi-restraints excluded: chain c residue 95 VAL Chi-restraints excluded: chain j residue 51 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain d residue 9 ASP Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 441 ASP Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 39 ILE Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain l residue 51 LEU Chi-restraints excluded: chain l residue 67 VAL Chi-restraints excluded: chain l residue 69 PHE Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 52 SER Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 265 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 386 GLU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 207 ASN Chi-restraints excluded: chain N residue 211 MET Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 314 LEU Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain N residue 494 GLU Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 9 ASP Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain n residue 51 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 783 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 463 optimal weight: 3.9990 chunk 593 optimal weight: 0.2980 chunk 459 optimal weight: 0.0870 chunk 684 optimal weight: 50.0000 chunk 453 optimal weight: 0.8980 chunk 809 optimal weight: 9.9990 chunk 506 optimal weight: 5.9990 chunk 493 optimal weight: 0.9990 chunk 373 optimal weight: 0.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** j 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 65457 Z= 0.143 Angle : 0.534 11.622 88396 Z= 0.265 Chirality : 0.043 0.198 10598 Planarity : 0.003 0.046 11312 Dihedral : 6.181 59.335 9519 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.53 % Allowed : 21.11 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.09), residues: 8470 helix: 2.01 (0.08), residues: 3976 sheet: 0.55 (0.17), residues: 945 loop : -0.19 (0.10), residues: 3549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 44 HIS 0.001 0.000 HIS J 266 PHE 0.019 0.001 PHE L 281 TYR 0.014 0.001 TYR g 8 ARG 0.010 0.000 ARG E 285 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 483 time to evaluate : 5.542 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: A 199 TYR cc_start: 0.7013 (OUTLIER) cc_final: 0.5960 (t80) REVERT: A 219 PHE cc_start: 0.8557 (m-80) cc_final: 0.8349 (m-80) REVERT: A 252 GLU cc_start: 0.8346 (tt0) cc_final: 0.7960 (tt0) REVERT: A 327 LYS cc_start: 0.8891 (tppt) cc_final: 0.8581 (tppt) REVERT: A 391 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.6915 (tm-30) REVERT: H 316 MET cc_start: -0.0106 (tpt) cc_final: -0.0925 (tpp) REVERT: H 363 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7242 (pm20) REVERT: a 38 GLN cc_start: 0.7885 (mt0) cc_final: 0.7586 (mm-40) REVERT: h 51 LEU cc_start: 0.1029 (OUTLIER) cc_final: 0.0572 (tp) REVERT: B 193 MET cc_start: 0.8617 (tpt) cc_final: 0.8217 (tpt) REVERT: B 219 PHE cc_start: 0.9017 (m-80) cc_final: 0.8654 (m-80) REVERT: b 38 GLN cc_start: 0.7488 (mt0) cc_final: 0.7264 (mm-40) REVERT: b 47 ASP cc_start: 0.8762 (p0) cc_final: 0.8503 (p0) REVERT: i 7 LEU cc_start: 0.2763 (mp) cc_final: 0.1844 (tp) REVERT: i 8 TYR cc_start: 0.4591 (p90) cc_final: 0.4310 (p90) REVERT: C 265 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8831 (t0) REVERT: C 445 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8993 (tttm) REVERT: c 41 GLU cc_start: 0.8295 (tp30) cc_final: 0.7800 (tp30) REVERT: j 8 TYR cc_start: 0.3789 (p90) cc_final: 0.3321 (p90) REVERT: D 176 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.8984 (p) REVERT: D 193 MET cc_start: 0.8183 (tpt) cc_final: 0.7886 (tpt) REVERT: D 199 TYR cc_start: 0.6658 (OUTLIER) cc_final: 0.5943 (t80) REVERT: D 288 TYR cc_start: 0.9143 (m-80) cc_final: 0.8719 (m-10) REVERT: D 391 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7025 (tm-30) REVERT: K 314 LEU cc_start: 0.6102 (OUTLIER) cc_final: 0.5759 (pp) REVERT: E 219 PHE cc_start: 0.8740 (m-80) cc_final: 0.8421 (m-80) REVERT: E 265 ASN cc_start: 0.9106 (OUTLIER) cc_final: 0.8712 (t0) REVERT: E 296 THR cc_start: 0.7386 (OUTLIER) cc_final: 0.7140 (p) REVERT: E 327 LYS cc_start: 0.8806 (tppt) cc_final: 0.8548 (tppt) REVERT: L 211 MET cc_start: 0.5820 (tpt) cc_final: 0.5102 (tmt) REVERT: l 51 LEU cc_start: 0.2313 (OUTLIER) cc_final: 0.2056 (tp) REVERT: l 69 PHE cc_start: 0.3859 (OUTLIER) cc_final: 0.3219 (p90) REVERT: F 176 THR cc_start: 0.9332 (OUTLIER) cc_final: 0.9053 (p) REVERT: F 193 MET cc_start: 0.8475 (tpt) cc_final: 0.8073 (tpt) REVERT: F 199 TYR cc_start: 0.6751 (OUTLIER) cc_final: 0.6276 (t80) REVERT: F 265 ASN cc_start: 0.9023 (OUTLIER) cc_final: 0.8671 (t0) REVERT: F 391 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6761 (tm-30) REVERT: M 59 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8746 (mm-30) REVERT: M 178 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8551 (mm-30) REVERT: m 1 MET cc_start: 0.4225 (ppp) cc_final: 0.3660 (pp-130) REVERT: G 219 PHE cc_start: 0.8985 (m-80) cc_final: 0.8565 (m-80) REVERT: G 265 ASN cc_start: 0.9113 (OUTLIER) cc_final: 0.8710 (t0) REVERT: G 285 ARG cc_start: 0.8662 (mmm-85) cc_final: 0.8026 (mmm-85) REVERT: N 59 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8633 (mm-30) REVERT: N 389 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8131 (tm) REVERT: N 461 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8529 (tm-30) REVERT: n 51 LEU cc_start: 0.1556 (OUTLIER) cc_final: 0.0322 (mm) outliers start: 173 outliers final: 107 residues processed: 621 average time/residue: 1.1776 time to fit residues: 993.1346 Evaluate side-chains 596 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 467 time to evaluate : 5.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 363 GLU Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 16 MET Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain a residue 50 LEU Chi-restraints excluded: chain h residue 51 LEU Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 67 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 52 SER Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 445 LYS Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain c residue 16 MET Chi-restraints excluded: chain c residue 29 ILE Chi-restraints excluded: chain c residue 39 ILE Chi-restraints excluded: chain c residue 95 VAL Chi-restraints excluded: chain j residue 39 ILE Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain K residue 314 LEU Chi-restraints excluded: chain d residue 9 ASP Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain e residue 39 ILE Chi-restraints excluded: chain l residue 51 LEU Chi-restraints excluded: chain l residue 67 VAL Chi-restraints excluded: chain l residue 69 PHE Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 265 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 207 ASN Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain N residue 494 GLU Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 9 ASP Chi-restraints excluded: chain g residue 16 MET Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 69 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 500 optimal weight: 10.0000 chunk 323 optimal weight: 5.9990 chunk 483 optimal weight: 0.9980 chunk 243 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 514 optimal weight: 10.0000 chunk 551 optimal weight: 8.9990 chunk 400 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 636 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 510 ASN I 510 ASN i 55 GLN J 510 ASN K 510 ASN L 510 ASN M 510 ASN N 510 ASN g 70 ASN n 55 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 65457 Z= 0.475 Angle : 0.629 12.240 88396 Z= 0.316 Chirality : 0.048 0.209 10598 Planarity : 0.004 0.050 11312 Dihedral : 6.884 59.189 9518 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.81 % Allowed : 21.06 % Favored : 76.14 % 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 (0.09), residues: 8470 helix: 1.72 (0.08), residues: 3955 sheet: 0.35 (0.16), residues: 1001 loop : -0.28 (0.10), residues: 3514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP G 44 HIS 0.003 0.001 HIS H 401 PHE 0.011 0.002 PHE C 62 TYR 0.013 0.001 TYR d 8 ARG 0.010 0.001 ARG E 285 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 484 time to evaluate : 5.476 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: A 199 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.6041 (t80) REVERT: A 327 LYS cc_start: 0.8941 (tppt) cc_final: 0.8608 (tppt) REVERT: A 391 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7289 (tm-30) REVERT: H 316 MET cc_start: 0.0297 (tpt) cc_final: -0.0849 (tpp) REVERT: H 363 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7254 (pm20) REVERT: a 5 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7552 (ttp80) REVERT: a 38 GLN cc_start: 0.7962 (mt0) cc_final: 0.7550 (mm-40) REVERT: h 51 LEU cc_start: 0.1303 (OUTLIER) cc_final: 0.0874 (tp) REVERT: B 176 THR cc_start: 0.9348 (OUTLIER) cc_final: 0.9035 (p) REVERT: B 193 MET cc_start: 0.8711 (tpt) cc_final: 0.8234 (tpt) REVERT: B 219 PHE cc_start: 0.9001 (m-80) cc_final: 0.8686 (m-80) REVERT: B 223 TYR cc_start: 0.8593 (t80) cc_final: 0.8297 (t80) REVERT: b 47 ASP cc_start: 0.8875 (p0) cc_final: 0.8644 (p0) REVERT: C 265 ASN cc_start: 0.9114 (OUTLIER) cc_final: 0.8808 (t0) REVERT: C 285 ARG cc_start: 0.8251 (mmm-85) cc_final: 0.7504 (mmm-85) REVERT: C 445 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8957 (tttm) REVERT: J 316 MET cc_start: -0.1538 (tmt) cc_final: -0.2060 (ttt) REVERT: D 37 GLU cc_start: 0.9384 (OUTLIER) cc_final: 0.9028 (mt-10) REVERT: D 176 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8852 (p) REVERT: D 199 TYR cc_start: 0.6868 (OUTLIER) cc_final: 0.5451 (t80) REVERT: D 285 ARG cc_start: 0.8125 (mmm-85) cc_final: 0.7874 (mmm-85) REVERT: D 288 TYR cc_start: 0.9185 (m-80) cc_final: 0.8770 (m-10) REVERT: D 391 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7546 (tm-30) REVERT: K 87 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8342 (t0) REVERT: K 314 LEU cc_start: 0.6048 (OUTLIER) cc_final: 0.5666 (pp) REVERT: E 37 GLU cc_start: 0.9402 (OUTLIER) cc_final: 0.8975 (mt-10) REVERT: E 265 ASN cc_start: 0.9181 (OUTLIER) cc_final: 0.8773 (t0) REVERT: E 316 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7213 (pmm) REVERT: L 211 MET cc_start: 0.5708 (tpt) cc_final: 0.4870 (tmt) REVERT: l 7 LEU cc_start: 0.2200 (pp) cc_final: 0.1697 (tp) REVERT: l 51 LEU cc_start: 0.2320 (OUTLIER) cc_final: 0.2116 (tp) REVERT: F 43 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8264 (mmtt) REVERT: F 176 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.8971 (p) REVERT: F 193 MET cc_start: 0.8595 (tpt) cc_final: 0.8207 (tpt) REVERT: F 199 TYR cc_start: 0.6945 (OUTLIER) cc_final: 0.5991 (t80) REVERT: F 265 ASN cc_start: 0.9088 (OUTLIER) cc_final: 0.8693 (t0) REVERT: F 391 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7315 (tm-30) REVERT: G 219 PHE cc_start: 0.9001 (m-80) cc_final: 0.8634 (m-80) REVERT: G 265 ASN cc_start: 0.9183 (OUTLIER) cc_final: 0.8735 (t0) REVERT: G 285 ARG cc_start: 0.8789 (mmm-85) cc_final: 0.8177 (mmm-85) REVERT: G 288 TYR cc_start: 0.9213 (m-80) cc_final: 0.8648 (m-10) REVERT: N 389 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8140 (tm) REVERT: N 461 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8563 (tm-30) REVERT: n 51 LEU cc_start: 0.1745 (OUTLIER) cc_final: 0.0544 (mm) outliers start: 192 outliers final: 117 residues processed: 637 average time/residue: 1.2219 time to fit residues: 1064.8720 Evaluate side-chains 610 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 468 time to evaluate : 5.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 363 GLU Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 16 MET Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain a residue 50 LEU Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain h residue 51 LEU Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 67 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain b residue 16 MET Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 52 SER Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 445 LYS Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain c residue 16 MET Chi-restraints excluded: chain c residue 39 ILE Chi-restraints excluded: chain c residue 95 VAL Chi-restraints excluded: chain j residue 39 ILE Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain K residue 211 MET Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 314 LEU Chi-restraints excluded: chain d residue 9 ASP Chi-restraints excluded: chain d residue 27 ILE Chi-restraints excluded: chain d residue 52 SER Chi-restraints excluded: chain E residue 37 GLU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain e residue 9 ASP Chi-restraints excluded: chain e residue 39 ILE Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 51 LEU Chi-restraints excluded: chain l residue 67 VAL Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 52 SER Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 265 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 296 THR Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 486 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 207 ASN Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 9 ASP Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 51 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 736 optimal weight: 6.9990 chunk 775 optimal weight: 0.5980 chunk 707 optimal weight: 30.0000 chunk 754 optimal weight: 1.9990 chunk 454 optimal weight: 0.9980 chunk 328 optimal weight: 0.7980 chunk 592 optimal weight: 20.0000 chunk 231 optimal weight: 9.9990 chunk 681 optimal weight: 20.0000 chunk 713 optimal weight: 6.9990 chunk 751 optimal weight: 30.0000 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 510 ASN K 229 ASN L 510 ASN g 70 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 65457 Z= 0.267 Angle : 0.582 13.516 88396 Z= 0.290 Chirality : 0.044 0.265 10598 Planarity : 0.003 0.049 11312 Dihedral : 6.601 59.421 9517 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.50 % Allowed : 21.47 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.09), residues: 8470 helix: 1.75 (0.08), residues: 3990 sheet: 0.28 (0.16), residues: 1036 loop : -0.25 (0.10), residues: 3444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 44 HIS 0.001 0.000 HIS K 401 PHE 0.018 0.001 PHE H 195 TYR 0.019 0.001 TYR I 288 ARG 0.011 0.000 ARG E 285 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 479 time to evaluate : 5.574 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 199 TYR cc_start: 0.7095 (OUTLIER) cc_final: 0.5987 (t80) REVERT: A 327 LYS cc_start: 0.8936 (tppt) cc_final: 0.8607 (tppt) REVERT: A 391 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7187 (tm-30) REVERT: H 316 MET cc_start: 0.0274 (tpt) cc_final: -0.0819 (tpp) REVERT: a 5 ARG cc_start: 0.7865 (ttp80) cc_final: 0.7428 (ttp80) REVERT: a 38 GLN cc_start: 0.7917 (mt0) cc_final: 0.7528 (mm-40) REVERT: a 84 TYR cc_start: 0.8101 (m-80) cc_final: 0.7898 (m-80) REVERT: h 51 LEU cc_start: 0.1213 (OUTLIER) cc_final: 0.0782 (tp) REVERT: B 176 THR cc_start: 0.9342 (OUTLIER) cc_final: 0.9047 (p) REVERT: B 193 MET cc_start: 0.8721 (tpt) cc_final: 0.8308 (tpt) REVERT: B 219 PHE cc_start: 0.8991 (m-80) cc_final: 0.8666 (m-80) REVERT: b 38 GLN cc_start: 0.7499 (mt0) cc_final: 0.7265 (mm-40) REVERT: b 47 ASP cc_start: 0.8860 (p0) cc_final: 0.8634 (p0) REVERT: C 176 THR cc_start: 0.9365 (OUTLIER) cc_final: 0.9051 (p) REVERT: C 265 ASN cc_start: 0.9096 (OUTLIER) cc_final: 0.8839 (t0) REVERT: C 285 ARG cc_start: 0.8259 (mmm-85) cc_final: 0.7650 (mmm-85) REVERT: C 445 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8954 (tttm) REVERT: j 8 TYR cc_start: 0.3929 (p90) cc_final: 0.3452 (p90) REVERT: D 176 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8898 (p) REVERT: D 288 TYR cc_start: 0.9195 (m-80) cc_final: 0.8783 (m-10) REVERT: D 391 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7368 (tm-30) REVERT: K 314 LEU cc_start: 0.5924 (OUTLIER) cc_final: 0.5534 (pp) REVERT: k 51 LEU cc_start: 0.1617 (OUTLIER) cc_final: 0.0326 (mm) REVERT: E 37 GLU cc_start: 0.9387 (OUTLIER) cc_final: 0.8924 (mt-10) REVERT: E 176 THR cc_start: 0.9351 (OUTLIER) cc_final: 0.9048 (p) REVERT: E 265 ASN cc_start: 0.9166 (OUTLIER) cc_final: 0.8768 (t0) REVERT: E 316 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7111 (pmm) REVERT: L 211 MET cc_start: 0.5787 (tpt) cc_final: 0.4983 (tmt) REVERT: l 51 LEU cc_start: 0.2320 (OUTLIER) cc_final: 0.2065 (tp) REVERT: F 176 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.8978 (p) REVERT: F 193 MET cc_start: 0.8590 (tpt) cc_final: 0.8262 (tpt) REVERT: F 265 ASN cc_start: 0.9060 (OUTLIER) cc_final: 0.8684 (t0) REVERT: F 391 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7131 (tm-30) REVERT: G 219 PHE cc_start: 0.9021 (m-80) cc_final: 0.8295 (m-80) REVERT: G 265 ASN cc_start: 0.9167 (OUTLIER) cc_final: 0.8720 (t0) REVERT: G 285 ARG cc_start: 0.8758 (mmm-85) cc_final: 0.8141 (mmm-85) REVERT: G 288 TYR cc_start: 0.9211 (m-80) cc_final: 0.8652 (m-10) REVERT: G 319 ARG cc_start: 0.8716 (mmm-85) cc_final: 0.8331 (mmm160) REVERT: N 389 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8145 (tm) REVERT: N 461 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8554 (tm-30) REVERT: n 51 LEU cc_start: 0.1667 (OUTLIER) cc_final: 0.0439 (mm) outliers start: 171 outliers final: 118 residues processed: 615 average time/residue: 1.2293 time to fit residues: 1025.1788 Evaluate side-chains 614 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 474 time to evaluate : 6.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 16 MET Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain a residue 50 LEU Chi-restraints excluded: chain h residue 51 LEU Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 67 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 52 SER Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 445 LYS Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain c residue 16 MET Chi-restraints excluded: chain c residue 39 ILE Chi-restraints excluded: chain c residue 95 VAL Chi-restraints excluded: chain j residue 39 ILE Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 314 LEU Chi-restraints excluded: chain d residue 9 ASP Chi-restraints excluded: chain d residue 27 ILE Chi-restraints excluded: chain k residue 51 LEU Chi-restraints excluded: chain E residue 37 GLU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 39 ILE Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 51 LEU Chi-restraints excluded: chain l residue 67 VAL Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 52 SER Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 265 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 296 THR Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 499 ASP Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 207 ASN Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 9 ASP Chi-restraints excluded: chain g residue 16 MET Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 52 SER Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 51 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 495 optimal weight: 1.9990 chunk 797 optimal weight: 7.9990 chunk 486 optimal weight: 0.8980 chunk 378 optimal weight: 8.9990 chunk 554 optimal weight: 30.0000 chunk 836 optimal weight: 30.0000 chunk 770 optimal weight: 0.8980 chunk 666 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 514 optimal weight: 4.9990 chunk 408 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 510 ASN ** j 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 510 ASN g 70 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 65457 Z= 0.273 Angle : 0.590 14.004 88396 Z= 0.293 Chirality : 0.044 0.197 10598 Planarity : 0.003 0.065 11312 Dihedral : 6.521 58.753 9517 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.22 % Allowed : 21.82 % Favored : 75.96 % 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: 1.12 (0.09), residues: 8470 helix: 1.77 (0.08), residues: 3976 sheet: 0.27 (0.16), residues: 1036 loop : -0.27 (0.10), residues: 3458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 44 HIS 0.001 0.000 HIS K 401 PHE 0.010 0.001 PHE H 195 TYR 0.024 0.001 TYR I 288 ARG 0.012 0.000 ARG E 285 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16940 Ramachandran restraints generated. 8470 Oldfield, 0 Emsley, 8470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 479 time to evaluate : 5.734 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: A 199 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.5908 (t80) REVERT: A 327 LYS cc_start: 0.8939 (tppt) cc_final: 0.8607 (tppt) REVERT: A 391 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: H 316 MET cc_start: 0.0303 (tpt) cc_final: -0.0801 (tpp) REVERT: a 5 ARG cc_start: 0.7847 (ttp80) cc_final: 0.7522 (ttp80) REVERT: a 38 GLN cc_start: 0.7904 (mt0) cc_final: 0.7521 (mm-40) REVERT: h 51 LEU cc_start: 0.1094 (OUTLIER) cc_final: 0.0670 (tp) REVERT: B 176 THR cc_start: 0.9350 (OUTLIER) cc_final: 0.9062 (p) REVERT: B 193 MET cc_start: 0.8780 (tpt) cc_final: 0.8318 (tpt) REVERT: B 219 PHE cc_start: 0.8992 (m-80) cc_final: 0.8653 (m-80) REVERT: B 223 TYR cc_start: 0.8633 (t80) cc_final: 0.8321 (t80) REVERT: b 47 ASP cc_start: 0.8878 (p0) cc_final: 0.8537 (p0) REVERT: C 176 THR cc_start: 0.9368 (OUTLIER) cc_final: 0.9052 (p) REVERT: C 265 ASN cc_start: 0.9122 (OUTLIER) cc_final: 0.8804 (t0) REVERT: C 445 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8964 (tttm) REVERT: j 8 TYR cc_start: 0.3889 (p90) cc_final: 0.3353 (p90) REVERT: D 176 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.8900 (p) REVERT: D 277 LYS cc_start: 0.8068 (mppt) cc_final: 0.7508 (mppt) REVERT: D 285 ARG cc_start: 0.8153 (mmm-85) cc_final: 0.7880 (mmm-85) REVERT: D 288 TYR cc_start: 0.9198 (m-80) cc_final: 0.8793 (m-10) REVERT: D 391 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7349 (tm-30) REVERT: K 314 LEU cc_start: 0.5906 (OUTLIER) cc_final: 0.5498 (pp) REVERT: k 51 LEU cc_start: 0.1575 (OUTLIER) cc_final: 0.0307 (mm) REVERT: E 37 GLU cc_start: 0.9393 (OUTLIER) cc_final: 0.8937 (mt-10) REVERT: E 176 THR cc_start: 0.9355 (OUTLIER) cc_final: 0.9055 (p) REVERT: E 265 ASN cc_start: 0.9166 (OUTLIER) cc_final: 0.8783 (t0) REVERT: E 316 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7155 (pmm) REVERT: L 211 MET cc_start: 0.5855 (tpt) cc_final: 0.5102 (tmt) REVERT: L 281 PHE cc_start: 0.7694 (t80) cc_final: 0.7395 (p90) REVERT: l 51 LEU cc_start: 0.2286 (OUTLIER) cc_final: 0.1991 (tp) REVERT: F 176 THR cc_start: 0.9299 (OUTLIER) cc_final: 0.8990 (p) REVERT: F 193 MET cc_start: 0.8598 (tpt) cc_final: 0.8199 (tpt) REVERT: F 265 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8665 (t0) REVERT: F 391 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7119 (tm-30) REVERT: m 51 LEU cc_start: 0.1238 (OUTLIER) cc_final: 0.0811 (tp) REVERT: G 219 PHE cc_start: 0.9018 (m-80) cc_final: 0.8533 (m-80) REVERT: G 265 ASN cc_start: 0.9158 (OUTLIER) cc_final: 0.8731 (t0) REVERT: G 285 ARG cc_start: 0.8778 (mmm-85) cc_final: 0.8152 (mmm-85) REVERT: G 288 TYR cc_start: 0.9200 (m-80) cc_final: 0.8618 (m-10) REVERT: G 319 ARG cc_start: 0.8714 (mmm-85) cc_final: 0.8249 (mmm-85) REVERT: N 389 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8159 (tm) REVERT: N 461 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8546 (tm-30) REVERT: n 51 LEU cc_start: 0.1668 (OUTLIER) cc_final: 0.0422 (mm) outliers start: 152 outliers final: 110 residues processed: 601 average time/residue: 1.2078 time to fit residues: 986.4856 Evaluate side-chains 604 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 471 time to evaluate : 5.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 16 MET Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain a residue 50 LEU Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain h residue 51 LEU Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 67 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 52 SER Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 445 LYS Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain c residue 39 ILE Chi-restraints excluded: chain c residue 95 VAL Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 314 LEU Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 9 ASP Chi-restraints excluded: chain d residue 27 ILE Chi-restraints excluded: chain k residue 51 LEU Chi-restraints excluded: chain E residue 37 GLU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain e residue 39 ILE Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 51 LEU Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 67 VAL Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 265 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 296 THR Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 499 ASP Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 207 ASN Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain g residue 9 ASP Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 51 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 529 optimal weight: 0.8980 chunk 709 optimal weight: 0.8980 chunk 204 optimal weight: 30.0000 chunk 614 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 667 optimal weight: 0.0060 chunk 279 optimal weight: 7.9990 chunk 685 optimal weight: 10.0000 chunk 84 optimal weight: 30.0000 chunk 122 optimal weight: 2.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 510 ASN I 510 ASN J 510 ASN ** j 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 510 ASN L 510 ASN M 510 ASN N 510 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.135515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.071343 restraints weight = 125129.667| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.82 r_work: 0.2717 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 65457 Z= 0.177 Angle : 0.571 13.711 88396 Z= 0.283 Chirality : 0.043 0.175 10598 Planarity : 0.003 0.050 11312 Dihedral : 6.244 58.991 9517 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.02 % Allowed : 22.08 % Favored : 75.90 % 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: 1.18 (0.09), residues: 8470 helix: 1.85 (0.08), residues: 3997 sheet: 0.38 (0.17), residues: 1001 loop : -0.30 (0.10), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 44 HIS 0.001 0.000 HIS J 266 PHE 0.021 0.001 PHE H 195 TYR 0.024 0.001 TYR I 288 ARG 0.012 0.000 ARG b 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20008.07 seconds wall clock time: 348 minutes 6.72 seconds (20886.72 seconds total)