Starting phenix.real_space_refine on Sat Feb 17 06:55:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0s_32923/02_2024/7x0s_32923_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0s_32923/02_2024/7x0s_32923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0s_32923/02_2024/7x0s_32923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0s_32923/02_2024/7x0s_32923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0s_32923/02_2024/7x0s_32923_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0s_32923/02_2024/7x0s_32923_updated.pdb" } resolution = 3.1 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= 0.014 sd= 0.165 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: 8 Type Number sf(0) Gaussians Al 16 5.89 5 P 32 5.49 5 Mg 16 5.21 5 S 421 5.16 5 C 42698 2.51 5 N 11901 2.21 5 O 13214 1.98 5 F 48 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 157": "NH1" <-> "NH2" Residue "K PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 243": "OE1" <-> "OE2" Residue "K PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 432": "NH1" <-> "NH2" Residue "K ARG 523": "NH1" <-> "NH2" Residue "J PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 247": "OD1" <-> "OD2" Residue "J TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "H PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 16": "NH1" <-> "NH2" Residue "G ASP 93": "OD1" <-> "OD2" Residue "G PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 293": "OE1" <-> "OE2" Residue "G TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 71": "OD1" <-> "OD2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 533": "OD1" <-> "OD2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 452": "OD1" <-> "OD2" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 518": "OD1" <-> "OD2" Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "R GLU 3": "OE1" <-> "OE2" Residue "R PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 243": "OE1" <-> "OE2" Residue "z PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 432": "NH1" <-> "NH2" Residue "z ARG 523": "NH1" <-> "NH2" Residue "P PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 247": "OD1" <-> "OD2" Residue "P TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 16": "NH1" <-> "NH2" Residue "N PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 293": "OE1" <-> "OE2" Residue "N TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 88": "OD1" <-> "OD2" Residue "a PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 238": "OD1" <-> "OD2" Residue "a PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 293": "OD1" <-> "OD2" Residue "a TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 533": "OD1" <-> "OD2" Residue "L PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 452": "OD1" <-> "OD2" Residue "L TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 518": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 68346 Number of models: 1 Model: "" Number of chains: 49 Chain: "K" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "J" Number of atoms: 4008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4008 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 511} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4037 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 16, 'TRANS': 509} Chain: "G" Number of atoms: 4094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4094 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "E" Number of atoms: 4126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4126 Classifications: {'peptide': 535} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 515} Chain: "I" Number of atoms: 3935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3935 Classifications: {'peptide': 521} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 505} Chain: "B" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3937 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 10, 'TRANS': 512} Chain: "A" Number of atoms: 4077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4077 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 14, 'TRANS': 522} Chain: "R" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3346 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "P" Number of atoms: 4008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4008 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 511} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4037 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 16, 'TRANS': 509} Chain: "N" Number of atoms: 4094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4094 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "e" Number of atoms: 4126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4126 Classifications: {'peptide': 535} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 515} Chain: "a" Number of atoms: 4077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4077 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 14, 'TRANS': 522} Chain: "M" Number of atoms: 3935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3935 Classifications: {'peptide': 521} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 505} Chain: "L" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3937 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 10, 'TRANS': 512} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 26.26, per 1000 atoms: 0.38 Number of scatterers: 68346 At special positions: 0 Unit cell: (180.566, 184.52, 175.294, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 421 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 13214 8.00 N 11901 7.00 C 42698 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=22, symmetry=0 Number of additional bonds: simple=22, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.85 Conformation dependent library (CDL) restraints added in 9.4 seconds 17664 Ramachandran restraints generated. 8832 Oldfield, 0 Emsley, 8832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16520 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 338 helices and 98 sheets defined 46.2% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.33 Creating SS restraints... Processing helix chain 'K' and resid 3 through 7 removed outlier: 3.521A pdb=" N LEU K 7 " --> pdb=" O ALA K 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 3 through 7' Processing helix chain 'K' and resid 16 through 36 removed outlier: 3.778A pdb=" N LEU K 20 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA K 21 " --> pdb=" O GLN K 17 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL K 33 " --> pdb=" O GLY K 29 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N THR K 36 " --> pdb=" O ASP K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 65 Processing helix chain 'K' and resid 72 through 87 removed outlier: 3.517A pdb=" N ALA K 83 " --> pdb=" O LYS K 79 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP K 85 " --> pdb=" O ALA K 81 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 102 removed outlier: 3.584A pdb=" N ILE K 98 " --> pdb=" O SER K 94 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE K 99 " --> pdb=" O ASN K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 110 removed outlier: 3.774A pdb=" N LEU K 108 " --> pdb=" O LYS K 104 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR K 109 " --> pdb=" O GLN K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 137 removed outlier: 3.559A pdb=" N GLU K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA K 125 " --> pdb=" O GLU K 121 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS K 129 " --> pdb=" O ALA K 125 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU K 135 " --> pdb=" O LEU K 131 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU K 136 " --> pdb=" O GLN K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 159 removed outlier: 3.845A pdb=" N THR K 158 " --> pdb=" O THR K 154 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS K 159 " --> pdb=" O SER K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 177 removed outlier: 4.320A pdb=" N GLU K 170 " --> pdb=" O ASP K 166 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP K 174 " --> pdb=" O GLU K 170 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER K 175 " --> pdb=" O ALA K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 190 No H-bonds generated for 'chain 'K' and resid 188 through 190' Processing helix chain 'K' and resid 201 through 203 No H-bonds generated for 'chain 'K' and resid 201 through 203' Processing helix chain 'K' and resid 254 through 263 removed outlier: 3.768A pdb=" N LYS K 258 " --> pdb=" O GLU K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 265 through 279 removed outlier: 3.784A pdb=" N ARG K 270 " --> pdb=" O PHE K 266 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE K 274 " --> pdb=" O ARG K 270 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU K 277 " --> pdb=" O LYS K 273 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG K 279 " --> pdb=" O ILE K 275 " (cutoff:3.500A) Processing helix chain 'K' and resid 299 through 308 removed outlier: 3.561A pdb=" N LYS K 307 " --> pdb=" O ASP K 303 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU K 308 " --> pdb=" O ALA K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 319 through 328 removed outlier: 3.993A pdb=" N ARG K 323 " --> pdb=" O ASN K 320 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU K 324 " --> pdb=" O MET K 321 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR K 325 " --> pdb=" O GLU K 322 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N CYS K 328 " --> pdb=" O THR K 325 " (cutoff:3.500A) Processing helix chain 'K' and resid 341 through 343 No H-bonds generated for 'chain 'K' and resid 341 through 343' Processing helix chain 'K' and resid 381 through 403 removed outlier: 3.742A pdb=" N THR K 385 " --> pdb=" O LYS K 381 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP K 393 " --> pdb=" O ASP K 389 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA K 397 " --> pdb=" O ASP K 393 " (cutoff:3.500A) Processing helix chain 'K' and resid 415 through 424 removed outlier: 3.552A pdb=" N ILE K 423 " --> pdb=" O ALA K 419 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS K 424 " --> pdb=" O GLU K 420 " (cutoff:3.500A) Processing helix chain 'K' and resid 426 through 428 No H-bonds generated for 'chain 'K' and resid 426 through 428' Processing helix chain 'K' and resid 432 through 454 removed outlier: 4.343A pdb=" N LEU K 435 " --> pdb=" O ARG K 432 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL K 437 " --> pdb=" O GLN K 434 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN K 438 " --> pdb=" O LEU K 435 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA K 439 " --> pdb=" O GLY K 436 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP K 442 " --> pdb=" O ALA K 439 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA K 443 " --> pdb=" O PHE K 440 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU K 444 " --> pdb=" O ALA K 441 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE K 446 " --> pdb=" O ALA K 443 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE K 447 " --> pdb=" O LEU K 444 " (cutoff:3.500A) Proline residue: K 448 - end of helix removed outlier: 3.943A pdb=" N LEU K 451 " --> pdb=" O PRO K 448 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA K 452 " --> pdb=" O LYS K 449 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN K 454 " --> pdb=" O LEU K 451 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 471 removed outlier: 3.762A pdb=" N LYS K 465 " --> pdb=" O GLU K 461 " (cutoff:3.500A) Processing helix chain 'K' and resid 489 through 492 No H-bonds generated for 'chain 'K' and resid 489 through 492' Processing helix chain 'K' and resid 498 through 504 Processing helix chain 'K' and resid 507 through 515 Processing helix chain 'J' and resid 29 through 42 removed outlier: 3.593A pdb=" N GLU J 38 " --> pdb=" O GLN J 34 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 73 removed outlier: 3.647A pdb=" N LEU J 73 " --> pdb=" O ALA J 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 69 through 73' Processing helix chain 'J' and resid 81 through 96 removed outlier: 3.635A pdb=" N MET J 85 " --> pdb=" O PRO J 81 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE J 86 " --> pdb=" O ALA J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 119 removed outlier: 3.866A pdb=" N LEU J 105 " --> pdb=" O THR J 101 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU J 117 " --> pdb=" O GLU J 113 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 142 removed outlier: 4.066A pdb=" N GLU J 130 " --> pdb=" O SER J 126 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA J 135 " --> pdb=" O GLY J 131 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU J 141 " --> pdb=" O ARG J 137 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE J 142 " --> pdb=" O LYS J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 163 Processing helix chain 'J' and resid 165 through 169 Processing helix chain 'J' and resid 178 through 187 removed outlier: 3.639A pdb=" N ALA J 186 " --> pdb=" O LEU J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 201 No H-bonds generated for 'chain 'J' and resid 199 through 201' Processing helix chain 'J' and resid 212 through 214 No H-bonds generated for 'chain 'J' and resid 212 through 214' Processing helix chain 'J' and resid 262 through 284 removed outlier: 3.558A pdb=" N ASN J 267 " --> pdb=" O GLU J 263 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE J 268 " --> pdb=" O GLU J 264 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER J 269 " --> pdb=" O LEU J 265 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS J 270 " --> pdb=" O MET J 266 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN J 279 " --> pdb=" O LEU J 275 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE J 283 " --> pdb=" O GLN J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 299 through 307 removed outlier: 3.526A pdb=" N TYR J 304 " --> pdb=" O MET J 300 " (cutoff:3.500A) Processing helix chain 'J' and resid 318 through 328 removed outlier: 3.531A pdb=" N LYS J 326 " --> pdb=" O ARG J 322 " (cutoff:3.500A) Processing helix chain 'J' and resid 382 through 404 removed outlier: 3.538A pdb=" N ASP J 386 " --> pdb=" O ASP J 382 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 428 removed outlier: 3.825A pdb=" N GLU J 418 " --> pdb=" O ALA J 414 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR J 424 " --> pdb=" O ALA J 420 " (cutoff:3.500A) Processing helix chain 'J' and resid 433 through 444 removed outlier: 3.998A pdb=" N TYR J 436 " --> pdb=" O LEU J 433 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA J 437 " --> pdb=" O GLU J 434 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS J 439 " --> pdb=" O TYR J 436 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS J 440 " --> pdb=" O ALA J 437 " (cutoff:3.500A) Processing helix chain 'J' and resid 446 through 455 removed outlier: 3.614A pdb=" N ARG J 450 " --> pdb=" O GLU J 446 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU J 452 " --> pdb=" O ILE J 448 " (cutoff:3.500A) Processing helix chain 'J' and resid 460 through 469 removed outlier: 3.590A pdb=" N LYS J 466 " --> pdb=" O GLU J 462 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU J 467 " --> pdb=" O VAL J 463 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR J 468 " --> pdb=" O ILE J 464 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA J 469 " --> pdb=" O SER J 465 " (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 520 removed outlier: 3.512A pdb=" N ILE J 508 " --> pdb=" O LYS J 504 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS J 509 " --> pdb=" O TYR J 505 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 32 removed outlier: 3.557A pdb=" N VAL H 31 " --> pdb=" O SER H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 77 through 89 removed outlier: 3.717A pdb=" N ALA H 83 " --> pdb=" O LEU H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 106 removed outlier: 3.674A pdb=" N LEU H 105 " --> pdb=" O ALA H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 112 No H-bonds generated for 'chain 'H' and resid 109 through 112' Processing helix chain 'H' and resid 119 through 137 removed outlier: 3.620A pdb=" N LYS H 137 " --> pdb=" O VAL H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 163 Processing helix chain 'H' and resid 172 through 183 removed outlier: 4.033A pdb=" N LYS H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET H 178 " --> pdb=" O PHE H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'H' and resid 205 through 207 No H-bonds generated for 'chain 'H' and resid 205 through 207' Processing helix chain 'H' and resid 260 through 281 removed outlier: 3.838A pdb=" N ALA H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL H 267 " --> pdb=" O TYR H 263 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP H 271 " --> pdb=" O VAL H 267 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 305 removed outlier: 3.531A pdb=" N PHE H 303 " --> pdb=" O ALA H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 316 through 326 removed outlier: 3.599A pdb=" N ARG H 321 " --> pdb=" O GLU H 317 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 336 No H-bonds generated for 'chain 'H' and resid 334 through 336' Processing helix chain 'H' and resid 379 through 401 removed outlier: 3.579A pdb=" N ILE H 395 " --> pdb=" O ASP H 391 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG H 398 " --> pdb=" O MET H 394 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE H 400 " --> pdb=" O VAL H 396 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS H 401 " --> pdb=" O ARG H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 426 removed outlier: 3.695A pdb=" N SER H 417 " --> pdb=" O GLU H 413 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG H 425 " --> pdb=" O ARG H 421 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 451 removed outlier: 3.574A pdb=" N GLY H 436 " --> pdb=" O GLN H 432 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA H 437 " --> pdb=" O LEU H 433 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU H 442 " --> pdb=" O TYR H 438 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ILE H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ILE H 445 " --> pdb=" O ALA H 441 " (cutoff:3.500A) Proline residue: H 446 - end of helix removed outlier: 3.542A pdb=" N LEU H 449 " --> pdb=" O ILE H 445 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N CYS H 450 " --> pdb=" O PRO H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 457 through 470 removed outlier: 3.508A pdb=" N LEU H 461 " --> pdb=" O ALA H 457 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN H 462 " --> pdb=" O THR H 458 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS H 463 " --> pdb=" O ASN H 459 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA H 469 " --> pdb=" O ARG H 465 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 513 Processing helix chain 'G' and resid 19 through 34 removed outlier: 3.579A pdb=" N VAL G 22 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN G 23 " --> pdb=" O ARG G 20 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N SER G 24 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN G 26 " --> pdb=" O GLN G 23 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE G 27 " --> pdb=" O SER G 24 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN G 28 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA G 29 " --> pdb=" O ASN G 26 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS G 31 " --> pdb=" O ASN G 28 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR G 32 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE G 33 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA G 34 " --> pdb=" O LYS G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 69 removed outlier: 3.640A pdb=" N LEU G 67 " --> pdb=" O GLY G 63 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 90 removed outlier: 3.581A pdb=" N SER G 79 " --> pdb=" O PRO G 75 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE G 81 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU G 82 " --> pdb=" O LYS G 78 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER G 84 " --> pdb=" O MET G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 113 removed outlier: 3.961A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 139 removed outlier: 3.570A pdb=" N ASP G 132 " --> pdb=" O LYS G 128 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER G 135 " --> pdb=" O ASP G 131 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR G 136 " --> pdb=" O ASP G 132 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU G 137 " --> pdb=" O MET G 133 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS G 139 " --> pdb=" O SER G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 160 removed outlier: 3.607A pdb=" N ASN G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE G 155 " --> pdb=" O MET G 151 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER G 159 " --> pdb=" O ILE G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 166 No H-bonds generated for 'chain 'G' and resid 164 through 166' Processing helix chain 'G' and resid 169 through 183 removed outlier: 4.225A pdb=" N ASN G 174 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL G 180 " --> pdb=" O ALA G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 211 No H-bonds generated for 'chain 'G' and resid 209 through 211' Processing helix chain 'G' and resid 262 through 282 removed outlier: 3.538A pdb=" N LEU G 268 " --> pdb=" O PHE G 264 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU G 272 " --> pdb=" O LEU G 268 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE G 275 " --> pdb=" O GLU G 271 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE G 282 " --> pdb=" O LEU G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 306 removed outlier: 3.676A pdb=" N TYR G 303 " --> pdb=" O LEU G 299 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG G 306 " --> pdb=" O HIS G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 326 removed outlier: 3.822A pdb=" N ARG G 325 " --> pdb=" O ASN G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 337 No H-bonds generated for 'chain 'G' and resid 335 through 337' Processing helix chain 'G' and resid 340 through 342 No H-bonds generated for 'chain 'G' and resid 340 through 342' Processing helix chain 'G' and resid 381 through 403 removed outlier: 3.674A pdb=" N GLU G 386 " --> pdb=" O GLU G 382 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL G 397 " --> pdb=" O ASP G 393 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS G 398 " --> pdb=" O ALA G 394 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL G 401 " --> pdb=" O VAL G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 428 removed outlier: 3.655A pdb=" N VAL G 418 " --> pdb=" O SER G 414 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA G 421 " --> pdb=" O ALA G 417 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ALA G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 434 through 455 removed outlier: 3.721A pdb=" N VAL G 440 " --> pdb=" O PRO G 436 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA G 441 " --> pdb=" O TYR G 437 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU G 445 " --> pdb=" O ALA G 441 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL G 446 " --> pdb=" O GLN G 442 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ILE G 447 " --> pdb=" O ALA G 443 " (cutoff:3.500A) Proline residue: G 448 - end of helix removed outlier: 3.599A pdb=" N LEU G 451 " --> pdb=" O ILE G 447 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE G 452 " --> pdb=" O PRO G 448 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N CYS G 455 " --> pdb=" O LEU G 451 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 469 removed outlier: 3.786A pdb=" N SER G 465 " --> pdb=" O ARG G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 493 No H-bonds generated for 'chain 'G' and resid 490 through 493' Processing helix chain 'G' and resid 499 through 517 removed outlier: 3.580A pdb=" N GLU G 511 " --> pdb=" O LYS G 507 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA G 513 " --> pdb=" O ALA G 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 47 removed outlier: 3.504A pdb=" N ALA E 38 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA E 41 " --> pdb=" O MET E 37 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL E 42 " --> pdb=" O ALA E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 77 removed outlier: 3.654A pdb=" N LEU E 76 " --> pdb=" O GLY E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 99 Processing helix chain 'E' and resid 106 through 123 removed outlier: 4.105A pdb=" N GLN E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 146 removed outlier: 3.518A pdb=" N GLN E 137 " --> pdb=" O ASP E 133 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 171 removed outlier: 3.552A pdb=" N THR E 169 " --> pdb=" O GLN E 165 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR E 170 " --> pdb=" O THR E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 192 removed outlier: 3.575A pdb=" N ALA E 187 " --> pdb=" O MET E 183 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 219 No H-bonds generated for 'chain 'E' and resid 217 through 219' Processing helix chain 'E' and resid 269 through 293 removed outlier: 3.561A pdb=" N GLU E 284 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE E 290 " --> pdb=" O MET E 286 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR E 293 " --> pdb=" O GLN E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 314 removed outlier: 3.969A pdb=" N HIS E 310 " --> pdb=" O ASP E 306 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU E 311 " --> pdb=" O GLU E 307 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU E 313 " --> pdb=" O ASN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 334 removed outlier: 4.021A pdb=" N GLU E 329 " --> pdb=" O GLY E 325 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU E 330 " --> pdb=" O PRO E 326 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE E 331 " --> pdb=" O GLU E 327 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 350 No H-bonds generated for 'chain 'E' and resid 348 through 350' Processing helix chain 'E' and resid 390 through 412 removed outlier: 3.525A pdb=" N GLU E 395 " --> pdb=" O MET E 391 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG E 408 " --> pdb=" O LEU E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 434 removed outlier: 3.508A pdb=" N ALA E 430 " --> pdb=" O SER E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 463 removed outlier: 3.535A pdb=" N GLU E 454 " --> pdb=" O ALA E 450 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL E 455 " --> pdb=" O ASP E 451 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE E 456 " --> pdb=" O ALA E 452 " (cutoff:3.500A) Proline residue: E 457 - end of helix removed outlier: 3.526A pdb=" N LEU E 460 " --> pdb=" O ILE E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 481 removed outlier: 4.313A pdb=" N GLU E 474 " --> pdb=" O GLN E 470 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL E 480 " --> pdb=" O ARG E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 502 No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 508 through 526 Processing helix chain 'I' and resid 33 through 47 Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 74 through 81 removed outlier: 3.565A pdb=" N LEU I 78 " --> pdb=" O GLY I 74 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN I 80 " --> pdb=" O THR I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 101 removed outlier: 3.974A pdb=" N MET I 90 " --> pdb=" O PRO I 86 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU I 91 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 123 removed outlier: 3.530A pdb=" N ASP I 118 " --> pdb=" O GLY I 114 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR I 121 " --> pdb=" O LEU I 117 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS I 122 " --> pdb=" O ASP I 118 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU I 123 " --> pdb=" O SER I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 151 removed outlier: 3.502A pdb=" N GLN I 138 " --> pdb=" O SER I 134 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU I 146 " --> pdb=" O GLU I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 171 removed outlier: 3.509A pdb=" N THR I 169 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER I 170 " --> pdb=" O SER I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 179 removed outlier: 4.414A pdb=" N GLN I 178 " --> pdb=" O VAL I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 189 removed outlier: 3.549A pdb=" N VAL I 188 " --> pdb=" O SER I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 207 No H-bonds generated for 'chain 'I' and resid 205 through 207' Processing helix chain 'I' and resid 218 through 220 No H-bonds generated for 'chain 'I' and resid 218 through 220' Processing helix chain 'I' and resid 273 through 291 removed outlier: 3.944A pdb=" N GLU I 278 " --> pdb=" O ARG I 274 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE I 283 " --> pdb=" O GLU I 279 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN I 285 " --> pdb=" O ALA I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 311 through 319 removed outlier: 3.581A pdb=" N HIS I 315 " --> pdb=" O ASP I 311 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE I 316 " --> pdb=" O LEU I 312 " (cutoff:3.500A) Processing helix chain 'I' and resid 333 through 339 Processing helix chain 'I' and resid 348 through 350 No H-bonds generated for 'chain 'I' and resid 348 through 350' Processing helix chain 'I' and resid 353 through 355 No H-bonds generated for 'chain 'I' and resid 353 through 355' Processing helix chain 'I' and resid 395 through 417 removed outlier: 3.827A pdb=" N GLU I 399 " --> pdb=" O LYS I 395 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL I 411 " --> pdb=" O ASP I 407 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE I 412 " --> pdb=" O ALA I 408 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS I 417 " --> pdb=" O ARG I 413 " (cutoff:3.500A) Processing helix chain 'I' and resid 427 through 441 removed outlier: 3.635A pdb=" N GLU I 431 " --> pdb=" O ALA I 427 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU I 436 " --> pdb=" O LEU I 432 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR I 437 " --> pdb=" O ALA I 433 " (cutoff:3.500A) Processing helix chain 'I' and resid 448 through 456 removed outlier: 3.743A pdb=" N ARG I 452 " --> pdb=" O SER I 448 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA I 453 " --> pdb=" O TYR I 449 " (cutoff:3.500A) Processing helix chain 'I' and resid 459 through 468 Processing helix chain 'I' and resid 473 through 486 removed outlier: 3.798A pdb=" N VAL I 477 " --> pdb=" O PRO I 473 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR I 478 " --> pdb=" O ILE I 474 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN I 486 " --> pdb=" O ASN I 482 " (cutoff:3.500A) Processing helix chain 'I' and resid 512 through 529 removed outlier: 3.628A pdb=" N ALA I 522 " --> pdb=" O ALA I 518 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER I 528 " --> pdb=" O GLU I 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 36 removed outlier: 3.637A pdb=" N ILE B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 42 Processing helix chain 'B' and resid 67 through 74 removed outlier: 3.915A pdb=" N ASN B 73 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 94 removed outlier: 3.532A pdb=" N VAL B 85 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 86 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU B 94 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 115 removed outlier: 3.515A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 143 removed outlier: 3.608A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 139 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 140 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 141 " --> pdb=" O ALA B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 169 removed outlier: 3.840A pdb=" N GLN B 157 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 188 removed outlier: 3.810A pdb=" N ALA B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 261 through 285 removed outlier: 3.523A pdb=" N ALA B 265 " --> pdb=" O THR B 261 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N HIS B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.741A pdb=" N LEU B 303 " --> pdb=" O TYR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 327 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 380 through 400 removed outlier: 3.612A pdb=" N ARG B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 397 " --> pdb=" O ALA B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 425 Processing helix chain 'B' and resid 430 through 454 removed outlier: 4.239A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ALA B 435 " --> pdb=" O LYS B 431 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Proline residue: B 447 - end of helix removed outlier: 3.665A pdb=" N ILE B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 469 removed outlier: 3.708A pdb=" N VAL B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 491 No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 497 through 515 removed outlier: 3.528A pdb=" N ALA B 507 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 35 removed outlier: 4.318A pdb=" N VAL A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 removed outlier: 3.845A pdb=" N LEU A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 64 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 85 removed outlier: 3.738A pdb=" N VAL A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 110 removed outlier: 3.638A pdb=" N LEU A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 132 removed outlier: 3.603A pdb=" N GLU A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 158 removed outlier: 3.522A pdb=" N CYS A 147 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 149 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN A 150 " --> pdb=" O CYS A 147 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A 151 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS A 153 " --> pdb=" O ASN A 150 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A 154 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET A 156 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 157 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER A 158 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 176 removed outlier: 3.510A pdb=" N VAL A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 257 through 277 removed outlier: 4.506A pdb=" N ASP A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN A 262 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN A 265 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A 267 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 271 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 272 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.830A pdb=" N ARG A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 322 " --> pdb=" O ARG A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 382 through 404 removed outlier: 3.682A pdb=" N VAL A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 401 " --> pdb=" O CYS A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 429 removed outlier: 3.750A pdb=" N ILE A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 455 removed outlier: 3.577A pdb=" N ARG A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix removed outlier: 3.519A pdb=" N LEU A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 453 " --> pdb=" O PRO A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 476 removed outlier: 3.851A pdb=" N PHE A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 473 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 508 through 526 removed outlier: 4.175A pdb=" N SER A 513 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 526 " --> pdb=" O ILE A 522 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 27 removed outlier: 3.635A pdb=" N GLN R 15 " --> pdb=" O GLN R 11 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TRP R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU R 22 " --> pdb=" O ALA R 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL R 23 " --> pdb=" O LYS R 19 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE R 24 " --> pdb=" O PHE R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 44 No H-bonds generated for 'chain 'R' and resid 41 through 44' Processing helix chain 'R' and resid 47 through 50 No H-bonds generated for 'chain 'R' and resid 47 through 50' Processing helix chain 'R' and resid 70 through 73 No H-bonds generated for 'chain 'R' and resid 70 through 73' Processing helix chain 'R' and resid 101 through 106 removed outlier: 3.567A pdb=" N HIS R 105 " --> pdb=" O TRP R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 125 removed outlier: 3.678A pdb=" N VAL R 113 " --> pdb=" O GLY R 109 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASP R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N SER R 115 " --> pdb=" O GLU R 111 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP R 118 " --> pdb=" O ASP R 114 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL R 119 " --> pdb=" O SER R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 158 removed outlier: 3.603A pdb=" N GLY R 148 " --> pdb=" O GLY R 144 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR R 149 " --> pdb=" O SER R 145 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU R 151 " --> pdb=" O MET R 147 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE R 152 " --> pdb=" O GLY R 148 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG R 156 " --> pdb=" O ILE R 152 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU R 157 " --> pdb=" O SER R 153 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU R 158 " --> pdb=" O LYS R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 190 removed outlier: 3.521A pdb=" N VAL R 189 " --> pdb=" O ALA R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 213 removed outlier: 3.766A pdb=" N ASP R 209 " --> pdb=" O ALA R 206 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS R 211 " --> pdb=" O TYR R 208 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE R 212 " --> pdb=" O ASP R 209 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG R 213 " --> pdb=" O ILE R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 236 removed outlier: 3.861A pdb=" N HIS R 227 " --> pdb=" O GLY R 223 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU R 228 " --> pdb=" O ASP R 224 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL R 229 " --> pdb=" O LEU R 225 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL R 236 " --> pdb=" O THR R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 250 through 255 removed outlier: 3.826A pdb=" N VAL R 255 " --> pdb=" O ARG R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 290 Processing helix chain 'R' and resid 296 through 298 No H-bonds generated for 'chain 'R' and resid 296 through 298' Processing helix chain 'R' and resid 305 through 307 No H-bonds generated for 'chain 'R' and resid 305 through 307' Processing helix chain 'R' and resid 324 through 336 removed outlier: 3.623A pdb=" N GLU R 328 " --> pdb=" O LYS R 324 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN R 332 " --> pdb=" O GLU R 328 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL R 333 " --> pdb=" O GLN R 329 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS R 336 " --> pdb=" O ASN R 332 " (cutoff:3.500A) Processing helix chain 'R' and resid 373 through 390 removed outlier: 3.835A pdb=" N LEU R 377 " --> pdb=" O ALA R 373 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG R 380 " --> pdb=" O GLU R 376 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE R 381 " --> pdb=" O LEU R 377 " (cutoff:3.500A) Processing helix chain 'R' and resid 396 through 399 No H-bonds generated for 'chain 'R' and resid 396 through 399' Processing helix chain 'R' and resid 405 through 422 removed outlier: 3.516A pdb=" N ASN R 414 " --> pdb=" O GLU R 410 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET R 415 " --> pdb=" O ALA R 411 " (cutoff:3.500A) Processing helix chain 'z' and resid 4 through 7 No H-bonds generated for 'chain 'z' and resid 4 through 7' Processing helix chain 'z' and resid 16 through 36 removed outlier: 3.726A pdb=" N LEU z 20 " --> pdb=" O ALA z 16 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA z 21 " --> pdb=" O GLN z 17 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL z 33 " --> pdb=" O GLY z 29 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N THR z 36 " --> pdb=" O ASP z 32 " (cutoff:3.500A) Processing helix chain 'z' and resid 60 through 65 Processing helix chain 'z' and resid 72 through 87 removed outlier: 3.515A pdb=" N ALA z 83 " --> pdb=" O LYS z 79 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP z 85 " --> pdb=" O ALA z 81 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE z 87 " --> pdb=" O ALA z 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 93 through 102 removed outlier: 3.704A pdb=" N LEU z 97 " --> pdb=" O THR z 93 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE z 98 " --> pdb=" O SER z 94 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE z 99 " --> pdb=" O ASN z 95 " (cutoff:3.500A) Processing helix chain 'z' and resid 107 through 110 No H-bonds generated for 'chain 'z' and resid 107 through 110' Processing helix chain 'z' and resid 116 through 137 removed outlier: 3.507A pdb=" N GLY z 122 " --> pdb=" O ILE z 118 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA z 125 " --> pdb=" O GLU z 121 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS z 129 " --> pdb=" O ALA z 125 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU z 135 " --> pdb=" O LEU z 131 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU z 136 " --> pdb=" O GLN z 132 " (cutoff:3.500A) Processing helix chain 'z' and resid 145 through 157 removed outlier: 3.555A pdb=" N ILE z 149 " --> pdb=" O ARG z 145 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP z 150 " --> pdb=" O GLU z 146 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER z 155 " --> pdb=" O VAL z 151 " (cutoff:3.500A) Processing helix chain 'z' and resid 165 through 177 removed outlier: 4.081A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP z 174 " --> pdb=" O GLU z 170 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER z 175 " --> pdb=" O ALA z 171 " (cutoff:3.500A) Processing helix chain 'z' and resid 188 through 190 No H-bonds generated for 'chain 'z' and resid 188 through 190' Processing helix chain 'z' and resid 201 through 203 No H-bonds generated for 'chain 'z' and resid 201 through 203' Processing helix chain 'z' and resid 254 through 263 removed outlier: 3.709A pdb=" N LYS z 258 " --> pdb=" O GLU z 254 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU z 259 " --> pdb=" O GLU z 255 " (cutoff:3.500A) Processing helix chain 'z' and resid 265 through 277 removed outlier: 3.813A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE z 274 " --> pdb=" O ARG z 270 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU z 277 " --> pdb=" O LYS z 273 " (cutoff:3.500A) Processing helix chain 'z' and resid 299 through 308 removed outlier: 3.601A pdb=" N LYS z 307 " --> pdb=" O ASP z 303 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 319 through 328 removed outlier: 3.973A pdb=" N ARG z 323 " --> pdb=" O ASN z 320 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU z 324 " --> pdb=" O MET z 321 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR z 325 " --> pdb=" O GLU z 322 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU z 326 " --> pdb=" O ARG z 323 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N CYS z 328 " --> pdb=" O THR z 325 " (cutoff:3.500A) Processing helix chain 'z' and resid 341 through 343 No H-bonds generated for 'chain 'z' and resid 341 through 343' Processing helix chain 'z' and resid 381 through 403 removed outlier: 3.517A pdb=" N THR z 385 " --> pdb=" O LYS z 381 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP z 393 " --> pdb=" O ASP z 389 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG z 396 " --> pdb=" O ARG z 392 " (cutoff:3.500A) Processing helix chain 'z' and resid 415 through 424 removed outlier: 3.505A pdb=" N LEU z 422 " --> pdb=" O MET z 418 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE z 423 " --> pdb=" O ALA z 419 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS z 424 " --> pdb=" O GLU z 420 " (cutoff:3.500A) Processing helix chain 'z' and resid 426 through 428 No H-bonds generated for 'chain 'z' and resid 426 through 428' Processing helix chain 'z' and resid 432 through 454 removed outlier: 4.390A pdb=" N LEU z 435 " --> pdb=" O ARG z 432 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL z 437 " --> pdb=" O GLN z 434 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN z 438 " --> pdb=" O LEU z 435 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA z 439 " --> pdb=" O GLY z 436 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP z 442 " --> pdb=" O ALA z 439 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA z 443 " --> pdb=" O PHE z 440 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU z 444 " --> pdb=" O ALA z 441 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU z 445 " --> pdb=" O ASP z 442 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE z 446 " --> pdb=" O ALA z 443 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE z 447 " --> pdb=" O LEU z 444 " (cutoff:3.500A) Proline residue: z 448 - end of helix removed outlier: 4.031A pdb=" N LEU z 451 " --> pdb=" O PRO z 448 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA z 452 " --> pdb=" O LYS z 449 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN z 454 " --> pdb=" O LEU z 451 " (cutoff:3.500A) Processing helix chain 'z' and resid 460 through 471 removed outlier: 3.721A pdb=" N LYS z 465 " --> pdb=" O GLU z 461 " (cutoff:3.500A) Processing helix chain 'z' and resid 489 through 492 No H-bonds generated for 'chain 'z' and resid 489 through 492' Processing helix chain 'z' and resid 498 through 515 removed outlier: 3.706A pdb=" N CYS z 508 " --> pdb=" O LEU z 504 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR z 509 " --> pdb=" O LEU z 505 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE z 515 " --> pdb=" O ILE z 511 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 42 removed outlier: 3.578A pdb=" N GLU P 38 " --> pdb=" O GLN P 34 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU P 39 " --> pdb=" O ALA P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 73 removed outlier: 3.642A pdb=" N LEU P 73 " --> pdb=" O ALA P 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 69 through 73' Processing helix chain 'P' and resid 81 through 96 removed outlier: 3.716A pdb=" N MET P 85 " --> pdb=" O PRO P 81 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE P 86 " --> pdb=" O ALA P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 119 removed outlier: 3.865A pdb=" N LEU P 105 " --> pdb=" O THR P 101 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU P 117 " --> pdb=" O GLU P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 142 removed outlier: 3.533A pdb=" N ILE P 129 " --> pdb=" O VAL P 125 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU P 130 " --> pdb=" O SER P 126 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE P 134 " --> pdb=" O GLU P 130 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA P 135 " --> pdb=" O GLY P 131 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU P 141 " --> pdb=" O ARG P 137 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE P 142 " --> pdb=" O LYS P 138 " (cutoff:3.500A) Processing helix chain 'P' and resid 160 through 163 No H-bonds generated for 'chain 'P' and resid 160 through 163' Processing helix chain 'P' and resid 165 through 169 Processing helix chain 'P' and resid 178 through 190 removed outlier: 3.616A pdb=" N ALA P 186 " --> pdb=" O LEU P 182 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL P 188 " --> pdb=" O ALA P 184 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER P 189 " --> pdb=" O GLN P 185 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE P 190 " --> pdb=" O ALA P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 199 through 201 No H-bonds generated for 'chain 'P' and resid 199 through 201' Processing helix chain 'P' and resid 212 through 214 No H-bonds generated for 'chain 'P' and resid 212 through 214' Processing helix chain 'P' and resid 262 through 284 removed outlier: 3.510A pdb=" N PHE P 268 " --> pdb=" O GLU P 264 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER P 269 " --> pdb=" O LEU P 265 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS P 270 " --> pdb=" O MET P 266 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU P 273 " --> pdb=" O SER P 269 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN P 279 " --> pdb=" O LEU P 275 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE P 283 " --> pdb=" O GLN P 279 " (cutoff:3.500A) Processing helix chain 'P' and resid 299 through 307 removed outlier: 3.523A pdb=" N TYR P 304 " --> pdb=" O MET P 300 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN P 306 " --> pdb=" O LEU P 302 " (cutoff:3.500A) Processing helix chain 'P' and resid 318 through 328 removed outlier: 3.787A pdb=" N ARG P 322 " --> pdb=" O LYS P 318 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG P 323 " --> pdb=" O TRP P 319 " (cutoff:3.500A) Processing helix chain 'P' and resid 382 through 404 removed outlier: 3.545A pdb=" N ASP P 387 " --> pdb=" O ASN P 383 " (cutoff:3.500A) Processing helix chain 'P' and resid 414 through 428 removed outlier: 3.655A pdb=" N GLU P 418 " --> pdb=" O ALA P 414 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE P 423 " --> pdb=" O LEU P 419 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR P 424 " --> pdb=" O ALA P 420 " (cutoff:3.500A) Processing helix chain 'P' and resid 433 through 454 removed outlier: 4.177A pdb=" N TYR P 436 " --> pdb=" O LEU P 433 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA P 437 " --> pdb=" O GLU P 434 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS P 440 " --> pdb=" O ALA P 437 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA P 442 " --> pdb=" O LYS P 439 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU P 443 " --> pdb=" O LYS P 440 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA P 447 " --> pdb=" O ALA P 444 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE P 448 " --> pdb=" O PHE P 445 " (cutoff:3.500A) Proline residue: P 449 - end of helix removed outlier: 3.854A pdb=" N GLU P 454 " --> pdb=" O ALA P 451 " (cutoff:3.500A) Processing helix chain 'P' and resid 460 through 469 removed outlier: 3.522A pdb=" N LYS P 466 " --> pdb=" O GLU P 462 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR P 468 " --> pdb=" O ILE P 464 " (cutoff:3.500A) Processing helix chain 'P' and resid 492 through 495 No H-bonds generated for 'chain 'P' and resid 492 through 495' Processing helix chain 'P' and resid 501 through 520 removed outlier: 3.501A pdb=" N ILE P 508 " --> pdb=" O LYS P 504 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS P 509 " --> pdb=" O TYR P 505 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 32 removed outlier: 4.102A pdb=" N VAL O 23 " --> pdb=" O PRO O 20 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER O 27 " --> pdb=" O SER O 24 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA O 28 " --> pdb=" O ASN O 25 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE O 32 " --> pdb=" O CYS O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 65 No H-bonds generated for 'chain 'O' and resid 62 through 65' Processing helix chain 'O' and resid 77 through 89 removed outlier: 3.613A pdb=" N ALA O 83 " --> pdb=" O LEU O 79 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP O 87 " --> pdb=" O ALA O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 106 removed outlier: 3.647A pdb=" N LEU O 105 " --> pdb=" O ALA O 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 109 through 112 No H-bonds generated for 'chain 'O' and resid 109 through 112' Processing helix chain 'O' and resid 119 through 137 removed outlier: 3.810A pdb=" N LYS O 137 " --> pdb=" O VAL O 133 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 162 removed outlier: 3.520A pdb=" N THR O 161 " --> pdb=" O LYS O 157 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 184 removed outlier: 4.187A pdb=" N LYS O 177 " --> pdb=" O ALA O 173 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET O 178 " --> pdb=" O PHE O 174 " (cutoff:3.500A) Processing helix chain 'O' and resid 192 through 194 No H-bonds generated for 'chain 'O' and resid 192 through 194' Processing helix chain 'O' and resid 205 through 207 No H-bonds generated for 'chain 'O' and resid 205 through 207' Processing helix chain 'O' and resid 260 through 281 removed outlier: 3.539A pdb=" N GLN O 264 " --> pdb=" O VAL O 260 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA O 265 " --> pdb=" O GLU O 261 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL O 267 " --> pdb=" O TYR O 263 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU O 274 " --> pdb=" O GLU O 270 " (cutoff:3.500A) Processing helix chain 'O' and resid 297 through 305 Processing helix chain 'O' and resid 316 through 326 removed outlier: 3.558A pdb=" N ARG O 321 " --> pdb=" O GLU O 317 " (cutoff:3.500A) Processing helix chain 'O' and resid 334 through 336 No H-bonds generated for 'chain 'O' and resid 334 through 336' Processing helix chain 'O' and resid 379 through 401 removed outlier: 3.539A pdb=" N ARG O 398 " --> pdb=" O MET O 394 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE O 400 " --> pdb=" O VAL O 396 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS O 401 " --> pdb=" O ARG O 397 " (cutoff:3.500A) Processing helix chain 'O' and resid 411 through 426 removed outlier: 3.738A pdb=" N SER O 417 " --> pdb=" O GLU O 413 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR O 426 " --> pdb=" O ASP O 422 " (cutoff:3.500A) Processing helix chain 'O' and resid 430 through 451 removed outlier: 3.521A pdb=" N LEU O 433 " --> pdb=" O LYS O 430 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE O 435 " --> pdb=" O GLN O 432 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLY O 436 " --> pdb=" O LEU O 433 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS O 440 " --> pdb=" O ALA O 437 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA O 441 " --> pdb=" O TYR O 438 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU O 443 " --> pdb=" O LYS O 440 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE O 444 " --> pdb=" O ALA O 441 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE O 445 " --> pdb=" O LEU O 442 " (cutoff:3.500A) Proline residue: O 446 - end of helix removed outlier: 3.733A pdb=" N LEU O 449 " --> pdb=" O PRO O 446 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP O 451 " --> pdb=" O GLN O 448 " (cutoff:3.500A) Processing helix chain 'O' and resid 457 through 468 removed outlier: 3.513A pdb=" N LEU O 461 " --> pdb=" O ALA O 457 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN O 462 " --> pdb=" O THR O 458 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS O 463 " --> pdb=" O ASN O 459 " (cutoff:3.500A) Processing helix chain 'O' and resid 496 through 513 Processing helix chain 'N' and resid 19 through 23 removed outlier: 3.679A pdb=" N VAL N 22 " --> pdb=" O GLY N 19 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN N 23 " --> pdb=" O ARG N 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 19 through 23' Processing helix chain 'N' and resid 25 through 36 removed outlier: 3.772A pdb=" N ILE N 33 " --> pdb=" O ALA N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 69 removed outlier: 3.627A pdb=" N LEU N 67 " --> pdb=" O GLY N 63 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU N 69 " --> pdb=" O ALA N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 90 removed outlier: 3.510A pdb=" N SER N 79 " --> pdb=" O PRO N 75 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET N 80 " --> pdb=" O ALA N 76 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU N 82 " --> pdb=" O LYS N 78 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER N 84 " --> pdb=" O MET N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 113 removed outlier: 3.966A pdb=" N HIS N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE N 112 " --> pdb=" O VAL N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 119 through 137 removed outlier: 3.558A pdb=" N ASP N 132 " --> pdb=" O LYS N 128 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER N 135 " --> pdb=" O ASP N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 160 removed outlier: 3.544A pdb=" N ASN N 154 " --> pdb=" O ASP N 150 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE N 155 " --> pdb=" O MET N 151 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER N 159 " --> pdb=" O ILE N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 164 through 166 No H-bonds generated for 'chain 'N' and resid 164 through 166' Processing helix chain 'N' and resid 169 through 182 removed outlier: 4.349A pdb=" N ASN N 174 " --> pdb=" O SER N 170 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL N 180 " --> pdb=" O ALA N 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 282 removed outlier: 3.638A pdb=" N GLU N 272 " --> pdb=" O LEU N 268 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE N 275 " --> pdb=" O GLU N 271 " (cutoff:3.500A) Processing helix chain 'N' and resid 298 through 306 removed outlier: 3.640A pdb=" N TYR N 303 " --> pdb=" O LEU N 299 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG N 306 " --> pdb=" O HIS N 302 " (cutoff:3.500A) Processing helix chain 'N' and resid 317 through 326 removed outlier: 3.747A pdb=" N ARG N 325 " --> pdb=" O ASN N 321 " (cutoff:3.500A) Processing helix chain 'N' and resid 335 through 337 No H-bonds generated for 'chain 'N' and resid 335 through 337' Processing helix chain 'N' and resid 340 through 342 No H-bonds generated for 'chain 'N' and resid 340 through 342' Processing helix chain 'N' and resid 381 through 403 removed outlier: 3.685A pdb=" N GLU N 386 " --> pdb=" O GLU N 382 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL N 397 " --> pdb=" O ASP N 393 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS N 398 " --> pdb=" O ALA N 394 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL N 401 " --> pdb=" O VAL N 397 " (cutoff:3.500A) Processing helix chain 'N' and resid 413 through 428 removed outlier: 3.674A pdb=" N VAL N 418 " --> pdb=" O SER N 414 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA N 421 " --> pdb=" O ALA N 417 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS N 427 " --> pdb=" O THR N 423 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ALA N 428 " --> pdb=" O GLU N 424 " (cutoff:3.500A) Processing helix chain 'N' and resid 434 through 455 removed outlier: 3.732A pdb=" N VAL N 440 " --> pdb=" O PRO N 436 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA N 441 " --> pdb=" O TYR N 437 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU N 445 " --> pdb=" O ALA N 441 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL N 446 " --> pdb=" O GLN N 442 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ILE N 447 " --> pdb=" O ALA N 443 " (cutoff:3.500A) Proline residue: N 448 - end of helix removed outlier: 3.501A pdb=" N LEU N 451 " --> pdb=" O ILE N 447 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE N 452 " --> pdb=" O PRO N 448 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N CYS N 455 " --> pdb=" O LEU N 451 " (cutoff:3.500A) Processing helix chain 'N' and resid 461 through 469 removed outlier: 3.936A pdb=" N SER N 465 " --> pdb=" O ARG N 461 " (cutoff:3.500A) Processing helix chain 'N' and resid 490 through 493 No H-bonds generated for 'chain 'N' and resid 490 through 493' Processing helix chain 'N' and resid 499 through 517 removed outlier: 3.590A pdb=" N GLU N 511 " --> pdb=" O LYS N 507 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA N 513 " --> pdb=" O ALA N 509 " (cutoff:3.500A) Processing helix chain 'e' and resid 20 through 22 No H-bonds generated for 'chain 'e' and resid 20 through 22' Processing helix chain 'e' and resid 31 through 46 removed outlier: 3.621A pdb=" N HIS e 35 " --> pdb=" O ALA e 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA e 41 " --> pdb=" O MET e 37 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL e 42 " --> pdb=" O ALA e 38 " (cutoff:3.500A) Processing helix chain 'e' and resid 72 through 77 removed outlier: 3.722A pdb=" N LEU e 76 " --> pdb=" O GLY e 72 " (cutoff:3.500A) Processing helix chain 'e' and resid 84 through 99 removed outlier: 3.610A pdb=" N LEU e 88 " --> pdb=" O GLN e 84 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET e 89 " --> pdb=" O ILE e 85 " (cutoff:3.500A) Processing helix chain 'e' and resid 106 through 123 removed outlier: 4.019A pdb=" N GLN e 120 " --> pdb=" O GLU e 116 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU e 121 " --> pdb=" O GLU e 117 " (cutoff:3.500A) Processing helix chain 'e' and resid 128 through 146 removed outlier: 3.531A pdb=" N GLN e 137 " --> pdb=" O ASP e 133 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL e 141 " --> pdb=" O GLN e 137 " (cutoff:3.500A) Processing helix chain 'e' and resid 161 through 173 removed outlier: 3.643A pdb=" N THR e 169 " --> pdb=" O GLN e 165 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR e 170 " --> pdb=" O THR e 166 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER e 173 " --> pdb=" O THR e 169 " (cutoff:3.500A) Processing helix chain 'e' and resid 177 through 179 No H-bonds generated for 'chain 'e' and resid 177 through 179' Processing helix chain 'e' and resid 182 through 192 removed outlier: 3.532A pdb=" N ALA e 187 " --> pdb=" O MET e 183 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL e 191 " --> pdb=" O ALA e 187 " (cutoff:3.500A) Processing helix chain 'e' and resid 217 through 219 No H-bonds generated for 'chain 'e' and resid 217 through 219' Processing helix chain 'e' and resid 269 through 293 removed outlier: 3.517A pdb=" N GLU e 284 " --> pdb=" O LYS e 280 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE e 287 " --> pdb=" O PHE e 283 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE e 290 " --> pdb=" O MET e 286 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR e 293 " --> pdb=" O GLN e 289 " (cutoff:3.500A) Processing helix chain 'e' and resid 306 through 314 removed outlier: 3.879A pdb=" N HIS e 310 " --> pdb=" O ASP e 306 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU e 311 " --> pdb=" O GLU e 307 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU e 312 " --> pdb=" O ALA e 308 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU e 313 " --> pdb=" O ASN e 309 " (cutoff:3.500A) Processing helix chain 'e' and resid 325 through 334 removed outlier: 3.955A pdb=" N GLU e 329 " --> pdb=" O GLY e 325 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU e 330 " --> pdb=" O PRO e 326 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE e 333 " --> pdb=" O GLU e 329 " (cutoff:3.500A) Processing helix chain 'e' and resid 390 through 412 removed outlier: 3.524A pdb=" N GLU e 395 " --> pdb=" O MET e 391 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP e 402 " --> pdb=" O ARG e 398 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE e 407 " --> pdb=" O ALA e 403 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG e 408 " --> pdb=" O LEU e 404 " (cutoff:3.500A) Processing helix chain 'e' and resid 422 through 434 Processing helix chain 'e' and resid 443 through 463 removed outlier: 3.539A pdb=" N GLU e 454 " --> pdb=" O ALA e 450 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL e 455 " --> pdb=" O ASP e 451 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE e 456 " --> pdb=" O ALA e 452 " (cutoff:3.500A) Proline residue: e 457 - end of helix Processing helix chain 'e' and resid 468 through 481 removed outlier: 3.577A pdb=" N THR e 473 " --> pdb=" O ILE e 469 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU e 474 " --> pdb=" O GLN e 470 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN e 479 " --> pdb=" O VAL e 475 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL e 480 " --> pdb=" O ARG e 476 " (cutoff:3.500A) Processing helix chain 'e' and resid 499 through 502 No H-bonds generated for 'chain 'e' and resid 499 through 502' Processing helix chain 'e' and resid 508 through 526 Processing helix chain 'a' and resid 15 through 35 removed outlier: 4.248A pdb=" N VAL a 22 " --> pdb=" O ARG a 18 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE a 28 " --> pdb=" O ALA a 24 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE a 31 " --> pdb=" O SER a 27 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N SER a 34 " --> pdb=" O ASN a 30 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N SER a 35 " --> pdb=" O ILE a 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 64 removed outlier: 3.826A pdb=" N LEU a 62 " --> pdb=" O GLY a 58 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU a 64 " --> pdb=" O THR a 60 " (cutoff:3.500A) Processing helix chain 'a' and resid 70 through 85 removed outlier: 3.701A pdb=" N VAL a 74 " --> pdb=" O PRO a 70 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP a 80 " --> pdb=" O CYS a 76 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP a 83 " --> pdb=" O ALA a 79 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS a 84 " --> pdb=" O ASP a 80 " (cutoff:3.500A) Processing helix chain 'a' and resid 92 through 110 removed outlier: 3.543A pdb=" N LEU a 101 " --> pdb=" O ALA a 97 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU a 106 " --> pdb=" O LYS a 102 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN a 110 " --> pdb=" O GLU a 106 " (cutoff:3.500A) Processing helix chain 'a' and resid 114 through 132 removed outlier: 3.563A pdb=" N LEU a 123 " --> pdb=" O SER a 119 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU a 127 " --> pdb=" O LEU a 123 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 158 removed outlier: 3.572A pdb=" N CYS a 147 " --> pdb=" O GLY a 144 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE a 149 " --> pdb=" O ASP a 146 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN a 150 " --> pdb=" O CYS a 147 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA a 151 " --> pdb=" O LEU a 148 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS a 153 " --> pdb=" O ASN a 150 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR a 154 " --> pdb=" O ALA a 151 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET a 156 " --> pdb=" O LYS a 153 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER a 157 " --> pdb=" O THR a 154 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER a 158 " --> pdb=" O SER a 155 " (cutoff:3.500A) Processing helix chain 'a' and resid 167 through 176 removed outlier: 3.506A pdb=" N VAL a 172 " --> pdb=" O PHE a 168 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA a 175 " --> pdb=" O MET a 171 " (cutoff:3.500A) Processing helix chain 'a' and resid 192 through 194 No H-bonds generated for 'chain 'a' and resid 192 through 194' Processing helix chain 'a' and resid 205 through 207 No H-bonds generated for 'chain 'a' and resid 205 through 207' Processing helix chain 'a' and resid 257 through 277 removed outlier: 4.646A pdb=" N ASP a 261 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN a 262 " --> pdb=" O LYS a 259 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG a 264 " --> pdb=" O ASP a 261 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN a 265 " --> pdb=" O GLN a 262 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU a 267 " --> pdb=" O ARG a 264 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP a 269 " --> pdb=" O ARG a 266 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE a 270 " --> pdb=" O GLU a 267 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS a 272 " --> pdb=" O ASP a 269 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG a 274 " --> pdb=" O THR a 271 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE a 275 " --> pdb=" O LYS a 272 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN a 276 " --> pdb=" O GLU a 273 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS a 277 " --> pdb=" O ARG a 274 " (cutoff:3.500A) Processing helix chain 'a' and resid 296 through 303 removed outlier: 3.518A pdb=" N TYR a 299 " --> pdb=" O CYS a 296 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE a 300 " --> pdb=" O LEU a 297 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU a 302 " --> pdb=" O TYR a 299 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA a 303 " --> pdb=" O PHE a 300 " (cutoff:3.500A) Processing helix chain 'a' and resid 313 through 322 removed outlier: 3.567A pdb=" N LYS a 317 " --> pdb=" O LYS a 313 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG a 318 " --> pdb=" O ARG a 314 " (cutoff:3.500A) Processing helix chain 'a' and resid 342 through 344 No H-bonds generated for 'chain 'a' and resid 342 through 344' Processing helix chain 'a' and resid 382 through 404 removed outlier: 3.600A pdb=" N VAL a 398 " --> pdb=" O ASP a 394 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL a 399 " --> pdb=" O ALA a 395 " (cutoff:3.500A) Processing helix chain 'a' and resid 414 through 429 removed outlier: 3.549A pdb=" N ALA a 418 " --> pdb=" O ALA a 414 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE a 421 " --> pdb=" O ALA a 417 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU a 424 " --> pdb=" O SER a 420 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) Processing helix chain 'a' and resid 435 through 455 removed outlier: 4.101A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ILE a 448 " --> pdb=" O SER a 444 " (cutoff:3.500A) Proline residue: a 449 - end of helix removed outlier: 3.628A pdb=" N LEU a 452 " --> pdb=" O ILE a 448 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA a 453 " --> pdb=" O PRO a 449 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL a 454 " --> pdb=" O ASN a 450 " (cutoff:3.500A) Processing helix chain 'a' and resid 463 through 476 removed outlier: 3.813A pdb=" N PHE a 470 " --> pdb=" O LYS a 466 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS a 471 " --> pdb=" O LEU a 467 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU a 473 " --> pdb=" O ALA a 469 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN a 475 " --> pdb=" O HIS a 471 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 501 No H-bonds generated for 'chain 'a' and resid 498 through 501' Processing helix chain 'a' and resid 508 through 526 removed outlier: 4.159A pdb=" N SER a 513 " --> pdb=" O VAL a 509 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR a 523 " --> pdb=" O GLU a 519 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE a 524 " --> pdb=" O ALA a 520 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG a 526 " --> pdb=" O ILE a 522 " (cutoff:3.500A) Processing helix chain 'M' and resid 33 through 47 Processing helix chain 'M' and resid 49 through 51 No H-bonds generated for 'chain 'M' and resid 49 through 51' Processing helix chain 'M' and resid 74 through 81 removed outlier: 3.549A pdb=" N LEU M 78 " --> pdb=" O GLY M 74 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN M 80 " --> pdb=" O THR M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 101 Processing helix chain 'M' and resid 108 through 124 removed outlier: 3.531A pdb=" N ASP M 118 " --> pdb=" O GLY M 114 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR M 121 " --> pdb=" O LEU M 117 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS M 122 " --> pdb=" O ASP M 118 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU M 123 " --> pdb=" O SER M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 150 removed outlier: 3.986A pdb=" N GLU M 146 " --> pdb=" O GLU M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 171 removed outlier: 3.771A pdb=" N SER M 170 " --> pdb=" O SER M 166 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU M 171 " --> pdb=" O ALA M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 179 removed outlier: 4.449A pdb=" N GLN M 178 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 192 removed outlier: 3.564A pdb=" N VAL M 188 " --> pdb=" O SER M 184 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL M 191 " --> pdb=" O SER M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 205 through 207 No H-bonds generated for 'chain 'M' and resid 205 through 207' Processing helix chain 'M' and resid 218 through 220 No H-bonds generated for 'chain 'M' and resid 218 through 220' Processing helix chain 'M' and resid 273 through 291 removed outlier: 3.989A pdb=" N GLU M 278 " --> pdb=" O ARG M 274 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE M 283 " --> pdb=" O GLU M 279 " (cutoff:3.500A) Processing helix chain 'M' and resid 311 through 319 removed outlier: 3.543A pdb=" N HIS M 315 " --> pdb=" O ASP M 311 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE M 316 " --> pdb=" O LEU M 312 " (cutoff:3.500A) Processing helix chain 'M' and resid 333 through 339 Processing helix chain 'M' and resid 348 through 350 No H-bonds generated for 'chain 'M' and resid 348 through 350' Processing helix chain 'M' and resid 353 through 355 No H-bonds generated for 'chain 'M' and resid 353 through 355' Processing helix chain 'M' and resid 395 through 417 removed outlier: 3.863A pdb=" N GLU M 399 " --> pdb=" O LYS M 395 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL M 411 " --> pdb=" O ASP M 407 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE M 412 " --> pdb=" O ALA M 408 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS M 417 " --> pdb=" O ARG M 413 " (cutoff:3.500A) Processing helix chain 'M' and resid 427 through 441 removed outlier: 3.659A pdb=" N GLU M 431 " --> pdb=" O ALA M 427 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU M 436 " --> pdb=" O LEU M 432 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR M 437 " --> pdb=" O ALA M 433 " (cutoff:3.500A) Processing helix chain 'M' and resid 448 through 456 removed outlier: 3.709A pdb=" N ARG M 452 " --> pdb=" O SER M 448 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA M 453 " --> pdb=" O TYR M 449 " (cutoff:3.500A) Processing helix chain 'M' and resid 459 through 468 Processing helix chain 'M' and resid 473 through 486 removed outlier: 3.887A pdb=" N VAL M 477 " --> pdb=" O PRO M 473 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR M 478 " --> pdb=" O ILE M 474 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN M 486 " --> pdb=" O ASN M 482 " (cutoff:3.500A) Processing helix chain 'M' and resid 512 through 529 removed outlier: 3.714A pdb=" N ALA M 522 " --> pdb=" O ALA M 518 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER M 528 " --> pdb=" O GLU M 524 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 42 removed outlier: 3.643A pdb=" N ILE L 35 " --> pdb=" O GLY L 31 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER L 41 " --> pdb=" O ASP L 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N THR L 42 " --> pdb=" O LEU L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 74 removed outlier: 3.938A pdb=" N ASN L 73 " --> pdb=" O THR L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 94 removed outlier: 3.506A pdb=" N VAL L 85 " --> pdb=" O LYS L 82 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET L 87 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN L 91 " --> pdb=" O SER L 88 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU L 94 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 115 removed outlier: 3.517A pdb=" N THR L 103 " --> pdb=" O THR L 99 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU L 110 " --> pdb=" O ALA L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 143 removed outlier: 3.645A pdb=" N GLU L 132 " --> pdb=" O ALA L 128 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU L 139 " --> pdb=" O LYS L 135 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA L 140 " --> pdb=" O ALA L 136 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU L 141 " --> pdb=" O ALA L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 169 removed outlier: 3.749A pdb=" N GLN L 157 " --> pdb=" O VAL L 153 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER L 168 " --> pdb=" O GLY L 164 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER L 169 " --> pdb=" O THR L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 188 removed outlier: 3.805A pdb=" N ALA L 186 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL L 187 " --> pdb=" O ALA L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 209 through 211 No H-bonds generated for 'chain 'L' and resid 209 through 211' Processing helix chain 'L' and resid 261 through 285 removed outlier: 3.566A pdb=" N ALA L 265 " --> pdb=" O THR L 261 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS L 284 " --> pdb=" O GLU L 280 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N HIS L 285 " --> pdb=" O ARG L 281 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 306 removed outlier: 3.879A pdb=" N LEU L 303 " --> pdb=" O TYR L 299 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 327 Processing helix chain 'L' and resid 338 through 340 No H-bonds generated for 'chain 'L' and resid 338 through 340' Processing helix chain 'L' and resid 380 through 400 removed outlier: 3.602A pdb=" N ARG L 388 " --> pdb=" O ASP L 384 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL L 396 " --> pdb=" O ASP L 392 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 425 Processing helix chain 'L' and resid 430 through 454 removed outlier: 4.206A pdb=" N VAL L 434 " --> pdb=" O GLY L 430 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ALA L 435 " --> pdb=" O LYS L 431 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU L 446 " --> pdb=" O ALA L 442 " (cutoff:3.500A) Proline residue: L 447 - end of helix removed outlier: 3.644A pdb=" N ILE L 450 " --> pdb=" O LEU L 446 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA L 454 " --> pdb=" O ILE L 450 " (cutoff:3.500A) Processing helix chain 'L' and resid 458 through 469 removed outlier: 3.700A pdb=" N VAL L 462 " --> pdb=" O SER L 458 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA L 463 " --> pdb=" O ALA L 459 " (cutoff:3.500A) Processing helix chain 'L' and resid 488 through 491 No H-bonds generated for 'chain 'L' and resid 488 through 491' Processing helix chain 'L' and resid 497 through 515 removed outlier: 3.510A pdb=" N ALA L 507 " --> pdb=" O VAL L 503 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 45 through 48 Processing sheet with id= B, first strand: chain 'K' and resid 191 through 195 removed outlier: 7.013A pdb=" N VAL K 372 " --> pdb=" O GLU K 192 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N MET K 194 " --> pdb=" O VAL K 372 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU K 374 " --> pdb=" O MET K 194 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER K 205 " --> pdb=" O LEU K 375 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 210 through 212 removed outlier: 3.716A pdb=" N LEU K 349 " --> pdb=" O GLU K 364 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 228 through 231 removed outlier: 7.077A pdb=" N GLY K 288 " --> pdb=" O TYR K 229 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU K 231 " --> pdb=" O GLY K 288 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL K 290 " --> pdb=" O LEU K 231 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'J' and resid 21 through 23 Processing sheet with id= F, first strand: chain 'J' and resid 54 through 57 removed outlier: 3.561A pdb=" N THR J 66 " --> pdb=" O LYS J 54 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 202 through 208 removed outlier: 7.039A pdb=" N SER J 373 " --> pdb=" O ARG J 203 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N CYS J 205 " --> pdb=" O SER J 373 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE J 375 " --> pdb=" O CYS J 205 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE J 207 " --> pdb=" O ILE J 375 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU J 377 " --> pdb=" O ILE J 207 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 239 through 241 removed outlier: 6.718A pdb=" N VAL J 290 " --> pdb=" O ALA J 240 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N MET J 311 " --> pdb=" O VAL J 291 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N THR J 293 " --> pdb=" O MET J 311 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL J 313 " --> pdb=" O THR J 293 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'J' and resid 349 through 354 Processing sheet with id= J, first strand: chain 'J' and resid 147 through 150 removed outlier: 3.613A pdb=" N CYS J 148 " --> pdb=" O LEU J 408 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU J 408 " --> pdb=" O CYS J 148 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'H' and resid 14 through 17 removed outlier: 3.914A pdb=" N ASP H 14 " --> pdb=" O LYS H 521 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR H 519 " --> pdb=" O SER H 16 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 47 through 50 Processing sheet with id= M, first strand: chain 'H' and resid 195 through 201 removed outlier: 7.106A pdb=" N CYS H 370 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N LYS H 198 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N PHE H 372 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL H 200 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU H 374 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN H 209 " --> pdb=" O ILE H 373 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 237 through 240 removed outlier: 6.912A pdb=" N VAL H 288 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU H 240 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N SER H 290 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N PHE H 309 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N SER H 291 " --> pdb=" O PHE H 309 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA H 311 " --> pdb=" O SER H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'H' and resid 347 through 351 removed outlier: 3.532A pdb=" N GLU H 349 " --> pdb=" O PHE H 360 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= Q, first strand: chain 'H' and resid 475 through 477 Processing sheet with id= R, first strand: chain 'G' and resid 15 through 18 removed outlier: 3.735A pdb=" N SER G 524 " --> pdb=" O LYS G 15 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU G 17 " --> pdb=" O ILE G 522 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 48 through 51 Processing sheet with id= T, first strand: chain 'G' and resid 200 through 205 removed outlier: 3.727A pdb=" N GLY G 378 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR G 373 " --> pdb=" O LEU G 215 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS G 213 " --> pdb=" O LEU G 375 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 218 through 220 Processing sheet with id= V, first strand: chain 'G' and resid 238 through 240 removed outlier: 6.459A pdb=" N VAL G 289 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR G 310 " --> pdb=" O VAL G 290 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'G' and resid 407 through 409 Processing sheet with id= X, first strand: chain 'E' and resid 57 through 60 Processing sheet with id= Y, first strand: chain 'E' and resid 207 through 213 removed outlier: 6.781A pdb=" N VAL E 381 " --> pdb=" O LYS E 208 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N GLU E 210 " --> pdb=" O VAL E 381 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE E 383 " --> pdb=" O GLU E 210 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LYS E 212 " --> pdb=" O ILE E 383 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE E 385 " --> pdb=" O LYS E 212 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS E 221 " --> pdb=" O PHE E 384 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 352 through 354 removed outlier: 6.738A pdb=" N LEU E 297 " --> pdb=" O ALA E 247 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU E 249 " --> pdb=" O LEU E 297 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ILE E 299 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N CYS E 300 " --> pdb=" O PRO E 318 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL E 320 " --> pdb=" O CYS E 300 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 357 through 360 removed outlier: 3.702A pdb=" N GLN E 358 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET E 369 " --> pdb=" O ILE E 360 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 416 through 418 Processing sheet with id= AC, first strand: chain 'I' and resid 59 through 61 Processing sheet with id= AD, first strand: chain 'I' and resid 208 through 212 removed outlier: 6.717A pdb=" N VAL I 386 " --> pdb=" O LYS I 209 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N VAL I 211 " --> pdb=" O VAL I 386 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE I 388 " --> pdb=" O VAL I 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'I' and resid 240 through 242 removed outlier: 3.581A pdb=" N GLU I 363 " --> pdb=" O LYS I 375 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU I 373 " --> pdb=" O VAL I 365 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'I' and resid 246 through 249 removed outlier: 6.600A pdb=" N VAL I 297 " --> pdb=" O GLY I 247 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ILE I 249 " --> pdb=" O VAL I 297 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LEU I 299 " --> pdb=" O ILE I 249 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N MET I 323 " --> pdb=" O LEU I 298 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE I 300 " --> pdb=" O MET I 323 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE I 325 " --> pdb=" O ILE I 300 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'I' and resid 421 through 423 Processing sheet with id= AH, first strand: chain 'I' and resid 491 through 494 Processing sheet with id= AI, first strand: chain 'B' and resid 17 through 20 removed outlier: 3.598A pdb=" N ASP B 17 " --> pdb=" O LYS B 522 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'B' and resid 50 through 52 removed outlier: 3.722A pdb=" N LYS B 50 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 52 " --> pdb=" O MET B 62 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.631A pdb=" N CYS B 371 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ILE B 202 " --> pdb=" O CYS B 371 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LYS B 204 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU B 375 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THR B 372 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR B 213 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'B' and resid 237 through 240 removed outlier: 5.917A pdb=" N CYS B 289 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA B 240 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE B 291 " --> pdb=" O ALA B 240 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'B' and resid 351 through 353 Processing sheet with id= AN, first strand: chain 'B' and resid 406 through 408 Processing sheet with id= AO, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= AP, first strand: chain 'A' and resid 10 through 13 Processing sheet with id= AQ, first strand: chain 'A' and resid 43 through 46 Processing sheet with id= AR, first strand: chain 'A' and resid 180 through 183 removed outlier: 3.793A pdb=" N GLN A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'A' and resid 197 through 201 removed outlier: 6.912A pdb=" N ILE A 375 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ALA A 200 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU A 377 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'A' and resid 213 through 216 removed outlier: 3.989A pdb=" N LEU A 361 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU A 350 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'A' and resid 234 through 237 removed outlier: 6.775A pdb=" N VAL A 285 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU A 237 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LEU A 287 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N MET A 306 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N THR A 288 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 308 " --> pdb=" O THR A 288 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain 'A' and resid 408 through 410 Processing sheet with id= AW, first strand: chain 'R' and resid 63 through 66 removed outlier: 8.559A pdb=" N ILE R 64 " --> pdb=" O ILE R 4 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N HIS R 6 " --> pdb=" O ILE R 64 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL R 66 " --> pdb=" O HIS R 6 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLN R 8 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL R 5 " --> pdb=" O GLN R 131 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE R 133 " --> pdb=" O VAL R 5 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE R 7 " --> pdb=" O PHE R 133 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU R 135 " --> pdb=" O ILE R 7 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA R 9 " --> pdb=" O LEU R 135 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N HIS R 137 " --> pdb=" O ALA R 9 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE R 163 " --> pdb=" O PHE R 133 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N LEU R 135 " --> pdb=" O ILE R 163 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASN R 165 " --> pdb=" O LEU R 135 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N HIS R 137 " --> pdb=" O ASN R 165 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE R 167 " --> pdb=" O HIS R 137 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER R 168 " --> pdb=" O TYR R 200 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'R' and resid 51 through 53 Processing sheet with id= AY, first strand: chain 'R' and resid 269 through 271 removed outlier: 3.789A pdb=" N ALA R 364 " --> pdb=" O ARG R 318 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL R 316 " --> pdb=" O THR R 366 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN R 370 " --> pdb=" O THR R 312 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR R 312 " --> pdb=" O ASN R 370 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA R 315 " --> pdb=" O LYS R 350 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS R 354 " --> pdb=" O PHE R 317 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'z' and resid 45 through 48 Processing sheet with id= BA, first strand: chain 'z' and resid 191 through 195 removed outlier: 6.969A pdb=" N VAL z 372 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N MET z 194 " --> pdb=" O VAL z 372 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU z 374 " --> pdb=" O MET z 194 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER z 205 " --> pdb=" O LEU z 375 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'z' and resid 210 through 212 removed outlier: 3.616A pdb=" N LEU z 349 " --> pdb=" O GLU z 364 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'z' and resid 228 through 231 removed outlier: 6.929A pdb=" N GLY z 288 " --> pdb=" O TYR z 229 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU z 231 " --> pdb=" O GLY z 288 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL z 290 " --> pdb=" O LEU z 231 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'P' and resid 21 through 23 Processing sheet with id= BE, first strand: chain 'P' and resid 54 through 57 removed outlier: 3.503A pdb=" N THR P 66 " --> pdb=" O LYS P 54 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'P' and resid 202 through 208 removed outlier: 7.234A pdb=" N SER P 373 " --> pdb=" O ARG P 203 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N CYS P 205 " --> pdb=" O SER P 373 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE P 375 " --> pdb=" O CYS P 205 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE P 207 " --> pdb=" O ILE P 375 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU P 377 " --> pdb=" O ILE P 207 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'P' and resid 239 through 241 removed outlier: 6.543A pdb=" N VAL P 290 " --> pdb=" O ALA P 240 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N MET P 311 " --> pdb=" O VAL P 291 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N THR P 293 " --> pdb=" O MET P 311 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL P 313 " --> pdb=" O THR P 293 " (cutoff:3.500A) No H-bonds generated for sheet with id= BG Processing sheet with id= BH, first strand: chain 'P' and resid 349 through 354 Processing sheet with id= BI, first strand: chain 'P' and resid 147 through 150 removed outlier: 3.741A pdb=" N CYS P 148 " --> pdb=" O LEU P 408 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU P 408 " --> pdb=" O CYS P 148 " (cutoff:3.500A) No H-bonds generated for sheet with id= BI Processing sheet with id= BJ, first strand: chain 'O' and resid 14 through 17 removed outlier: 4.199A pdb=" N ASP O 14 " --> pdb=" O LYS O 521 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS O 521 " --> pdb=" O ASP O 14 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER O 16 " --> pdb=" O THR O 519 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR O 519 " --> pdb=" O SER O 16 " (cutoff:3.500A) No H-bonds generated for sheet with id= BJ Processing sheet with id= BK, first strand: chain 'O' and resid 47 through 50 Processing sheet with id= BL, first strand: chain 'O' and resid 195 through 201 removed outlier: 7.099A pdb=" N CYS O 370 " --> pdb=" O GLY O 196 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N LYS O 198 " --> pdb=" O CYS O 370 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE O 372 " --> pdb=" O LYS O 198 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL O 200 " --> pdb=" O PHE O 372 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU O 374 " --> pdb=" O VAL O 200 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'O' and resid 237 through 240 removed outlier: 7.130A pdb=" N VAL O 288 " --> pdb=" O ALA O 238 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU O 240 " --> pdb=" O VAL O 288 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N SER O 290 " --> pdb=" O LEU O 240 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N PHE O 309 " --> pdb=" O VAL O 289 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N SER O 291 " --> pdb=" O PHE O 309 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA O 311 " --> pdb=" O SER O 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= BM Processing sheet with id= BN, first strand: chain 'O' and resid 347 through 351 removed outlier: 3.534A pdb=" N GLU O 349 " --> pdb=" O PHE O 360 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'O' and resid 405 through 407 Processing sheet with id= BP, first strand: chain 'O' and resid 475 through 477 Processing sheet with id= BQ, first strand: chain 'N' and resid 15 through 18 removed outlier: 3.795A pdb=" N SER N 524 " --> pdb=" O LYS N 15 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU N 17 " --> pdb=" O ILE N 522 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'N' and resid 48 through 51 Processing sheet with id= BS, first strand: chain 'N' and resid 199 through 205 removed outlier: 6.827A pdb=" N CYS N 372 " --> pdb=" O ARG N 200 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLU N 202 " --> pdb=" O CYS N 372 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE N 374 " --> pdb=" O GLU N 202 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ILE N 204 " --> pdb=" O ILE N 374 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU N 376 " --> pdb=" O ILE N 204 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR N 373 " --> pdb=" O LEU N 215 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'N' and resid 218 through 220 Processing sheet with id= BU, first strand: chain 'N' and resid 238 through 240 removed outlier: 6.432A pdb=" N VAL N 289 " --> pdb=" O VAL N 239 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR N 310 " --> pdb=" O VAL N 290 " (cutoff:3.500A) No H-bonds generated for sheet with id= BU Processing sheet with id= BV, first strand: chain 'N' and resid 407 through 409 Processing sheet with id= BW, first strand: chain 'e' and resid 57 through 60 Processing sheet with id= BX, first strand: chain 'e' and resid 207 through 213 removed outlier: 6.856A pdb=" N VAL e 381 " --> pdb=" O LYS e 208 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N GLU e 210 " --> pdb=" O VAL e 381 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE e 383 " --> pdb=" O GLU e 210 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LYS e 212 " --> pdb=" O ILE e 383 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE e 385 " --> pdb=" O LYS e 212 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS e 221 " --> pdb=" O PHE e 384 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'e' and resid 352 through 354 removed outlier: 6.665A pdb=" N LEU e 297 " --> pdb=" O ALA e 247 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU e 249 " --> pdb=" O LEU e 297 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE e 299 " --> pdb=" O LEU e 249 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N CYS e 300 " --> pdb=" O PRO e 318 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL e 320 " --> pdb=" O CYS e 300 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'e' and resid 357 through 360 removed outlier: 3.591A pdb=" N GLN e 358 " --> pdb=" O VAL e 371 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET e 369 " --> pdb=" O ILE e 360 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'e' and resid 416 through 418 Processing sheet with id= CB, first strand: chain 'a' and resid 10 through 12 Processing sheet with id= CC, first strand: chain 'a' and resid 43 through 46 Processing sheet with id= CD, first strand: chain 'a' and resid 180 through 183 removed outlier: 3.788A pdb=" N GLN a 187 " --> pdb=" O ASP a 183 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'a' and resid 197 through 201 removed outlier: 6.780A pdb=" N ILE a 375 " --> pdb=" O LEU a 198 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ALA a 200 " --> pdb=" O ILE a 375 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU a 377 " --> pdb=" O ALA a 200 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'a' and resid 213 through 216 removed outlier: 3.958A pdb=" N LEU a 361 " --> pdb=" O GLU a 354 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU a 350 " --> pdb=" O LYS a 365 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'a' and resid 234 through 237 removed outlier: 6.759A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N MET a 306 " --> pdb=" O ILE a 286 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N THR a 288 " --> pdb=" O MET a 306 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL a 308 " --> pdb=" O THR a 288 " (cutoff:3.500A) No H-bonds generated for sheet with id= CG Processing sheet with id= CH, first strand: chain 'a' and resid 408 through 410 Processing sheet with id= CI, first strand: chain 'M' and resid 59 through 61 Processing sheet with id= CJ, first strand: chain 'M' and resid 208 through 212 removed outlier: 6.701A pdb=" N VAL M 386 " --> pdb=" O LYS M 209 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL M 211 " --> pdb=" O VAL M 386 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE M 388 " --> pdb=" O VAL M 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= CJ Processing sheet with id= CK, first strand: chain 'M' and resid 240 through 242 removed outlier: 3.615A pdb=" N GLU M 363 " --> pdb=" O LYS M 375 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU M 373 " --> pdb=" O VAL M 365 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'M' and resid 246 through 249 removed outlier: 6.627A pdb=" N VAL M 297 " --> pdb=" O GLY M 247 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ILE M 249 " --> pdb=" O VAL M 297 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU M 299 " --> pdb=" O ILE M 249 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N MET M 323 " --> pdb=" O LEU M 298 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE M 300 " --> pdb=" O MET M 323 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE M 325 " --> pdb=" O ILE M 300 " (cutoff:3.500A) No H-bonds generated for sheet with id= CL Processing sheet with id= CM, first strand: chain 'M' and resid 421 through 423 Processing sheet with id= CN, first strand: chain 'M' and resid 491 through 494 Processing sheet with id= CO, first strand: chain 'L' and resid 17 through 20 removed outlier: 3.729A pdb=" N ASP L 17 " --> pdb=" O LYS L 522 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain 'L' and resid 199 through 205 removed outlier: 6.586A pdb=" N CYS L 371 " --> pdb=" O HIS L 200 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE L 202 " --> pdb=" O CYS L 371 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE L 373 " --> pdb=" O ILE L 202 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LYS L 204 " --> pdb=" O ILE L 373 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU L 375 " --> pdb=" O LYS L 204 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR L 372 " --> pdb=" O ASP L 215 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR L 213 " --> pdb=" O VAL L 374 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain 'L' and resid 237 through 240 removed outlier: 5.914A pdb=" N CYS L 289 " --> pdb=" O LEU L 238 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA L 240 " --> pdb=" O CYS L 289 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE L 291 " --> pdb=" O ALA L 240 " (cutoff:3.500A) No H-bonds generated for sheet with id= CQ Processing sheet with id= CR, first strand: chain 'L' and resid 351 through 353 Processing sheet with id= CS, first strand: chain 'L' and resid 406 through 408 Processing sheet with id= CT, first strand: chain 'L' and resid 476 through 479 2372 hydrogen bonds defined for protein. 6702 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: 24.44 Time building geometry restraints manager: 21.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 9463 1.24 - 1.38: 15169 1.38 - 1.53: 33013 1.53 - 1.67: 10760 1.67 - 1.81: 748 Bond restraints: 69153 Sorted by residual: bond pdb=" CA THR M 106 " pdb=" C THR M 106 " ideal model delta sigma weight residual 1.523 1.359 0.164 1.34e-02 5.57e+03 1.50e+02 bond pdb=" CA THR I 106 " pdb=" C THR I 106 " ideal model delta sigma weight residual 1.519 1.379 0.140 1.19e-02 7.06e+03 1.39e+02 bond pdb=" CA THR O 94 " pdb=" C THR O 94 " ideal model delta sigma weight residual 1.523 1.366 0.157 1.34e-02 5.57e+03 1.37e+02 bond pdb=" CA ASN P 102 " pdb=" C ASN P 102 " ideal model delta sigma weight residual 1.521 1.376 0.144 1.27e-02 6.20e+03 1.29e+02 bond pdb=" C VAL H 90 " pdb=" O VAL H 90 " ideal model delta sigma weight residual 1.233 1.121 0.112 1.02e-02 9.61e+03 1.21e+02 ... (remaining 69148 not shown) Histogram of bond angle deviations from ideal: 97.90 - 105.59: 1250 105.59 - 113.28: 39796 113.28 - 120.97: 32766 120.97 - 128.65: 19265 128.65 - 136.34: 324 Bond angle restraints: 93401 Sorted by residual: angle pdb=" O GLY A 87 " pdb=" C GLY A 87 " pdb=" N ASP A 88 " ideal model delta sigma weight residual 122.77 114.21 8.56 9.40e-01 1.13e+00 8.29e+01 angle pdb=" C GLY M 105 " pdb=" N THR M 106 " pdb=" CA THR M 106 " ideal model delta sigma weight residual 121.54 105.13 16.41 1.91e+00 2.74e-01 7.39e+01 angle pdb=" CA GLY A 87 " pdb=" C GLY A 87 " pdb=" N ASP A 88 " ideal model delta sigma weight residual 117.63 126.46 -8.83 1.17e+00 7.31e-01 5.70e+01 angle pdb=" C GLY O 93 " pdb=" N THR O 94 " pdb=" CA THR O 94 " ideal model delta sigma weight residual 121.54 108.26 13.28 1.91e+00 2.74e-01 4.84e+01 angle pdb=" N ASN P 102 " pdb=" CA ASN P 102 " pdb=" C ASN P 102 " ideal model delta sigma weight residual 113.97 105.74 8.23 1.28e+00 6.10e-01 4.14e+01 ... (remaining 93396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.97: 41821 27.97 - 55.93: 836 55.93 - 83.90: 33 83.90 - 111.87: 7 111.87 - 139.83: 22 Dihedral angle restraints: 42719 sinusoidal: 17202 harmonic: 25517 Sorted by residual: dihedral pdb=" CA THR a 90 " pdb=" C THR a 90 " pdb=" N THR a 91 " pdb=" CA THR a 91 " ideal model delta harmonic sigma weight residual 180.00 124.86 55.14 0 5.00e+00 4.00e-02 1.22e+02 dihedral pdb=" C5' ADP M 601 " pdb=" O5' ADP M 601 " pdb=" PA ADP M 601 " pdb=" O2A ADP M 601 " ideal model delta sinusoidal sigma weight residual -60.00 79.84 -139.83 1 2.00e+01 2.50e-03 4.23e+01 dihedral pdb=" C5' ADP a 601 " pdb=" O5' ADP a 601 " pdb=" PA ADP a 601 " pdb=" O2A ADP a 601 " ideal model delta sinusoidal sigma weight residual -60.00 79.82 -139.82 1 2.00e+01 2.50e-03 4.23e+01 ... (remaining 42716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.216: 11085 0.216 - 0.432: 6 0.432 - 0.647: 2 0.647 - 0.863: 3 0.863 - 1.079: 1 Chirality restraints: 11097 Sorted by residual: chirality pdb=" CA THR M 106 " pdb=" N THR M 106 " pdb=" C THR M 106 " pdb=" CB THR M 106 " both_signs ideal model delta sigma weight residual False 2.53 1.45 1.08 2.00e-01 2.50e+01 2.91e+01 chirality pdb=" CA THR I 106 " pdb=" N THR I 106 " pdb=" C THR I 106 " pdb=" CB THR I 106 " both_signs ideal model delta sigma weight residual False 2.53 1.68 0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" CA THR O 94 " pdb=" N THR O 94 " pdb=" C THR O 94 " pdb=" CB THR O 94 " both_signs ideal model delta sigma weight residual False 2.53 1.71 0.82 2.00e-01 2.50e+01 1.67e+01 ... (remaining 11094 not shown) Planarity restraints: 11940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY O 93 " 0.039 2.00e-02 2.50e+03 8.09e-02 6.54e+01 pdb=" C GLY O 93 " -0.140 2.00e-02 2.50e+03 pdb=" O GLY O 93 " 0.054 2.00e-02 2.50e+03 pdb=" N THR O 94 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY M 105 " 0.033 2.00e-02 2.50e+03 6.82e-02 4.65e+01 pdb=" C GLY M 105 " -0.118 2.00e-02 2.50e+03 pdb=" O GLY M 105 " 0.045 2.00e-02 2.50e+03 pdb=" N THR M 106 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR P 101 " 0.031 2.00e-02 2.50e+03 6.09e-02 3.71e+01 pdb=" C THR P 101 " -0.105 2.00e-02 2.50e+03 pdb=" O THR P 101 " 0.039 2.00e-02 2.50e+03 pdb=" N ASN P 102 " 0.036 2.00e-02 2.50e+03 ... (remaining 11937 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.79: 45 1.79 - 2.57: 796 2.57 - 3.35: 79106 3.35 - 4.12: 165707 4.12 - 4.90: 304008 Nonbonded interactions: 549662 Sorted by model distance: nonbonded pdb=" OD2 ASP e 71 " pdb=" O HOH e 701 " model vdw 1.018 2.440 nonbonded pdb=" OD1 ASP z 90 " pdb="MG MG z 602 " model vdw 1.042 2.170 nonbonded pdb=" OD2 ASP M 73 " pdb=" O HOH M 701 " model vdw 1.056 2.440 nonbonded pdb=" OD1 ASP L 66 " pdb=" F2 AF3 L 603 " model vdw 1.070 2.390 nonbonded pdb=" OG1 THR G 95 " pdb=" F3 AF3 G 603 " model vdw 1.098 2.390 ... (remaining 549657 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'G' selection = chain 'N' } ncs_group { reference = (chain 'H' and resid 1 through 526) selection = (chain 'O' and resid 1 through 526) } ncs_group { reference = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'P' } ncs_group { reference = chain 'K' selection = chain 'z' } 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 6.370 Check model and map are aligned: 0.780 Set scattering table: 0.450 Process input model: 138.810 Find NCS groups from input model: 6.040 Set up NCS constraints: 0.590 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.261 69153 Z= 0.293 Angle : 0.605 16.414 93401 Z= 0.334 Chirality : 0.046 1.079 11097 Planarity : 0.005 0.081 11940 Dihedral : 10.919 139.832 26199 Min Nonbonded Distance : 1.018 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.76 % Favored : 95.22 % Rotamer: Outliers : 3.51 % Allowed : 5.70 % Favored : 90.79 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.05 % Twisted Proline : 0.39 % Twisted General : 0.02 % 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: -5.89 (0.06), residues: 8832 helix: -4.90 (0.02), residues: 4186 sheet: -2.12 (0.14), residues: 1092 loop : -2.94 (0.08), residues: 3554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 302 HIS 0.003 0.001 HIS J 80 PHE 0.014 0.001 PHE a 239 TYR 0.008 0.001 TYR R 425 ARG 0.013 0.000 ARG z 157 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17664 Ramachandran restraints generated. 8832 Oldfield, 0 Emsley, 8832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17664 Ramachandran restraints generated. 8832 Oldfield, 0 Emsley, 8832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2549 residues out of total 7408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 2289 time to evaluate : 5.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 65 HIS cc_start: 0.7696 (m170) cc_final: 0.7436 (m170) REVERT: K 157 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7205 (mmm160) REVERT: K 418 MET cc_start: 0.8244 (ttm) cc_final: 0.7841 (mtp) REVERT: J 67 ASN cc_start: 0.7334 (p0) cc_final: 0.6900 (t0) REVERT: J 121 ILE cc_start: 0.7498 (tp) cc_final: 0.7181 (tp) REVERT: J 387 ASP cc_start: 0.6995 (t70) cc_final: 0.6653 (t0) REVERT: J 522 ASP cc_start: 0.6839 (t70) cc_final: 0.6573 (t0) REVERT: H 1 MET cc_start: 0.5082 (mtt) cc_final: 0.4336 (tpt) REVERT: H 32 ILE cc_start: 0.8732 (tt) cc_final: 0.8463 (tt) REVERT: G 88 ASP cc_start: 0.7161 (t70) cc_final: 0.6752 (t70) REVERT: G 293 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7347 (mt-10) REVERT: G 333 SER cc_start: 0.8536 (p) cc_final: 0.8169 (m) REVERT: E 279 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6500 (mt-10) REVERT: E 443 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7445 (pm20) REVERT: E 521 MET cc_start: 0.7927 (mmp) cc_final: 0.7702 (mmt) REVERT: B 274 LYS cc_start: 0.7207 (mmtt) cc_final: 0.6831 (mmtt) REVERT: A 20 GLN cc_start: 0.8177 (mt0) cc_final: 0.7950 (mt0) REVERT: A 270 ILE cc_start: 0.7133 (mt) cc_final: 0.6919 (mm) REVERT: A 352 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8222 (p) REVERT: R 76 VAL cc_start: 0.7108 (OUTLIER) cc_final: 0.6903 (t) REVERT: R 86 ARG cc_start: 0.5865 (mtt180) cc_final: 0.5291 (mtp85) REVERT: R 87 PRO cc_start: 0.6246 (Cg_exo) cc_final: 0.6000 (Cg_endo) REVERT: R 114 ASP cc_start: 0.7099 (t0) cc_final: 0.6793 (t70) REVERT: R 276 ARG cc_start: 0.3488 (mtt90) cc_final: 0.2080 (mmt-90) REVERT: R 330 MET cc_start: 0.1238 (mmp) cc_final: 0.0495 (mtt) REVERT: R 380 ARG cc_start: 0.5162 (ttp-110) cc_final: 0.4792 (mtp-110) REVERT: R 403 MET cc_start: 0.5996 (mmm) cc_final: 0.5593 (mtp) REVERT: R 412 GLU cc_start: 0.5493 (tt0) cc_final: 0.4519 (tp30) REVERT: z 44 MET cc_start: 0.8434 (mmm) cc_final: 0.8206 (mmt) REVERT: z 79 LYS cc_start: 0.8452 (mttt) cc_final: 0.8205 (mmtp) REVERT: z 508 CYS cc_start: 0.7483 (m) cc_final: 0.7196 (m) REVERT: z 522 MET cc_start: 0.7472 (ptt) cc_final: 0.7264 (ptt) REVERT: P 382 ASP cc_start: 0.7589 (m-30) cc_final: 0.7187 (m-30) REVERT: P 426 TYR cc_start: 0.5675 (m-80) cc_final: 0.5370 (m-80) REVERT: O 10 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7764 (mtmm) REVERT: O 32 ILE cc_start: 0.8609 (tt) cc_final: 0.8346 (tt) REVERT: O 38 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.8790 (m) REVERT: O 58 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8804 (mp) REVERT: e 169 THR cc_start: 0.8542 (m) cc_final: 0.8320 (p) REVERT: e 394 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7619 (mm-30) REVERT: e 443 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.6763 (pm20) REVERT: a 54 ILE cc_start: 0.8858 (mt) cc_final: 0.8642 (mt) REVERT: a 80 ASP cc_start: 0.7077 (t70) cc_final: 0.6842 (t0) REVERT: M 373 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8407 (pp) REVERT: M 397 VAL cc_start: 0.8919 (t) cc_final: 0.8252 (t) REVERT: L 93 ASP cc_start: 0.7109 (m-30) cc_final: 0.6811 (m-30) outliers start: 260 outliers final: 55 residues processed: 2457 average time/residue: 0.7075 time to fit residues: 2822.1627 Evaluate side-chains 1202 residues out of total 7408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1138 time to evaluate : 5.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 157 ARG Chi-restraints excluded: chain K residue 479 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 257 VAL Chi-restraints excluded: chain H residue 516 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 443 GLN Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 175 VAL Chi-restraints excluded: chain R residue 257 MET Chi-restraints excluded: chain z residue 477 VAL Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 217 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 253 THR Chi-restraints excluded: chain P residue 292 VAL Chi-restraints excluded: chain P residue 297 VAL Chi-restraints excluded: chain P residue 498 LEU Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain e residue 18 LYS Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain e residue 443 GLN Chi-restraints excluded: chain e residue 472 MET Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 352 VAL Chi-restraints excluded: chain a residue 399 VAL Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 241 VAL Chi-restraints excluded: chain M residue 373 LEU Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 64 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 741 optimal weight: 9.9990 chunk 665 optimal weight: 5.9990 chunk 369 optimal weight: 8.9990 chunk 227 optimal weight: 6.9990 chunk 448 optimal weight: 2.9990 chunk 355 optimal weight: 6.9990 chunk 688 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 chunk 418 optimal weight: 5.9990 chunk 512 optimal weight: 0.0980 chunk 797 optimal weight: 1.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 8 ASN K 84 GLN K 161 HIS K 214 HIS K 334 ASN K 425 HIS ** K 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 50 ASN J 219 HIS J 303 HIS J 383 ASN ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 264 GLN H 301 GLN ** H 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 ASN G 390 ASN G 454 ASN G 481 ASN E 180 HIS E 234 HIS I 394 ASN I 486 GLN B 148 HIS B 288 ASN A 56 ASN A 205 GLN A 251 GLN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 165 ASN R 227 HIS R 279 GLN ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 384 GLN R 414 ASN z 214 HIS z 386 GLN z 503 GLN P 21 HIS P 41 GLN P 53 ASN P 303 HIS ** P 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 201 GLN O 258 HIS O 331 GLN ** O 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 GLN N 64 ASN N 116 GLN N 302 HIS N 390 ASN ** e 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 443 GLN a 103 ASN a 205 GLN a 242 GLN a 492 ASN ** a 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 GLN ** M 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 394 ASN M 484 HIS L 288 ASN L 419 HIS L 502 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 69153 Z= 0.298 Angle : 0.685 13.594 93401 Z= 0.341 Chirality : 0.045 0.297 11097 Planarity : 0.005 0.067 11940 Dihedral : 7.922 179.184 9707 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.48 % Allowed : 12.34 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.07), residues: 8832 helix: -2.53 (0.06), residues: 4241 sheet: -1.47 (0.15), residues: 1101 loop : -2.35 (0.09), residues: 3490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 101 HIS 0.011 0.001 HIS L 178 PHE 0.026 0.002 PHE A 8 TYR 0.020 0.002 TYR N 303 ARG 0.008 0.001 ARG K 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17664 Ramachandran restraints generated. 8832 Oldfield, 0 Emsley, 8832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17664 Ramachandran restraints generated. 8832 Oldfield, 0 Emsley, 8832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1368 residues out of total 7408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1110 time to evaluate : 6.056 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: K 79 LYS cc_start: 0.8701 (mptt) cc_final: 0.8389 (mptt) REVERT: K 157 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7294 (mmm160) REVERT: K 514 ASN cc_start: 0.8345 (m-40) cc_final: 0.8122 (m-40) REVERT: J 67 ASN cc_start: 0.7623 (OUTLIER) cc_final: 0.7402 (p0) REVERT: J 522 ASP cc_start: 0.7102 (t70) cc_final: 0.6853 (t0) REVERT: H 32 ILE cc_start: 0.8769 (tt) cc_final: 0.8525 (tt) REVERT: G 27 ILE cc_start: 0.8737 (mm) cc_final: 0.8435 (mt) REVERT: G 31 LYS cc_start: 0.7912 (mttt) cc_final: 0.7591 (mttm) REVERT: G 95 THR cc_start: 0.7678 (p) cc_final: 0.7421 (p) REVERT: G 270 MET cc_start: 0.8187 (mtp) cc_final: 0.7984 (mtp) REVERT: G 305 MET cc_start: 0.7713 (tpp) cc_final: 0.7457 (tpp) REVERT: G 330 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7916 (mpt-90) REVERT: E 82 ASP cc_start: 0.7664 (p0) cc_final: 0.7349 (p0) REVERT: E 443 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7180 (pm20) REVERT: E 529 ASP cc_start: 0.7833 (p0) cc_final: 0.7633 (p0) REVERT: B 417 MET cc_start: 0.8838 (mtm) cc_final: 0.8618 (mtp) REVERT: B 439 TYR cc_start: 0.9325 (t80) cc_final: 0.9085 (t80) REVERT: A 101 LEU cc_start: 0.8873 (mt) cc_final: 0.8627 (mt) REVERT: A 137 ILE cc_start: 0.1128 (OUTLIER) cc_final: 0.0913 (tt) REVERT: R 69 GLU cc_start: 0.6490 (tt0) cc_final: 0.6227 (tt0) REVERT: R 76 VAL cc_start: 0.7213 (OUTLIER) cc_final: 0.7003 (t) REVERT: R 86 ARG cc_start: 0.6009 (mtt180) cc_final: 0.5493 (mtp85) REVERT: R 87 PRO cc_start: 0.6443 (Cg_exo) cc_final: 0.6242 (Cg_endo) REVERT: R 114 ASP cc_start: 0.7842 (t0) cc_final: 0.7318 (t70) REVERT: R 212 PHE cc_start: 0.4011 (t80) cc_final: 0.3721 (t80) REVERT: R 224 ASP cc_start: 0.5332 (m-30) cc_final: 0.4921 (m-30) REVERT: R 276 ARG cc_start: 0.4043 (mtt90) cc_final: 0.2599 (mmt-90) REVERT: R 330 MET cc_start: 0.1174 (mmp) cc_final: 0.0777 (mtt) REVERT: R 388 MET cc_start: 0.6733 (mtm) cc_final: 0.6402 (mtm) REVERT: z 56 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8695 (tp) REVERT: z 504 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8864 (tp) REVERT: P 37 LYS cc_start: 0.8058 (tttt) cc_final: 0.7752 (tttt) REVERT: O 10 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7672 (mmtt) REVERT: O 34 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7419 (mm-30) REVERT: O 38 THR cc_start: 0.9376 (OUTLIER) cc_final: 0.8903 (m) REVERT: O 184 MET cc_start: 0.7413 (mmm) cc_final: 0.7090 (mmm) REVERT: O 308 MET cc_start: 0.8158 (mtp) cc_final: 0.7946 (mtp) REVERT: N 49 MET cc_start: 0.8732 (mtp) cc_final: 0.8515 (mtm) REVERT: N 167 ARG cc_start: 0.6971 (mmm160) cc_final: 0.6660 (mmm160) REVERT: N 515 LEU cc_start: 0.9075 (tp) cc_final: 0.8839 (tp) REVERT: e 32 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8404 (mt) REVERT: e 40 LYS cc_start: 0.8123 (mtmt) cc_final: 0.7879 (mtpt) REVERT: e 94 LYS cc_start: 0.8654 (ttpp) cc_final: 0.8303 (tttp) REVERT: e 176 VAL cc_start: 0.8435 (t) cc_final: 0.8105 (t) REVERT: e 434 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.7046 (tt0) REVERT: M 73 ASP cc_start: 0.7487 (t70) cc_final: 0.7210 (t0) REVERT: M 93 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7527 (mm-30) REVERT: M 458 MET cc_start: 0.9011 (mmp) cc_final: 0.8682 (mmt) REVERT: L 408 TYR cc_start: 0.8126 (m-80) cc_final: 0.7907 (m-80) REVERT: L 432 GLU cc_start: 0.7124 (mp0) cc_final: 0.6902 (mp0) outliers start: 258 outliers final: 145 residues processed: 1296 average time/residue: 0.6506 time to fit residues: 1424.5855 Evaluate side-chains 1013 residues out of total 7408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 856 time to evaluate : 5.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 157 ARG Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 354 THR Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain K residue 477 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 117 GLU Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain J residue 347 CYS Chi-restraints excluded: chain J residue 380 SER Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 257 VAL Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain H residue 386 GLU Chi-restraints excluded: chain H residue 521 LYS Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 330 ARG Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 472 GLN Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 443 GLN Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain E residue 530 ASP Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 207 ASP Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 269 TYR Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 397 VAL Chi-restraints excluded: chain I residue 404 SER Chi-restraints excluded: chain I residue 503 ILE Chi-restraints excluded: chain I residue 523 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 105 HIS Chi-restraints excluded: chain R residue 108 GLU Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 163 ILE Chi-restraints excluded: chain R residue 175 VAL Chi-restraints excluded: chain R residue 227 HIS Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 321 MET Chi-restraints excluded: chain R residue 327 ASP Chi-restraints excluded: chain z residue 56 LEU Chi-restraints excluded: chain z residue 263 GLU Chi-restraints excluded: chain z residue 504 LEU Chi-restraints excluded: chain P residue 67 ASN Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 126 SER Chi-restraints excluded: chain P residue 217 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 251 THR Chi-restraints excluded: chain P residue 253 THR Chi-restraints excluded: chain P residue 283 ILE Chi-restraints excluded: chain P residue 292 VAL Chi-restraints excluded: chain P residue 297 VAL Chi-restraints excluded: chain P residue 344 MET Chi-restraints excluded: chain P residue 347 CYS Chi-restraints excluded: chain P residue 373 SER Chi-restraints excluded: chain P residue 380 SER Chi-restraints excluded: chain P residue 498 LEU Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 412 ILE Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 116 GLN Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 350 LEU Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain e residue 21 ASP Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 82 ASP Chi-restraints excluded: chain e residue 147 ASP Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 249 LEU Chi-restraints excluded: chain e residue 250 THR Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain e residue 434 GLU Chi-restraints excluded: chain e residue 443 GLN Chi-restraints excluded: chain e residue 456 ILE Chi-restraints excluded: chain e residue 472 MET Chi-restraints excluded: chain a residue 49 ILE Chi-restraints excluded: chain a residue 382 ASP Chi-restraints excluded: chain a residue 434 GLU Chi-restraints excluded: chain a residue 447 VAL Chi-restraints excluded: chain M residue 65 LYS Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 186 MET Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 241 VAL Chi-restraints excluded: chain M residue 295 CYS Chi-restraints excluded: chain M residue 340 ILE Chi-restraints excluded: chain M residue 490 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 77 ASP Chi-restraints excluded: chain L residue 216 GLU Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 288 ASN Chi-restraints excluded: chain L residue 474 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 443 optimal weight: 7.9990 chunk 247 optimal weight: 0.9980 chunk 663 optimal weight: 0.5980 chunk 542 optimal weight: 0.6980 chunk 219 optimal weight: 1.9990 chunk 798 optimal weight: 4.9990 chunk 862 optimal weight: 0.9990 chunk 711 optimal weight: 0.0470 chunk 792 optimal weight: 7.9990 chunk 272 optimal weight: 3.9990 chunk 640 optimal weight: 8.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 8 ASN K 346 HIS ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 241 ASN ** H 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 ASN G 253 GLN E 180 HIS ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS B 148 HIS ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 293 ASN P 41 GLN P 175 ASN ** P 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 264 GLN ** O 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 GLN ** e 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 180 HIS ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 493 HIS a 262 GLN a 333 ASN ** a 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 288 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 69153 Z= 0.153 Angle : 0.570 26.048 93401 Z= 0.274 Chirality : 0.041 0.292 11097 Planarity : 0.003 0.050 11940 Dihedral : 7.503 177.373 9676 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.96 % Allowed : 13.91 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.08), residues: 8832 helix: -1.03 (0.07), residues: 4274 sheet: -1.27 (0.16), residues: 1088 loop : -2.12 (0.09), residues: 3470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 101 HIS 0.008 0.001 HIS L 178 PHE 0.027 0.001 PHE H 360 TYR 0.017 0.001 TYR A 181 ARG 0.011 0.000 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17664 Ramachandran restraints generated. 8832 Oldfield, 0 Emsley, 8832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17664 Ramachandran restraints generated. 8832 Oldfield, 0 Emsley, 8832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 7408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 957 time to evaluate : 5.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 65 HIS cc_start: 0.7949 (m-70) cc_final: 0.7636 (m170) REVERT: K 157 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7285 (mmm-85) REVERT: K 194 MET cc_start: 0.7883 (tpt) cc_final: 0.7658 (mmt) REVERT: J 359 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7369 (mt0) REVERT: J 522 ASP cc_start: 0.7064 (t70) cc_final: 0.6689 (t0) REVERT: H 32 ILE cc_start: 0.8742 (tt) cc_final: 0.8470 (tt) REVERT: H 372 PHE cc_start: 0.7116 (OUTLIER) cc_final: 0.6644 (m-80) REVERT: G 27 ILE cc_start: 0.8730 (mm) cc_final: 0.8418 (mt) REVERT: G 31 LYS cc_start: 0.7908 (mttt) cc_final: 0.7630 (mttm) REVERT: G 88 ASP cc_start: 0.7956 (t70) cc_final: 0.7698 (t0) REVERT: G 305 MET cc_start: 0.7627 (tpp) cc_final: 0.7400 (tpp) REVERT: E 82 ASP cc_start: 0.7668 (p0) cc_final: 0.7409 (p0) REVERT: E 242 GLU cc_start: 0.7347 (tp30) cc_final: 0.6975 (tt0) REVERT: E 443 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.7115 (pm20) REVERT: I 447 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7205 (mm-30) REVERT: B 439 TYR cc_start: 0.9387 (t80) cc_final: 0.9171 (t80) REVERT: A 101 LEU cc_start: 0.8869 (mt) cc_final: 0.8656 (mt) REVERT: A 382 ASP cc_start: 0.7798 (m-30) cc_final: 0.7552 (m-30) REVERT: R 86 ARG cc_start: 0.6062 (mtt180) cc_final: 0.5507 (mtp85) REVERT: R 114 ASP cc_start: 0.7844 (t0) cc_final: 0.7294 (t70) REVERT: R 147 MET cc_start: 0.5471 (tpt) cc_final: 0.4941 (tpt) REVERT: R 212 PHE cc_start: 0.3921 (t80) cc_final: 0.3650 (t80) REVERT: R 276 ARG cc_start: 0.4111 (mtt90) cc_final: 0.2618 (mmt-90) REVERT: R 300 MET cc_start: 0.2819 (mmp) cc_final: 0.2412 (mmm) REVERT: R 327 ASP cc_start: 0.4984 (OUTLIER) cc_final: 0.3903 (p0) REVERT: R 330 MET cc_start: 0.1011 (mmp) cc_final: 0.0734 (mtt) REVERT: O 10 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7685 (mmtt) REVERT: O 38 THR cc_start: 0.9385 (OUTLIER) cc_final: 0.8949 (m) REVERT: N 20 ARG cc_start: 0.7497 (tpp80) cc_final: 0.7276 (tpp80) REVERT: N 49 MET cc_start: 0.8722 (mtp) cc_final: 0.8501 (mtm) REVERT: e 40 LYS cc_start: 0.7819 (mtmt) cc_final: 0.7597 (mtpt) REVERT: e 94 LYS cc_start: 0.8584 (ttpp) cc_final: 0.8276 (tttp) REVERT: e 183 MET cc_start: 0.7572 (mtp) cc_final: 0.7367 (mtp) REVERT: e 499 MET cc_start: 0.8729 (mmp) cc_final: 0.8310 (mmp) REVERT: M 73 ASP cc_start: 0.7298 (t70) cc_final: 0.6814 (t0) REVERT: M 93 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7603 (mm-30) REVERT: L 276 LYS cc_start: 0.8138 (tttt) cc_final: 0.7518 (mptt) REVERT: L 417 MET cc_start: 0.8536 (mtm) cc_final: 0.8235 (mtp) REVERT: L 432 GLU cc_start: 0.7033 (mp0) cc_final: 0.6822 (mp0) outliers start: 219 outliers final: 136 residues processed: 1104 average time/residue: 0.6183 time to fit residues: 1176.0716 Evaluate side-chains 985 residues out of total 7408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 841 time to evaluate : 5.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 12 GLU Chi-restraints excluded: chain K residue 157 ARG Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain K residue 471 SER Chi-restraints excluded: chain K residue 477 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain J residue 359 GLN Chi-restraints excluded: chain J residue 517 THR Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 257 VAL Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain H residue 372 PHE Chi-restraints excluded: chain H residue 386 GLU Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain H residue 521 LYS Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 472 GLN Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 120 GLN Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 443 GLN Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 166 SER Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 257 LYS Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 447 GLU Chi-restraints excluded: chain I residue 459 GLU Chi-restraints excluded: chain I residue 535 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 105 HIS Chi-restraints excluded: chain R residue 108 GLU Chi-restraints excluded: chain R residue 321 MET Chi-restraints excluded: chain R residue 327 ASP Chi-restraints excluded: chain R residue 404 ASP Chi-restraints excluded: chain z residue 47 LEU Chi-restraints excluded: chain z residue 201 GLU Chi-restraints excluded: chain z residue 263 GLU Chi-restraints excluded: chain P residue 67 ASN Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 191 PHE Chi-restraints excluded: chain P residue 217 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 249 MET Chi-restraints excluded: chain P residue 251 THR Chi-restraints excluded: chain P residue 253 THR Chi-restraints excluded: chain P residue 283 ILE Chi-restraints excluded: chain P residue 292 VAL Chi-restraints excluded: chain P residue 297 VAL Chi-restraints excluded: chain P residue 344 MET Chi-restraints excluded: chain P residue 498 LEU Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 216 PHE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 395 ILE Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 412 ILE Chi-restraints excluded: chain O residue 420 LEU Chi-restraints excluded: chain O residue 479 ILE Chi-restraints excluded: chain O residue 497 MET Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 459 THR Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain e residue 21 ASP Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain e residue 82 ASP Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 227 ILE Chi-restraints excluded: chain e residue 249 LEU Chi-restraints excluded: chain e residue 250 THR Chi-restraints excluded: chain e residue 392 ILE Chi-restraints excluded: chain e residue 436 ASP Chi-restraints excluded: chain e residue 443 GLN Chi-restraints excluded: chain e residue 472 MET Chi-restraints excluded: chain e residue 489 ILE Chi-restraints excluded: chain a residue 7 VAL Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 48 ASP Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 334 LEU Chi-restraints excluded: chain a residue 382 ASP Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain a residue 434 GLU Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 132 ILE Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 241 VAL Chi-restraints excluded: chain M residue 252 CYS Chi-restraints excluded: chain M residue 315 HIS Chi-restraints excluded: chain M residue 490 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain L residue 77 ASP Chi-restraints excluded: chain L residue 232 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 789 optimal weight: 6.9990 chunk 600 optimal weight: 0.8980 chunk 414 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 381 optimal weight: 6.9990 chunk 536 optimal weight: 8.9990 chunk 801 optimal weight: 6.9990 chunk 848 optimal weight: 9.9990 chunk 418 optimal weight: 7.9990 chunk 759 optimal weight: 0.9990 chunk 228 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 71 HIS K 460 GLN K 514 ASN J 80 HIS J 475 ASN H 21 GLN ** H 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 ASN G 73 GLN ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 ASN E 182 GLN ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 ASN ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 315 HIS I 394 ASN I 484 HIS B 124 GLN B 519 ASN A 205 GLN A 333 ASN ** R 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 99 ASN ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 245 GLN R 247 ASN ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 332 ASN ** R 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 337 ASN z 293 ASN ** P 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 ASN P 472 GLN P 475 ASN ** O 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 258 HIS O 390 HIS ** O 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 522 ASN ** N 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN a 284 ASN a 366 ASN M 129 HIS ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 148 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 69153 Z= 0.430 Angle : 0.735 31.569 93401 Z= 0.362 Chirality : 0.048 0.341 11097 Planarity : 0.004 0.052 11940 Dihedral : 8.022 178.065 9669 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.07 % Favored : 93.92 % Rotamer: Outliers : 4.23 % Allowed : 13.75 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.80 (0.08), residues: 8832 helix: -0.46 (0.08), residues: 4323 sheet: -1.24 (0.15), residues: 1105 loop : -2.03 (0.10), residues: 3404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 319 HIS 0.009 0.002 HIS B 148 PHE 0.032 0.002 PHE E 232 TYR 0.027 0.002 TYR K 353 ARG 0.016 0.001 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17664 Ramachandran restraints generated. 8832 Oldfield, 0 Emsley, 8832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17664 Ramachandran restraints generated. 8832 Oldfield, 0 Emsley, 8832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1148 residues out of total 7408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 835 time to evaluate : 5.988 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: K 157 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7289 (mmm160) REVERT: K 321 MET cc_start: 0.8388 (mmp) cc_final: 0.7872 (mmp) REVERT: J 121 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7319 (tp) REVERT: J 359 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7465 (mt0) REVERT: J 472 GLN cc_start: 0.5427 (OUTLIER) cc_final: 0.5067 (pp30) REVERT: J 522 ASP cc_start: 0.7192 (t70) cc_final: 0.6828 (t0) REVERT: H 32 ILE cc_start: 0.8891 (tt) cc_final: 0.8645 (tt) REVERT: G 88 ASP cc_start: 0.8015 (t70) cc_final: 0.7777 (t0) REVERT: G 330 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7757 (mpt-90) REVERT: E 279 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6776 (mt-10) REVERT: E 443 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7279 (pm20) REVERT: I 447 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7169 (mm-30) REVERT: B 51 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8604 (mt) REVERT: B 439 TYR cc_start: 0.9404 (t80) cc_final: 0.9157 (t80) REVERT: A 270 ILE cc_start: 0.8662 (mt) cc_final: 0.8406 (mt) REVERT: R 86 ARG cc_start: 0.6192 (mtt180) cc_final: 0.5554 (mtp85) REVERT: R 216 LYS cc_start: 0.5242 (mmtm) cc_final: 0.4983 (tptp) REVERT: R 267 MET cc_start: 0.4131 (OUTLIER) cc_final: 0.3481 (mmt) REVERT: R 276 ARG cc_start: 0.4617 (mtt90) cc_final: 0.3072 (mmt180) REVERT: R 362 LYS cc_start: 0.4413 (tttt) cc_final: 0.4113 (mttm) REVERT: R 406 MET cc_start: 0.6074 (ttt) cc_final: 0.5823 (mmp) REVERT: P 44 ARG cc_start: 0.8138 (ttm-80) cc_final: 0.7838 (ttt-90) REVERT: P 68 ASP cc_start: 0.8243 (t0) cc_final: 0.8035 (t0) REVERT: O 10 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7332 (mmtt) REVERT: O 38 THR cc_start: 0.9427 (OUTLIER) cc_final: 0.8953 (m) REVERT: O 402 ASN cc_start: 0.7757 (t0) cc_final: 0.7257 (p0) REVERT: N 49 MET cc_start: 0.8815 (mtp) cc_final: 0.8598 (mtm) REVERT: N 349 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8259 (tt) REVERT: e 40 LYS cc_start: 0.8023 (mtmt) cc_final: 0.7729 (mtpt) REVERT: a 44 MET cc_start: 0.8143 (mtt) cc_final: 0.7907 (ttm) REVERT: a 209 MET cc_start: 0.7215 (mmt) cc_final: 0.6991 (mmt) REVERT: M 458 MET cc_start: 0.9062 (mmp) cc_final: 0.8718 (mmt) REVERT: M 531 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8434 (tptt) REVERT: L 317 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7912 (t80) outliers start: 313 outliers final: 208 residues processed: 1076 average time/residue: 0.6224 time to fit residues: 1153.9468 Evaluate side-chains 988 residues out of total 7408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 766 time to evaluate : 5.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 12 GLU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 155 SER Chi-restraints excluded: chain K residue 157 ARG Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 380 ASN Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain K residue 477 VAL Chi-restraints excluded: chain K residue 503 GLN Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 117 GLU Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 213 SER Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain J residue 347 CYS Chi-restraints excluded: chain J residue 359 GLN Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain J residue 448 ILE Chi-restraints excluded: chain J residue 472 GLN Chi-restraints excluded: chain J residue 517 THR Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain H residue 386 GLU Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 330 ARG Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 472 GLN Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 443 GLN Chi-restraints excluded: chain E residue 530 ASP Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 207 ASP Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 257 LYS Chi-restraints excluded: chain I residue 269 TYR Chi-restraints excluded: chain I residue 273 ASP Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 319 LYS Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 397 VAL Chi-restraints excluded: chain I residue 422 ILE Chi-restraints excluded: chain I residue 447 GLU Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 105 HIS Chi-restraints excluded: chain R residue 108 GLU Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 163 ILE Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 267 MET Chi-restraints excluded: chain R residue 321 MET Chi-restraints excluded: chain R residue 327 ASP Chi-restraints excluded: chain R residue 370 ASN Chi-restraints excluded: chain R residue 404 ASP Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 12 GLU Chi-restraints excluded: chain z residue 82 THR Chi-restraints excluded: chain z residue 86 ASP Chi-restraints excluded: chain z residue 143 MET Chi-restraints excluded: chain z residue 263 GLU Chi-restraints excluded: chain z residue 386 GLN Chi-restraints excluded: chain z residue 389 ASP Chi-restraints excluded: chain z residue 504 LEU Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 67 ASN Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 126 SER Chi-restraints excluded: chain P residue 169 MET Chi-restraints excluded: chain P residue 193 ASP Chi-restraints excluded: chain P residue 217 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 251 THR Chi-restraints excluded: chain P residue 292 VAL Chi-restraints excluded: chain P residue 297 VAL Chi-restraints excluded: chain P residue 314 ARG Chi-restraints excluded: chain P residue 344 MET Chi-restraints excluded: chain P residue 352 LEU Chi-restraints excluded: chain P residue 373 SER Chi-restraints excluded: chain P residue 380 SER Chi-restraints excluded: chain P residue 498 LEU Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 347 VAL Chi-restraints excluded: chain O residue 395 ILE Chi-restraints excluded: chain O residue 420 LEU Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 170 SER Chi-restraints excluded: chain N residue 349 LEU Chi-restraints excluded: chain N residue 350 LEU Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain N residue 484 THR Chi-restraints excluded: chain e residue 21 ASP Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 82 ASP Chi-restraints excluded: chain e residue 147 ASP Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 213 VAL Chi-restraints excluded: chain e residue 226 VAL Chi-restraints excluded: chain e residue 227 ILE Chi-restraints excluded: chain e residue 249 LEU Chi-restraints excluded: chain e residue 262 HIS Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain e residue 392 ILE Chi-restraints excluded: chain e residue 472 MET Chi-restraints excluded: chain a residue 7 VAL Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 48 ASP Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 261 ASP Chi-restraints excluded: chain a residue 301 VAL Chi-restraints excluded: chain a residue 382 ASP Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain a residue 434 GLU Chi-restraints excluded: chain M residue 28 ASP Chi-restraints excluded: chain M residue 65 LYS Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 241 VAL Chi-restraints excluded: chain M residue 252 CYS Chi-restraints excluded: chain M residue 323 MET Chi-restraints excluded: chain M residue 398 ILE Chi-restraints excluded: chain M residue 490 THR Chi-restraints excluded: chain M residue 515 SER Chi-restraints excluded: chain M residue 531 LYS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 77 ASP Chi-restraints excluded: chain L residue 288 ASN Chi-restraints excluded: chain L residue 317 PHE Chi-restraints excluded: chain L residue 441 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 706 optimal weight: 6.9990 chunk 481 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 631 optimal weight: 3.9990 chunk 350 optimal weight: 0.9990 chunk 724 optimal weight: 0.8980 chunk 586 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 433 optimal weight: 1.9990 chunk 761 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 477 ASN H 21 GLN H 331 GLN ** H 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 221 ASN G 390 ASN E 53 ASN ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 279 GLN ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS P 50 ASN ** O 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 501 ASN e 53 ASN ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN ** a 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 69153 Z= 0.183 Angle : 0.586 27.935 93401 Z= 0.283 Chirality : 0.042 0.272 11097 Planarity : 0.003 0.045 11940 Dihedral : 7.556 175.164 9658 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.00 % Allowed : 15.42 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.05 % 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: 8832 helix: 0.15 (0.08), residues: 4298 sheet: -0.98 (0.16), residues: 1050 loop : -1.86 (0.10), residues: 3484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 435 HIS 0.011 0.001 HIS L 174 PHE 0.030 0.001 PHE A 8 TYR 0.018 0.001 TYR A 181 ARG 0.010 0.000 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17664 Ramachandran restraints generated. 8832 Oldfield, 0 Emsley, 8832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17664 Ramachandran restraints generated. 8832 Oldfield, 0 Emsley, 8832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1054 residues out of total 7408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 832 time to evaluate : 6.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 12 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8088 (pt0) REVERT: K 84 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8120 (mm110) REVERT: K 107 ASP cc_start: 0.6927 (t70) cc_final: 0.6720 (t70) REVERT: K 157 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7403 (mmm-85) REVERT: K 321 MET cc_start: 0.8311 (mmp) cc_final: 0.7856 (mmp) REVERT: J 121 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7297 (tp) REVERT: J 472 GLN cc_start: 0.5571 (OUTLIER) cc_final: 0.5226 (pp30) REVERT: J 522 ASP cc_start: 0.7094 (t70) cc_final: 0.6742 (t0) REVERT: H 32 ILE cc_start: 0.8817 (tt) cc_final: 0.8579 (tt) REVERT: G 330 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7891 (tpt-90) REVERT: E 7 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.7502 (m-10) REVERT: E 27 MET cc_start: 0.6131 (pmm) cc_final: 0.5860 (pmm) REVERT: I 447 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7236 (mm-30) REVERT: B 51 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8468 (mt) REVERT: B 439 TYR cc_start: 0.9378 (t80) cc_final: 0.9166 (t80) REVERT: R 86 ARG cc_start: 0.6184 (mtt180) cc_final: 0.5542 (mtp85) REVERT: R 216 LYS cc_start: 0.5189 (mmtm) cc_final: 0.4942 (tptp) REVERT: R 276 ARG cc_start: 0.4359 (mtt90) cc_final: 0.2525 (mmt180) REVERT: R 323 MET cc_start: 0.0940 (mmp) cc_final: 0.0518 (mmm) REVERT: R 388 MET cc_start: 0.6385 (mtm) cc_final: 0.6141 (mtm) REVERT: z 135 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: z 210 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9056 (mt) REVERT: O 10 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7283 (mmtt) REVERT: O 38 THR cc_start: 0.9384 (OUTLIER) cc_final: 0.8882 (m) REVERT: O 402 ASN cc_start: 0.7802 (t0) cc_final: 0.7292 (p0) REVERT: N 49 MET cc_start: 0.8785 (mtp) cc_final: 0.8527 (mtm) REVERT: e 239 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8331 (mttm) REVERT: a 209 MET cc_start: 0.7218 (mmt) cc_final: 0.6966 (mmt) REVERT: M 314 LEU cc_start: 0.8815 (tp) cc_final: 0.8553 (tp) REVERT: M 373 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8479 (pp) REVERT: L 299 TYR cc_start: 0.7715 (t80) cc_final: 0.7499 (t80) REVERT: L 436 MET cc_start: 0.8602 (mtt) cc_final: 0.8373 (mtt) outliers start: 222 outliers final: 143 residues processed: 1000 average time/residue: 0.6397 time to fit residues: 1111.3062 Evaluate side-chains 929 residues out of total 7408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 771 time to evaluate : 6.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 12 GLU Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 84 GLN Chi-restraints excluded: chain K residue 157 ARG Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 374 LEU Chi-restraints excluded: chain K residue 380 ASN Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain K residue 477 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain J residue 472 GLN Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain H residue 386 GLU Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 330 ARG Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 472 GLN Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain I residue 257 LYS Chi-restraints excluded: chain I residue 269 TYR Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 422 ILE Chi-restraints excluded: chain I residue 447 GLU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 105 HIS Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 404 ASP Chi-restraints excluded: chain z residue 12 GLU Chi-restraints excluded: chain z residue 47 LEU Chi-restraints excluded: chain z residue 135 GLU Chi-restraints excluded: chain z residue 210 LEU Chi-restraints excluded: chain z residue 263 GLU Chi-restraints excluded: chain z residue 386 GLN Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 67 ASN Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 126 SER Chi-restraints excluded: chain P residue 169 MET Chi-restraints excluded: chain P residue 193 ASP Chi-restraints excluded: chain P residue 217 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 251 THR Chi-restraints excluded: chain P residue 292 VAL Chi-restraints excluded: chain P residue 297 VAL Chi-restraints excluded: chain P residue 314 ARG Chi-restraints excluded: chain P residue 344 MET Chi-restraints excluded: chain P residue 380 SER Chi-restraints excluded: chain P residue 498 LEU Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 389 LEU Chi-restraints excluded: chain O residue 395 ILE Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 412 ILE Chi-restraints excluded: chain O residue 420 LEU Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 170 SER Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain N residue 484 THR Chi-restraints excluded: chain e residue 21 ASP Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 82 ASP Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 226 VAL Chi-restraints excluded: chain e residue 227 ILE Chi-restraints excluded: chain e residue 239 LYS Chi-restraints excluded: chain e residue 249 LEU Chi-restraints excluded: chain e residue 250 THR Chi-restraints excluded: chain e residue 375 CYS Chi-restraints excluded: chain e residue 392 ILE Chi-restraints excluded: chain e residue 436 ASP Chi-restraints excluded: chain e residue 472 MET Chi-restraints excluded: chain a residue 7 VAL Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 48 ASP Chi-restraints excluded: chain a residue 261 ASP Chi-restraints excluded: chain a residue 382 ASP Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain a residue 434 GLU Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 241 VAL Chi-restraints excluded: chain M residue 373 LEU Chi-restraints excluded: chain M residue 398 ILE Chi-restraints excluded: chain M residue 474 ILE Chi-restraints excluded: chain M residue 490 THR Chi-restraints excluded: chain M residue 503 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 77 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 285 optimal weight: 1.9990 chunk 764 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 498 optimal weight: 1.9990 chunk 209 optimal weight: 5.9990 chunk 849 optimal weight: 2.9990 chunk 705 optimal weight: 0.0980 chunk 393 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 281 optimal weight: 0.0270 chunk 445 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 21 GLN ** H 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 221 ASN ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN B 124 GLN ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 131 GLN ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS z 293 ASN ** z 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 ASN P 102 ASN ** O 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 174 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 69153 Z= 0.143 Angle : 0.556 24.804 93401 Z= 0.267 Chirality : 0.041 0.240 11097 Planarity : 0.003 0.079 11940 Dihedral : 7.271 173.919 9652 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.80 % Allowed : 15.84 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.09), residues: 8832 helix: 0.59 (0.08), residues: 4272 sheet: -0.86 (0.16), residues: 1060 loop : -1.69 (0.10), residues: 3500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 101 HIS 0.007 0.001 HIS L 174 PHE 0.030 0.001 PHE H 360 TYR 0.022 0.001 TYR K 353 ARG 0.010 0.000 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17664 Ramachandran restraints generated. 8832 Oldfield, 0 Emsley, 8832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17664 Ramachandran restraints generated. 8832 Oldfield, 0 Emsley, 8832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1041 residues out of total 7408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 834 time to evaluate : 6.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 12 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7930 (pt0) REVERT: K 107 ASP cc_start: 0.6870 (t70) cc_final: 0.6666 (t70) REVERT: K 157 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7188 (mmm-85) REVERT: K 522 MET cc_start: 0.8220 (ptt) cc_final: 0.7981 (ptt) REVERT: J 472 GLN cc_start: 0.5571 (OUTLIER) cc_final: 0.5200 (pp30) REVERT: J 522 ASP cc_start: 0.7042 (t70) cc_final: 0.6699 (t0) REVERT: H 32 ILE cc_start: 0.8808 (tt) cc_final: 0.8560 (tt) REVERT: H 116 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8411 (mp) REVERT: H 270 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: G 330 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7868 (tpt-90) REVERT: I 447 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7198 (mm-30) REVERT: B 456 TYR cc_start: 0.8272 (m-80) cc_final: 0.8054 (m-10) REVERT: R 1 MET cc_start: 0.5579 (ppp) cc_final: 0.5182 (ppp) REVERT: R 86 ARG cc_start: 0.6155 (mtt180) cc_final: 0.5492 (mtp85) REVERT: R 216 LYS cc_start: 0.5201 (mmtm) cc_final: 0.4837 (tptp) REVERT: R 276 ARG cc_start: 0.4525 (mtt90) cc_final: 0.2559 (mmt180) REVERT: R 300 MET cc_start: 0.2226 (mmp) cc_final: 0.1764 (mmm) REVERT: R 323 MET cc_start: 0.1087 (mmp) cc_final: 0.0819 (mmm) REVERT: R 388 MET cc_start: 0.6458 (mtm) cc_final: 0.6228 (mtm) REVERT: R 406 MET cc_start: 0.7250 (mmp) cc_final: 0.6462 (ttt) REVERT: z 135 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: O 10 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7360 (mmtt) REVERT: O 38 THR cc_start: 0.9349 (OUTLIER) cc_final: 0.8770 (m) REVERT: O 402 ASN cc_start: 0.7739 (t0) cc_final: 0.7199 (p0) REVERT: N 49 MET cc_start: 0.8740 (mtp) cc_final: 0.8439 (mtm) REVERT: a 209 MET cc_start: 0.7228 (mmt) cc_final: 0.6963 (mmt) REVERT: M 314 LEU cc_start: 0.8858 (tp) cc_final: 0.8629 (tp) REVERT: M 373 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8513 (pp) REVERT: M 458 MET cc_start: 0.9079 (mmp) cc_final: 0.8735 (mmt) REVERT: L 299 TYR cc_start: 0.7890 (t80) cc_final: 0.7515 (t80) REVERT: L 436 MET cc_start: 0.8568 (mtt) cc_final: 0.8339 (mtt) outliers start: 207 outliers final: 143 residues processed: 990 average time/residue: 0.6581 time to fit residues: 1133.4051 Evaluate side-chains 932 residues out of total 7408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 778 time to evaluate : 5.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 12 GLU Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 157 ARG Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 374 LEU Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain K residue 477 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain J residue 472 GLN Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain H residue 386 GLU Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 330 ARG Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 472 GLN Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain I residue 24 TYR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain I residue 257 LYS Chi-restraints excluded: chain I residue 269 TYR Chi-restraints excluded: chain I residue 273 ASP Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 397 VAL Chi-restraints excluded: chain I residue 447 GLU Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 105 HIS Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 375 GLN Chi-restraints excluded: chain R residue 404 ASP Chi-restraints excluded: chain z residue 63 LEU Chi-restraints excluded: chain z residue 135 GLU Chi-restraints excluded: chain z residue 143 MET Chi-restraints excluded: chain z residue 190 MET Chi-restraints excluded: chain z residue 263 GLU Chi-restraints excluded: chain z residue 386 GLN Chi-restraints excluded: chain P residue 67 ASN Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 191 PHE Chi-restraints excluded: chain P residue 193 ASP Chi-restraints excluded: chain P residue 217 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 251 THR Chi-restraints excluded: chain P residue 297 VAL Chi-restraints excluded: chain P residue 314 ARG Chi-restraints excluded: chain P residue 344 MET Chi-restraints excluded: chain P residue 352 LEU Chi-restraints excluded: chain P residue 357 ASP Chi-restraints excluded: chain P residue 380 SER Chi-restraints excluded: chain P residue 498 LEU Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 216 PHE Chi-restraints excluded: chain O residue 395 ILE Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 412 ILE Chi-restraints excluded: chain O residue 420 LEU Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 170 SER Chi-restraints excluded: chain N residue 452 ILE Chi-restraints excluded: chain N residue 459 THR Chi-restraints excluded: chain N residue 484 THR Chi-restraints excluded: chain e residue 21 ASP Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 82 ASP Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 213 VAL Chi-restraints excluded: chain e residue 226 VAL Chi-restraints excluded: chain e residue 227 ILE Chi-restraints excluded: chain e residue 249 LEU Chi-restraints excluded: chain e residue 250 THR Chi-restraints excluded: chain e residue 375 CYS Chi-restraints excluded: chain e residue 392 ILE Chi-restraints excluded: chain e residue 436 ASP Chi-restraints excluded: chain e residue 506 GLU Chi-restraints excluded: chain a residue 7 VAL Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 48 ASP Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 261 ASP Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain a residue 434 GLU Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 241 VAL Chi-restraints excluded: chain M residue 373 LEU Chi-restraints excluded: chain M residue 474 ILE Chi-restraints excluded: chain M residue 490 THR Chi-restraints excluded: chain M residue 503 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 77 ASP Chi-restraints excluded: chain L residue 177 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 819 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 484 optimal weight: 10.0000 chunk 620 optimal weight: 3.9990 chunk 480 optimal weight: 9.9990 chunk 715 optimal weight: 7.9990 chunk 474 optimal weight: 0.0670 chunk 846 optimal weight: 10.0000 chunk 529 optimal weight: 8.9990 chunk 515 optimal weight: 6.9990 chunk 390 optimal weight: 0.3980 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 513 ASN ** H 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS P 53 ASN ** O 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 501 ASN ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 174 HIS ** L 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 69153 Z= 0.190 Angle : 0.571 24.034 93401 Z= 0.275 Chirality : 0.042 0.318 11097 Planarity : 0.003 0.073 11940 Dihedral : 7.251 179.069 9648 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.82 % Allowed : 16.18 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.09), residues: 8832 helix: 0.82 (0.08), residues: 4261 sheet: -0.80 (0.16), residues: 1075 loop : -1.64 (0.10), residues: 3496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 101 HIS 0.008 0.001 HIS L 174 PHE 0.032 0.001 PHE H 360 TYR 0.023 0.001 TYR I 282 ARG 0.013 0.000 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17664 Ramachandran restraints generated. 8832 Oldfield, 0 Emsley, 8832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17664 Ramachandran restraints generated. 8832 Oldfield, 0 Emsley, 8832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 7408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 789 time to evaluate : 6.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 12 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7944 (pt0) REVERT: K 107 ASP cc_start: 0.6909 (t70) cc_final: 0.6653 (t0) REVERT: J 121 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7340 (tp) REVERT: J 472 GLN cc_start: 0.5665 (OUTLIER) cc_final: 0.5260 (pp30) REVERT: J 522 ASP cc_start: 0.7025 (t70) cc_final: 0.6675 (t0) REVERT: H 32 ILE cc_start: 0.8793 (tt) cc_final: 0.8537 (tt) REVERT: H 116 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8433 (mp) REVERT: H 270 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7756 (tt0) REVERT: H 316 GLU cc_start: 0.7228 (tp30) cc_final: 0.6856 (tm-30) REVERT: H 379 GLU cc_start: 0.7345 (tp30) cc_final: 0.7062 (tp30) REVERT: G 330 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7872 (tpt-90) REVERT: E 284 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: B 349 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8914 (mm) REVERT: R 1 MET cc_start: 0.5642 (ppp) cc_final: 0.5200 (ppp) REVERT: R 86 ARG cc_start: 0.6185 (mtt180) cc_final: 0.5542 (mtp85) REVERT: R 216 LYS cc_start: 0.5252 (mmtm) cc_final: 0.4834 (tptp) REVERT: R 267 MET cc_start: 0.3948 (OUTLIER) cc_final: 0.3208 (mmt) REVERT: R 276 ARG cc_start: 0.4178 (mtt90) cc_final: 0.2506 (mmt180) REVERT: R 300 MET cc_start: 0.2098 (mmp) cc_final: 0.1649 (mmm) REVERT: R 323 MET cc_start: 0.1109 (mmp) cc_final: 0.0903 (mmm) REVERT: R 388 MET cc_start: 0.6482 (mtm) cc_final: 0.5778 (mmm) REVERT: R 406 MET cc_start: 0.7396 (mmp) cc_final: 0.6547 (ttt) REVERT: z 135 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: O 10 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7363 (mmtt) REVERT: O 38 THR cc_start: 0.9380 (OUTLIER) cc_final: 0.8847 (m) REVERT: O 402 ASN cc_start: 0.7690 (t0) cc_final: 0.7147 (p0) REVERT: N 49 MET cc_start: 0.8731 (mtp) cc_final: 0.8457 (mtm) REVERT: N 520 ASP cc_start: 0.7939 (p0) cc_final: 0.7141 (p0) REVERT: e 446 MET cc_start: 0.8434 (mmm) cc_final: 0.8166 (mmm) REVERT: e 458 MET cc_start: 0.8344 (mtm) cc_final: 0.7739 (mtm) REVERT: a 209 MET cc_start: 0.7167 (mmt) cc_final: 0.6899 (mmt) REVERT: M 373 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8521 (pp) REVERT: M 458 MET cc_start: 0.9086 (mmp) cc_final: 0.8747 (mmt) outliers start: 209 outliers final: 168 residues processed: 952 average time/residue: 0.6145 time to fit residues: 1022.5537 Evaluate side-chains 939 residues out of total 7408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 758 time to evaluate : 6.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 12 GLU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 374 LEU Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 477 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain J residue 472 GLN Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain H residue 386 GLU Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 330 ARG Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 472 GLN Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 436 ASP Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain I residue 24 TYR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 257 LYS Chi-restraints excluded: chain I residue 269 TYR Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 397 VAL Chi-restraints excluded: chain I residue 422 ILE Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 105 HIS Chi-restraints excluded: chain R residue 163 ILE Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 267 MET Chi-restraints excluded: chain R residue 321 MET Chi-restraints excluded: chain R residue 370 ASN Chi-restraints excluded: chain R residue 404 ASP Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 12 GLU Chi-restraints excluded: chain z residue 63 LEU Chi-restraints excluded: chain z residue 135 GLU Chi-restraints excluded: chain z residue 190 MET Chi-restraints excluded: chain z residue 263 GLU Chi-restraints excluded: chain z residue 386 GLN Chi-restraints excluded: chain P residue 67 ASN Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 126 SER Chi-restraints excluded: chain P residue 193 ASP Chi-restraints excluded: chain P residue 217 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 251 THR Chi-restraints excluded: chain P residue 266 MET Chi-restraints excluded: chain P residue 297 VAL Chi-restraints excluded: chain P residue 314 ARG Chi-restraints excluded: chain P residue 352 LEU Chi-restraints excluded: chain P residue 357 ASP Chi-restraints excluded: chain P residue 373 SER Chi-restraints excluded: chain P residue 380 SER Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 216 PHE Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain O residue 389 LEU Chi-restraints excluded: chain O residue 395 ILE Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 420 LEU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 170 SER Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 452 ILE Chi-restraints excluded: chain N residue 459 THR Chi-restraints excluded: chain N residue 484 THR Chi-restraints excluded: chain e residue 21 ASP Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 82 ASP Chi-restraints excluded: chain e residue 147 ASP Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 213 VAL Chi-restraints excluded: chain e residue 226 VAL Chi-restraints excluded: chain e residue 227 ILE Chi-restraints excluded: chain e residue 249 LEU Chi-restraints excluded: chain e residue 250 THR Chi-restraints excluded: chain e residue 375 CYS Chi-restraints excluded: chain e residue 392 ILE Chi-restraints excluded: chain e residue 436 ASP Chi-restraints excluded: chain e residue 506 GLU Chi-restraints excluded: chain a residue 7 VAL Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 382 ASP Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain a residue 434 GLU Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 241 VAL Chi-restraints excluded: chain M residue 373 LEU Chi-restraints excluded: chain M residue 474 ILE Chi-restraints excluded: chain M residue 490 THR Chi-restraints excluded: chain M residue 503 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 77 ASP Chi-restraints excluded: chain L residue 177 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 523 optimal weight: 0.7980 chunk 337 optimal weight: 4.9990 chunk 505 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 538 optimal weight: 6.9990 chunk 576 optimal weight: 4.9990 chunk 418 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 665 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN R 279 GLN ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS ** O 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 501 ASN ** N 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 205 GLN ** a 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 174 HIS ** L 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 69153 Z= 0.244 Angle : 0.597 21.485 93401 Z= 0.290 Chirality : 0.043 0.332 11097 Planarity : 0.003 0.087 11940 Dihedral : 7.261 175.570 9642 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.11 % Allowed : 15.92 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.09), residues: 8832 helix: 0.88 (0.08), residues: 4282 sheet: -0.82 (0.16), residues: 1100 loop : -1.63 (0.10), residues: 3450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 101 HIS 0.011 0.001 HIS E 262 PHE 0.031 0.001 PHE H 360 TYR 0.025 0.001 TYR I 282 ARG 0.013 0.000 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17664 Ramachandran restraints generated. 8832 Oldfield, 0 Emsley, 8832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17664 Ramachandran restraints generated. 8832 Oldfield, 0 Emsley, 8832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 7408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 776 time to evaluate : 6.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 12 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8122 (pt0) REVERT: K 107 ASP cc_start: 0.6967 (t70) cc_final: 0.6709 (t0) REVERT: J 77 GLU cc_start: 0.6745 (mt-10) cc_final: 0.6448 (mt-10) REVERT: J 121 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7359 (tp) REVERT: J 472 GLN cc_start: 0.5775 (OUTLIER) cc_final: 0.5312 (pp30) REVERT: J 522 ASP cc_start: 0.7095 (t70) cc_final: 0.6740 (t0) REVERT: H 32 ILE cc_start: 0.8835 (tt) cc_final: 0.8582 (tt) REVERT: H 116 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8465 (mp) REVERT: H 316 GLU cc_start: 0.7233 (tp30) cc_final: 0.6866 (tm-30) REVERT: H 379 GLU cc_start: 0.7348 (tp30) cc_final: 0.7030 (tp30) REVERT: G 330 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7903 (tpt-90) REVERT: I 355 MET cc_start: 0.8135 (mmm) cc_final: 0.7835 (mmt) REVERT: B 310 MET cc_start: 0.7198 (tpp) cc_final: 0.6923 (mmm) REVERT: B 408 TYR cc_start: 0.8190 (m-80) cc_final: 0.7943 (m-80) REVERT: R 86 ARG cc_start: 0.6220 (mtt180) cc_final: 0.5586 (mtp85) REVERT: R 267 MET cc_start: 0.3971 (OUTLIER) cc_final: 0.3124 (mmt) REVERT: R 276 ARG cc_start: 0.4438 (mtt90) cc_final: 0.2593 (mmt180) REVERT: R 300 MET cc_start: 0.2142 (mmp) cc_final: 0.1655 (mmm) REVERT: R 323 MET cc_start: 0.1107 (mmp) cc_final: 0.0895 (mmm) REVERT: R 388 MET cc_start: 0.6658 (mtm) cc_final: 0.6009 (mmm) REVERT: R 406 MET cc_start: 0.7357 (mmp) cc_final: 0.6606 (ttt) REVERT: z 135 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: O 10 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7380 (mmtt) REVERT: O 38 THR cc_start: 0.9405 (OUTLIER) cc_final: 0.8880 (m) REVERT: O 402 ASN cc_start: 0.7798 (t0) cc_final: 0.7128 (p0) REVERT: N 49 MET cc_start: 0.8753 (mtp) cc_final: 0.8467 (mtm) REVERT: N 73 GLN cc_start: 0.7481 (mp10) cc_final: 0.7120 (mp10) REVERT: a 209 MET cc_start: 0.7195 (mmt) cc_final: 0.6922 (mmt) REVERT: M 314 LEU cc_start: 0.8813 (tp) cc_final: 0.8544 (tp) REVERT: M 458 MET cc_start: 0.9070 (mmp) cc_final: 0.8747 (mmt) outliers start: 230 outliers final: 182 residues processed: 950 average time/residue: 0.6378 time to fit residues: 1056.9151 Evaluate side-chains 932 residues out of total 7408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 741 time to evaluate : 5.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 12 GLU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 155 SER Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 374 LEU Chi-restraints excluded: chain K residue 380 ASN Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 477 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain J residue 472 GLN Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 330 ARG Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 472 GLN Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 436 ASP Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain E residue 530 ASP Chi-restraints excluded: chain I residue 24 TYR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain I residue 257 LYS Chi-restraints excluded: chain I residue 269 TYR Chi-restraints excluded: chain I residue 422 ILE Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 163 ILE Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain R residue 267 MET Chi-restraints excluded: chain R residue 321 MET Chi-restraints excluded: chain R residue 370 ASN Chi-restraints excluded: chain R residue 404 ASP Chi-restraints excluded: chain R residue 414 ASN Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 12 GLU Chi-restraints excluded: chain z residue 63 LEU Chi-restraints excluded: chain z residue 135 GLU Chi-restraints excluded: chain z residue 143 MET Chi-restraints excluded: chain z residue 190 MET Chi-restraints excluded: chain z residue 263 GLU Chi-restraints excluded: chain z residue 386 GLN Chi-restraints excluded: chain P residue 67 ASN Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 126 SER Chi-restraints excluded: chain P residue 193 ASP Chi-restraints excluded: chain P residue 217 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 251 THR Chi-restraints excluded: chain P residue 266 MET Chi-restraints excluded: chain P residue 283 ILE Chi-restraints excluded: chain P residue 297 VAL Chi-restraints excluded: chain P residue 314 ARG Chi-restraints excluded: chain P residue 352 LEU Chi-restraints excluded: chain P residue 357 ASP Chi-restraints excluded: chain P residue 373 SER Chi-restraints excluded: chain P residue 380 SER Chi-restraints excluded: chain P residue 499 ASP Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain O residue 389 LEU Chi-restraints excluded: chain O residue 395 ILE Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 420 LEU Chi-restraints excluded: chain O residue 479 ILE Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 170 SER Chi-restraints excluded: chain N residue 350 LEU Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 452 ILE Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain N residue 484 THR Chi-restraints excluded: chain e residue 21 ASP Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 82 ASP Chi-restraints excluded: chain e residue 147 ASP Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 226 VAL Chi-restraints excluded: chain e residue 227 ILE Chi-restraints excluded: chain e residue 249 LEU Chi-restraints excluded: chain e residue 250 THR Chi-restraints excluded: chain e residue 262 HIS Chi-restraints excluded: chain e residue 375 CYS Chi-restraints excluded: chain e residue 392 ILE Chi-restraints excluded: chain e residue 436 ASP Chi-restraints excluded: chain e residue 506 GLU Chi-restraints excluded: chain a residue 7 VAL Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 48 ASP Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 382 ASP Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain a residue 434 GLU Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 241 VAL Chi-restraints excluded: chain M residue 323 MET Chi-restraints excluded: chain M residue 398 ILE Chi-restraints excluded: chain M residue 490 THR Chi-restraints excluded: chain M residue 503 ILE Chi-restraints excluded: chain M residue 515 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 77 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 769 optimal weight: 6.9990 chunk 810 optimal weight: 7.9990 chunk 739 optimal weight: 6.9990 chunk 788 optimal weight: 4.9990 chunk 474 optimal weight: 4.9990 chunk 343 optimal weight: 9.9990 chunk 619 optimal weight: 0.6980 chunk 242 optimal weight: 0.0030 chunk 712 optimal weight: 3.9990 chunk 745 optimal weight: 9.9990 chunk 785 optimal weight: 5.9990 overall best weight: 2.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 335 ASN ** H 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS ** O 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 174 HIS ** L 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 302 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 69153 Z= 0.309 Angle : 0.645 20.921 93401 Z= 0.314 Chirality : 0.045 0.311 11097 Planarity : 0.004 0.095 11940 Dihedral : 7.402 176.554 9640 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.07 % Favored : 93.91 % Rotamer: Outliers : 3.15 % Allowed : 16.02 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.09), residues: 8832 helix: 0.85 (0.08), residues: 4287 sheet: -0.82 (0.16), residues: 1120 loop : -1.67 (0.10), residues: 3425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 319 HIS 0.010 0.001 HIS E 262 PHE 0.032 0.002 PHE A 8 TYR 0.024 0.002 TYR I 282 ARG 0.010 0.001 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17664 Ramachandran restraints generated. 8832 Oldfield, 0 Emsley, 8832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17664 Ramachandran restraints generated. 8832 Oldfield, 0 Emsley, 8832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 7408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 759 time to evaluate : 6.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 12 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8114 (pt0) REVERT: K 107 ASP cc_start: 0.7002 (t70) cc_final: 0.6750 (t0) REVERT: J 38 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7584 (tt0) REVERT: J 77 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6521 (mt-10) REVERT: J 121 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7313 (tp) REVERT: J 472 GLN cc_start: 0.5978 (OUTLIER) cc_final: 0.5385 (pp30) REVERT: J 522 ASP cc_start: 0.7135 (t70) cc_final: 0.6776 (t0) REVERT: H 32 ILE cc_start: 0.8910 (tt) cc_final: 0.8633 (tt) REVERT: H 116 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8453 (mp) REVERT: H 482 GLU cc_start: 0.7082 (mp0) cc_final: 0.6841 (mp0) REVERT: G 330 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7865 (tpt-90) REVERT: B 51 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8508 (mt) REVERT: B 310 MET cc_start: 0.7285 (tpp) cc_final: 0.7057 (mmm) REVERT: B 408 TYR cc_start: 0.8318 (m-80) cc_final: 0.8092 (m-80) REVERT: B 456 TYR cc_start: 0.8227 (m-10) cc_final: 0.8020 (m-10) REVERT: R 86 ARG cc_start: 0.6248 (mtt180) cc_final: 0.5566 (mtp85) REVERT: R 105 HIS cc_start: 0.5969 (OUTLIER) cc_final: 0.5599 (m170) REVERT: R 267 MET cc_start: 0.4083 (OUTLIER) cc_final: 0.3117 (mmt) REVERT: R 276 ARG cc_start: 0.4450 (mtt90) cc_final: 0.2641 (mmt180) REVERT: R 300 MET cc_start: 0.2460 (mmp) cc_final: 0.1986 (mmm) REVERT: R 388 MET cc_start: 0.6628 (mtm) cc_final: 0.6021 (mmm) REVERT: z 135 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: P 52 MET cc_start: 0.8121 (mmp) cc_final: 0.7866 (mmt) REVERT: O 10 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7367 (mmtt) REVERT: O 38 THR cc_start: 0.9413 (OUTLIER) cc_final: 0.8951 (m) REVERT: O 402 ASN cc_start: 0.7833 (t0) cc_final: 0.7149 (p0) REVERT: N 49 MET cc_start: 0.8843 (mtp) cc_final: 0.8592 (mtm) REVERT: N 73 GLN cc_start: 0.7420 (mp10) cc_final: 0.7080 (mp10) REVERT: a 209 MET cc_start: 0.7223 (mmt) cc_final: 0.6954 (mmt) REVERT: M 458 MET cc_start: 0.9072 (mmp) cc_final: 0.8727 (mmt) REVERT: M 506 GLU cc_start: 0.6992 (tm-30) cc_final: 0.6383 (tm-30) outliers start: 233 outliers final: 192 residues processed: 941 average time/residue: 0.6421 time to fit residues: 1055.2181 Evaluate side-chains 939 residues out of total 7408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 736 time to evaluate : 6.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 12 GLU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 155 SER Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 244 VAL Chi-restraints excluded: chain K residue 374 LEU Chi-restraints excluded: chain K residue 380 ASN Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 477 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain J residue 347 CYS Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain J residue 472 GLN Chi-restraints excluded: chain J residue 502 LEU Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 330 ARG Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 472 GLN Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 436 ASP Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain E residue 530 ASP Chi-restraints excluded: chain I residue 24 TYR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain I residue 257 LYS Chi-restraints excluded: chain I residue 269 TYR Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 105 HIS Chi-restraints excluded: chain R residue 163 ILE Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 267 MET Chi-restraints excluded: chain R residue 321 MET Chi-restraints excluded: chain R residue 370 ASN Chi-restraints excluded: chain R residue 414 ASN Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 12 GLU Chi-restraints excluded: chain z residue 47 LEU Chi-restraints excluded: chain z residue 63 LEU Chi-restraints excluded: chain z residue 135 GLU Chi-restraints excluded: chain z residue 143 MET Chi-restraints excluded: chain z residue 190 MET Chi-restraints excluded: chain z residue 263 GLU Chi-restraints excluded: chain z residue 386 GLN Chi-restraints excluded: chain P residue 67 ASN Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 126 SER Chi-restraints excluded: chain P residue 193 ASP Chi-restraints excluded: chain P residue 217 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 251 THR Chi-restraints excluded: chain P residue 266 MET Chi-restraints excluded: chain P residue 292 VAL Chi-restraints excluded: chain P residue 297 VAL Chi-restraints excluded: chain P residue 314 ARG Chi-restraints excluded: chain P residue 352 LEU Chi-restraints excluded: chain P residue 357 ASP Chi-restraints excluded: chain P residue 373 SER Chi-restraints excluded: chain P residue 380 SER Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain O residue 389 LEU Chi-restraints excluded: chain O residue 395 ILE Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 412 ILE Chi-restraints excluded: chain O residue 420 LEU Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain O residue 479 ILE Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 170 SER Chi-restraints excluded: chain N residue 350 LEU Chi-restraints excluded: chain N residue 388 GLU Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 452 ILE Chi-restraints excluded: chain N residue 459 THR Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain N residue 484 THR Chi-restraints excluded: chain e residue 21 ASP Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 82 ASP Chi-restraints excluded: chain e residue 147 ASP Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 213 VAL Chi-restraints excluded: chain e residue 226 VAL Chi-restraints excluded: chain e residue 227 ILE Chi-restraints excluded: chain e residue 249 LEU Chi-restraints excluded: chain e residue 250 THR Chi-restraints excluded: chain e residue 262 HIS Chi-restraints excluded: chain e residue 375 CYS Chi-restraints excluded: chain e residue 392 ILE Chi-restraints excluded: chain e residue 436 ASP Chi-restraints excluded: chain e residue 506 GLU Chi-restraints excluded: chain a residue 7 VAL Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 48 ASP Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 382 ASP Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain a residue 434 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 241 VAL Chi-restraints excluded: chain M residue 323 MET Chi-restraints excluded: chain M residue 398 ILE Chi-restraints excluded: chain M residue 490 THR Chi-restraints excluded: chain M residue 503 ILE Chi-restraints excluded: chain M residue 515 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 77 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 517 optimal weight: 4.9990 chunk 833 optimal weight: 2.9990 chunk 508 optimal weight: 0.9990 chunk 395 optimal weight: 3.9990 chunk 579 optimal weight: 0.9980 chunk 874 optimal weight: 0.9980 chunk 805 optimal weight: 0.9990 chunk 696 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 538 optimal weight: 3.9990 chunk 427 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 233 HIS H 335 ASN ** H 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 227 HIS ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS z 425 HIS ** O 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 501 ASN ** N 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN ** a 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 174 HIS ** L 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 69153 Z= 0.195 Angle : 0.596 18.692 93401 Z= 0.288 Chirality : 0.043 0.307 11097 Planarity : 0.003 0.096 11940 Dihedral : 7.194 176.155 9640 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.64 % Favored : 94.35 % Rotamer: Outliers : 2.59 % Allowed : 16.69 % Favored : 80.71 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.09), residues: 8832 helix: 1.06 (0.08), residues: 4275 sheet: -0.75 (0.16), residues: 1130 loop : -1.59 (0.10), residues: 3427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 101 HIS 0.010 0.001 HIS L 174 PHE 0.033 0.001 PHE H 360 TYR 0.023 0.001 TYR a 181 ARG 0.010 0.000 ARG L 481 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17664 Ramachandran restraints generated. 8832 Oldfield, 0 Emsley, 8832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17664 Ramachandran restraints generated. 8832 Oldfield, 0 Emsley, 8832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 967 residues out of total 7408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 775 time to evaluate : 6.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 12 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8078 (pt0) REVERT: K 107 ASP cc_start: 0.6975 (t70) cc_final: 0.6724 (t0) REVERT: K 217 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.6882 (mpt90) REVERT: J 121 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7370 (tp) REVERT: J 472 GLN cc_start: 0.5942 (OUTLIER) cc_final: 0.5500 (pp30) REVERT: J 522 ASP cc_start: 0.7077 (t70) cc_final: 0.6738 (t0) REVERT: H 32 ILE cc_start: 0.8854 (tt) cc_final: 0.8605 (tt) REVERT: H 116 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8437 (mp) REVERT: H 482 GLU cc_start: 0.6898 (mp0) cc_final: 0.6650 (mp0) REVERT: G 330 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7867 (tpt-90) REVERT: E 89 MET cc_start: 0.8081 (mmm) cc_final: 0.7834 (mmp) REVERT: I 319 LYS cc_start: 0.7122 (tttt) cc_final: 0.6795 (ttpt) REVERT: B 310 MET cc_start: 0.7172 (tpp) cc_final: 0.6942 (mmm) REVERT: B 408 TYR cc_start: 0.8309 (m-80) cc_final: 0.8000 (m-80) REVERT: R 86 ARG cc_start: 0.6279 (mtt180) cc_final: 0.5618 (mtp85) REVERT: R 105 HIS cc_start: 0.5943 (OUTLIER) cc_final: 0.5519 (m170) REVERT: R 233 MET cc_start: 0.5672 (tpp) cc_final: 0.5388 (tpp) REVERT: R 267 MET cc_start: 0.4013 (OUTLIER) cc_final: 0.3257 (mmt) REVERT: R 276 ARG cc_start: 0.4425 (mtt90) cc_final: 0.2620 (mmt180) REVERT: R 300 MET cc_start: 0.2097 (mmp) cc_final: 0.1567 (mmm) REVERT: R 321 MET cc_start: 0.2418 (ptp) cc_final: 0.1194 (ppp) REVERT: R 323 MET cc_start: 0.2514 (mmm) cc_final: 0.1132 (ptt) REVERT: R 388 MET cc_start: 0.6520 (mtm) cc_final: 0.6112 (mmm) REVERT: R 406 MET cc_start: 0.7101 (mmp) cc_final: 0.6421 (ttt) REVERT: z 135 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: P 52 MET cc_start: 0.8072 (mmp) cc_final: 0.7835 (mmp) REVERT: O 38 THR cc_start: 0.9406 (OUTLIER) cc_final: 0.8920 (m) REVERT: O 402 ASN cc_start: 0.7801 (t0) cc_final: 0.7149 (p0) REVERT: N 49 MET cc_start: 0.8816 (mtp) cc_final: 0.8558 (mtm) REVERT: N 73 GLN cc_start: 0.7405 (mp10) cc_final: 0.7068 (mp10) REVERT: a 209 MET cc_start: 0.7263 (mmt) cc_final: 0.6978 (mmt) REVERT: M 314 LEU cc_start: 0.8645 (tp) cc_final: 0.8376 (tp) REVERT: M 458 MET cc_start: 0.9064 (mmp) cc_final: 0.8718 (mmt) REVERT: M 506 GLU cc_start: 0.6978 (tm-30) cc_final: 0.6329 (tm-30) REVERT: M 532 ILE cc_start: 0.7310 (mt) cc_final: 0.7088 (mp) outliers start: 192 outliers final: 166 residues processed: 921 average time/residue: 0.6194 time to fit residues: 991.7376 Evaluate side-chains 921 residues out of total 7408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 745 time to evaluate : 5.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 12 GLU Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 217 ARG Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 244 VAL Chi-restraints excluded: chain K residue 374 LEU Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 477 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 117 GLU Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain J residue 347 CYS Chi-restraints excluded: chain J residue 472 GLN Chi-restraints excluded: chain J residue 502 LEU Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 330 ARG Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 472 GLN Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 436 ASP Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain E residue 530 ASP Chi-restraints excluded: chain I residue 24 TYR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 257 LYS Chi-restraints excluded: chain I residue 269 TYR Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 105 HIS Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 227 HIS Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 267 MET Chi-restraints excluded: chain R residue 370 ASN Chi-restraints excluded: chain R residue 414 ASN Chi-restraints excluded: chain z residue 12 GLU Chi-restraints excluded: chain z residue 47 LEU Chi-restraints excluded: chain z residue 63 LEU Chi-restraints excluded: chain z residue 135 GLU Chi-restraints excluded: chain z residue 190 MET Chi-restraints excluded: chain z residue 263 GLU Chi-restraints excluded: chain z residue 386 GLN Chi-restraints excluded: chain P residue 67 ASN Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 126 SER Chi-restraints excluded: chain P residue 193 ASP Chi-restraints excluded: chain P residue 217 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 251 THR Chi-restraints excluded: chain P residue 297 VAL Chi-restraints excluded: chain P residue 314 ARG Chi-restraints excluded: chain P residue 352 LEU Chi-restraints excluded: chain P residue 357 ASP Chi-restraints excluded: chain P residue 380 SER Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain O residue 395 ILE Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 412 ILE Chi-restraints excluded: chain O residue 420 LEU Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain O residue 479 ILE Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 170 SER Chi-restraints excluded: chain N residue 388 GLU Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 452 ILE Chi-restraints excluded: chain N residue 459 THR Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain N residue 484 THR Chi-restraints excluded: chain e residue 21 ASP Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 82 ASP Chi-restraints excluded: chain e residue 147 ASP Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 226 VAL Chi-restraints excluded: chain e residue 227 ILE Chi-restraints excluded: chain e residue 249 LEU Chi-restraints excluded: chain e residue 250 THR Chi-restraints excluded: chain e residue 262 HIS Chi-restraints excluded: chain e residue 375 CYS Chi-restraints excluded: chain e residue 392 ILE Chi-restraints excluded: chain e residue 436 ASP Chi-restraints excluded: chain e residue 506 GLU Chi-restraints excluded: chain a residue 7 VAL Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 382 ASP Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain a residue 434 GLU Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 241 VAL Chi-restraints excluded: chain M residue 398 ILE Chi-restraints excluded: chain M residue 490 THR Chi-restraints excluded: chain M residue 503 ILE Chi-restraints excluded: chain M residue 515 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 432 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 553 optimal weight: 5.9990 chunk 741 optimal weight: 10.0000 chunk 213 optimal weight: 0.5980 chunk 642 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 193 optimal weight: 7.9990 chunk 697 optimal weight: 20.0000 chunk 291 optimal weight: 0.5980 chunk 716 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN R 227 HIS ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS ** O 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 501 ASN ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.112410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.100709 restraints weight = 120113.010| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.00 r_work: 0.3177 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.5625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 69153 Z= 0.196 Angle : 0.592 20.239 93401 Z= 0.286 Chirality : 0.043 0.293 11097 Planarity : 0.003 0.094 11940 Dihedral : 7.047 176.077 9632 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.73 % Favored : 94.26 % Rotamer: Outliers : 2.63 % Allowed : 16.65 % Favored : 80.71 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.09), residues: 8832 helix: 1.12 (0.08), residues: 4278 sheet: -0.75 (0.16), residues: 1154 loop : -1.55 (0.10), residues: 3400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 506 HIS 0.007 0.001 HIS E 262 PHE 0.033 0.001 PHE H 360 TYR 0.022 0.001 TYR I 282 ARG 0.007 0.000 ARG B 481 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18977.19 seconds wall clock time: 333 minutes 12.94 seconds (19992.94 seconds total)