Starting phenix.real_space_refine on Thu Feb 15 09:51:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0v_32926/02_2024/7x0v_32926_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0v_32926/02_2024/7x0v_32926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0v_32926/02_2024/7x0v_32926.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0v_32926/02_2024/7x0v_32926.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0v_32926/02_2024/7x0v_32926_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0v_32926/02_2024/7x0v_32926_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 396 5.16 5 C 40592 2.51 5 N 11328 2.21 5 O 12572 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 "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: 65000 Number of models: 1 Model: "" Number of chains: 48 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: "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: 25.64, per 1000 atoms: 0.39 Number of scatterers: 65000 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 396 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 12572 8.00 N 11328 7.00 C 40592 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 9.6 seconds 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15736 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 319 helices and 95 sheets defined 46.5% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.19 Creating SS restraints... Processing helix chain 'K' and resid 3 through 7 removed outlier: 3.522A 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: 4.047A pdb=" N ALA K 21 " --> pdb=" O GLN K 17 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL K 33 " --> pdb=" O GLY K 29 " (cutoff:3.500A) removed outlier: 4.950A 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: 3.570A 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: 3.773A 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: 3.593A pdb=" N GLU K 135 " --> pdb=" O LEU K 131 " (cutoff:3.500A) removed outlier: 3.685A 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: 4.319A 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: 3.533A pdb=" N LEU K 277 " --> pdb=" O LYS K 273 " (cutoff:3.500A) removed outlier: 3.645A 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: 3.790A 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: 3.743A pdb=" N THR K 385 " --> pdb=" O LYS K 381 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP K 393 " --> pdb=" O ASP K 389 " (cutoff:3.500A) removed outlier: 3.561A 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: 3.960A 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: 3.551A pdb=" N ALA K 452 " --> pdb=" O LYS K 449 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN K 454 " --> pdb=" O LEU K 451 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 471 removed outlier: 3.761A 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: 3.864A 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: 3.720A 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: 3.767A 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: 3.532A pdb=" N LYS J 326 " --> pdb=" O ARG J 322 " (cutoff:3.500A) Processing helix chain 'J' and resid 382 through 404 removed outlier: 3.537A 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 455 removed outlier: 3.997A 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: 3.537A pdb=" N LYS J 439 " --> pdb=" O TYR J 436 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS J 440 " --> pdb=" O ALA J 437 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA J 447 " --> pdb=" O ALA J 444 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE J 448 " --> pdb=" O PHE J 445 " (cutoff:3.500A) Proline residue: J 449 - end of helix removed outlier: 3.843A pdb=" N GLU J 454 " --> pdb=" O ALA J 451 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN J 455 " --> pdb=" O LEU J 452 " (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: 3.511A 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: 3.673A 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: 3.621A 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: 4.034A pdb=" N LYS H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 3.672A 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: 3.837A 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: 3.710A 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: 3.709A 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: 3.504A 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: 3.573A 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: 4.132A 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: 3.543A pdb=" N LEU H 449 " --> pdb=" O ILE H 445 " (cutoff:3.500A) removed outlier: 3.687A 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: 3.846A 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: 3.634A pdb=" N THR G 32 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE G 33 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 3.643A 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: 3.738A 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: 3.569A 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: 3.970A pdb=" N SER G 135 " --> pdb=" O ASP G 131 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR G 136 " --> pdb=" O ASP G 132 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU G 137 " --> pdb=" O MET G 133 " (cutoff:3.500A) removed outlier: 3.612A 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: 3.549A 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: 3.588A 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: 3.516A 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: 3.691A 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: 3.720A 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: 4.621A pdb=" N VAL G 446 " --> pdb=" O GLN G 442 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ILE G 447 " --> pdb=" O ALA G 443 " (cutoff:3.500A) Proline residue: G 448 - end of helix removed outlier: 3.600A 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: 3.911A 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: 4.070A 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: 3.686A 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: 3.560A 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: 3.986A pdb=" N THR E 293 " --> pdb=" O GLN E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 314 removed outlier: 3.968A 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: 3.598A 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: 3.829A 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: 3.509A 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: 3.850A 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: 3.566A pdb=" N LEU I 78 " --> pdb=" O GLY I 74 " (cutoff:3.500A) removed outlier: 3.664A 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: 3.558A 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: 3.511A pdb=" N ILE I 283 " --> pdb=" O GLU I 279 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN I 285 " --> pdb=" O ALA I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 311 through 319 removed outlier: 3.580A 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: 3.738A 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 447 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: 3.627A 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: 3.916A pdb=" N ASN B 73 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 94 removed outlier: 3.531A 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: 3.601A pdb=" N GLN B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 3.744A 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: 3.548A pdb=" N LEU B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 143 removed outlier: 3.607A 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: 3.608A 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: 3.667A 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: 4.676A pdb=" N HIS B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.740A 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: 3.611A pdb=" N ARG B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) removed outlier: 3.555A 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: 3.529A pdb=" N ALA B 507 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 35 removed outlier: 4.317A pdb=" N VAL A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 3.719A 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: 3.630A 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: 3.584A pdb=" N ASP A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.614A 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: 3.639A 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: 3.755A 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: 3.523A 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: 3.635A 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: 3.509A 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: 4.164A 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: 3.666A 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: 3.515A 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: 3.829A pdb=" N ARG A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 3.555A 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: 4.167A 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: 4.121A 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: 3.852A 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: 3.510A 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 '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: 3.591A 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: 3.787A 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: 3.554A pdb=" N ILE z 149 " --> pdb=" O ARG z 145 " (cutoff:3.500A) removed outlier: 3.680A 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: 3.708A 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: 3.812A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE z 274 " --> pdb=" O ARG z 270 " (cutoff:3.500A) removed outlier: 3.572A 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: 3.972A pdb=" N ARG z 323 " --> pdb=" O ASN z 320 " (cutoff:3.500A) removed outlier: 5.263A 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: 4.031A 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: 3.562A pdb=" N ILE z 423 " --> pdb=" O ALA z 419 " (cutoff:3.500A) removed outlier: 3.800A 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: 3.865A 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: 3.983A 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: 3.707A 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: 3.781A pdb=" N LEU P 39 " --> pdb=" O ALA P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 73 removed outlier: 3.641A 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: 3.659A 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: 4.198A pdb=" N GLU P 130 " --> pdb=" O SER P 126 " (cutoff:3.500A) removed outlier: 3.533A 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: 4.466A 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: 3.786A 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: 3.544A pdb=" N ASP P 387 " --> pdb=" O ASN P 383 " (cutoff:3.500A) Processing helix chain 'P' and resid 414 through 428 removed outlier: 3.654A 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: 3.528A pdb=" N LYS P 440 " --> pdb=" O ALA P 437 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA P 442 " --> pdb=" O LYS P 439 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU P 443 " --> pdb=" O LYS P 440 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA P 447 " --> pdb=" O ALA P 444 " (cutoff:3.500A) removed outlier: 3.583A 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: 3.614A 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: 3.591A 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: 4.200A pdb=" N LYS O 401 " --> pdb=" O ARG O 397 " (cutoff:3.500A) Processing helix chain 'O' and resid 411 through 426 removed outlier: 3.739A 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: 3.520A 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: 3.540A pdb=" N ALA O 441 " --> pdb=" O TYR O 438 " (cutoff:3.500A) removed outlier: 3.524A 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: 3.934A 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: 4.123A 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: 3.678A pdb=" N VAL N 22 " --> pdb=" O GLY N 19 " (cutoff:3.500A) removed outlier: 3.858A 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: 3.771A 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: 3.509A 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: 3.523A 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: 3.559A 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: 3.557A 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: 3.686A 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: 3.859A 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: 3.675A 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: 4.914A pdb=" N ALA N 428 " --> pdb=" O GLU N 424 " (cutoff:3.500A) Processing helix chain 'N' and resid 434 through 455 removed outlier: 3.731A 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: 5.191A pdb=" N ILE N 447 " --> pdb=" O ALA N 443 " (cutoff:3.500A) Proline residue: N 448 - end of helix removed outlier: 3.502A 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: 3.843A 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: 3.591A 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: 3.620A pdb=" N HIS e 35 " --> pdb=" O ALA e 31 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA e 41 " --> pdb=" O MET e 37 " (cutoff:3.500A) removed outlier: 3.948A 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: 3.532A pdb=" N GLN e 137 " --> pdb=" O ASP e 133 " (cutoff:3.500A) removed outlier: 4.116A 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: 3.518A 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: 4.057A 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: 4.140A pdb=" N VAL e 455 " --> pdb=" O ASP e 451 " (cutoff:3.500A) removed outlier: 4.587A 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: 3.576A pdb=" N THR e 473 " --> pdb=" O ILE e 469 " (cutoff:3.500A) removed outlier: 3.641A 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: 3.812A 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: 3.561A 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: 3.521A 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: 3.686A pdb=" N ILE a 149 " --> pdb=" O ASP a 146 " (cutoff:3.500A) removed outlier: 3.677A 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: 3.722A 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: 4.056A 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: 3.575A 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: 4.647A pdb=" N ASP a 261 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 4.151A 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: 3.686A 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: 4.782A 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: 3.517A 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: 3.578A pdb=" N GLN a 276 " --> pdb=" O GLU a 273 " (cutoff:3.500A) removed outlier: 3.541A 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: 3.555A pdb=" N PHE a 300 " --> pdb=" O LEU a 297 " (cutoff:3.500A) removed outlier: 4.224A 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: 3.566A 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: 3.548A 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: 4.217A pdb=" N GLU a 424 " --> pdb=" O SER a 420 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) Processing helix chain 'a' and resid 435 through 455 removed outlier: 4.102A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE a 448 " --> pdb=" O SER a 444 " (cutoff:3.500A) Proline residue: a 449 - end of helix removed outlier: 3.629A 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: 3.526A 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: 3.633A 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: 4.160A 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: 4.647A 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: 4.448A 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: 3.544A pdb=" N HIS M 315 " --> pdb=" O ASP M 311 " (cutoff:3.500A) removed outlier: 3.752A 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: 3.724A 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: 3.725A 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: 3.710A 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: 3.577A 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: 4.782A 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: 3.939A pdb=" N ASN L 73 " --> pdb=" O THR L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 94 removed outlier: 3.507A 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: 3.559A 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: 3.518A pdb=" N THR L 103 " --> pdb=" O THR L 99 " (cutoff:3.500A) removed outlier: 3.630A 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: 4.130A 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: 3.677A 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: 4.382A 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: 4.207A 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: 3.759A 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: 4.080A 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: 7.076A 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: 7.040A 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: 6.772A pdb=" N ILE J 375 " --> pdb=" O CYS J 205 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE J 207 " --> pdb=" O ILE J 375 " (cutoff:3.500A) removed outlier: 6.036A 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: 3.614A 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: 3.915A 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: 7.107A 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: 6.647A 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: 6.183A 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: 6.911A 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: 6.877A pdb=" N PHE H 309 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 8.505A 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: 3.531A 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: 3.736A 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: 3.728A 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: 3.526A 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: 6.460A pdb=" N VAL G 289 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 6.563A 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: 8.021A 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: 7.601A pdb=" N LYS E 212 " --> pdb=" O ILE E 383 " (cutoff:3.500A) removed outlier: 6.273A 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: 6.737A pdb=" N LEU E 297 " --> pdb=" O ALA E 247 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU E 249 " --> pdb=" O LEU E 297 " (cutoff:3.500A) removed outlier: 5.727A 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: 6.559A 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: 8.053A 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: 3.604A 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: 5.916A 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: 3.770A 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: 6.215A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.208A 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: 4.592A pdb=" N THR B 372 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 3.655A 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: 8.196A 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: 7.521A 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: 6.853A pdb=" N MET A 306 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 8.224A 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 'z' and resid 45 through 48 Processing sheet with id= AX, 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= AY, 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= AZ, first strand: chain 'z' and resid 228 through 231 removed outlier: 6.930A 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: 6.648A pdb=" N VAL z 290 " --> pdb=" O LEU z 231 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'P' and resid 21 through 23 Processing sheet with id= BB, 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= BC, 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: 6.101A pdb=" N LEU P 377 " --> pdb=" O ILE P 207 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'P' and resid 239 through 241 removed outlier: 6.544A pdb=" N VAL P 290 " --> pdb=" O ALA P 240 " (cutoff:3.500A) removed outlier: 6.406A 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= BD Processing sheet with id= BE, first strand: chain 'P' and resid 349 through 354 Processing sheet with id= BF, 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= BF Processing sheet with id= BG, first strand: chain 'O' and resid 14 through 17 removed outlier: 4.200A 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: 4.057A pdb=" N THR O 519 " --> pdb=" O SER O 16 " (cutoff:3.500A) No H-bonds generated for sheet with id= BG Processing sheet with id= BH, first strand: chain 'O' and resid 47 through 50 Processing sheet with id= BI, 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= BJ, first strand: chain 'O' and resid 237 through 240 removed outlier: 7.131A 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: 6.497A pdb=" N SER O 290 " --> pdb=" O LEU O 240 " (cutoff:3.500A) removed outlier: 6.925A 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= BJ Processing sheet with id= BK, first strand: chain 'O' and resid 347 through 351 removed outlier: 3.535A pdb=" N GLU O 349 " --> pdb=" O PHE O 360 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'O' and resid 405 through 407 Processing sheet with id= BM, first strand: chain 'O' and resid 475 through 477 Processing sheet with id= BN, 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= BO, first strand: chain 'N' and resid 48 through 51 Processing sheet with id= BP, 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: 7.686A 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: 7.260A pdb=" N ILE N 204 " --> pdb=" O ILE N 374 " (cutoff:3.500A) removed outlier: 6.407A 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= BQ, first strand: chain 'N' and resid 218 through 220 Processing sheet with id= BR, 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: 6.482A pdb=" N THR N 310 " --> pdb=" O VAL N 290 " (cutoff:3.500A) No H-bonds generated for sheet with id= BR Processing sheet with id= BS, first strand: chain 'N' and resid 407 through 409 Processing sheet with id= BT, first strand: chain 'e' and resid 57 through 60 Processing sheet with id= BU, 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: 6.288A 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= BV, 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: 7.499A 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: 8.254A 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= BW, 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: 3.629A pdb=" N MET e 369 " --> pdb=" O ILE e 360 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'e' and resid 416 through 418 Processing sheet with id= BY, first strand: chain 'a' and resid 10 through 12 Processing sheet with id= BZ, first strand: chain 'a' and resid 43 through 46 Processing sheet with id= CA, 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= CB, 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: 8.077A pdb=" N ALA a 200 " --> pdb=" O ILE a 375 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU a 377 " --> pdb=" O ALA a 200 " (cutoff:3.500A) Processing sheet with id= CC, 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= CD, first strand: chain 'a' and resid 234 through 237 removed outlier: 6.758A 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= CD Processing sheet with id= CE, first strand: chain 'a' and resid 408 through 410 Processing sheet with id= CF, first strand: chain 'M' and resid 59 through 61 Processing sheet with id= CG, 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: 8.035A pdb=" N VAL M 211 " --> pdb=" O VAL M 386 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE M 388 " --> pdb=" O VAL M 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= CG Processing sheet with id= CH, 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= CI, 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: 6.729A pdb=" N MET M 323 " --> pdb=" O LEU M 298 " (cutoff:3.500A) removed outlier: 7.773A 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= CI Processing sheet with id= CJ, first strand: chain 'M' and resid 421 through 423 Processing sheet with id= CK, first strand: chain 'M' and resid 491 through 494 Processing sheet with id= CL, 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= CM, 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: 7.188A 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: 3.647A pdb=" N TYR L 213 " --> pdb=" O VAL L 374 " (cutoff:3.500A) Processing sheet with id= CN, 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: 6.112A pdb=" N ILE L 291 " --> pdb=" O ALA L 240 " (cutoff:3.500A) No H-bonds generated for sheet with id= CN Processing sheet with id= CO, first strand: chain 'L' and resid 351 through 353 Processing sheet with id= CP, first strand: chain 'L' and resid 406 through 408 Processing sheet with id= CQ, first strand: chain 'L' and resid 476 through 479 2291 hydrogen bonds defined for protein. 6456 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: 25.05 Time building geometry restraints manager: 21.91 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: 8981 1.24 - 1.38: 14308 1.38 - 1.53: 31314 1.53 - 1.67: 10423 1.67 - 1.81: 706 Bond restraints: 65732 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 1.51e+02 bond pdb=" CA THR I 106 " pdb=" C THR I 106 " ideal model delta sigma weight residual 1.519 1.378 0.141 1.19e-02 7.06e+03 1.40e+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 0.145 1.27e-02 6.20e+03 1.30e+02 bond pdb=" C THR M 106 " pdb=" O THR M 106 " ideal model delta sigma weight residual 1.235 1.097 0.138 1.26e-02 6.30e+03 1.21e+02 ... (remaining 65727 not shown) Histogram of bond angle deviations from ideal: 97.93 - 105.62: 1166 105.62 - 113.30: 38015 113.30 - 120.98: 31096 120.98 - 128.66: 18186 128.66 - 136.35: 301 Bond angle restraints: 88764 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 122.77 114.20 8.57 9.40e-01 1.13e+00 8.32e+01 angle pdb=" C GLY M 105 " pdb=" N THR M 106 " pdb=" CA THR M 106 " ideal model delta sigma weight residual 121.54 105.16 16.38 1.91e+00 2.74e-01 7.35e+01 angle pdb=" CA GLY A 87 " pdb=" C GLY A 87 " pdb=" N ASP A 88 " ideal model delta sigma weight residual 117.63 126.48 -8.85 1.17e+00 7.31e-01 5.72e+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 4.83e+01 angle pdb=" N ASN P 102 " pdb=" CA ASN P 102 " pdb=" C ASN P 102 " ideal model delta sigma weight residual 113.97 105.73 8.24 1.28e+00 6.10e-01 4.14e+01 ... (remaining 88759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.97: 39833 27.97 - 55.94: 785 55.94 - 83.91: 32 83.91 - 111.88: 6 111.88 - 139.85: 22 Dihedral angle restraints: 40678 sinusoidal: 16386 harmonic: 24292 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 P 601 " pdb=" O5' ADP P 601 " pdb=" PA ADP P 601 " pdb=" O2A ADP P 601 " ideal model delta sinusoidal sigma weight residual -60.00 79.85 -139.85 1 2.00e+01 2.50e-03 4.23e+01 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 79.85 -139.85 1 2.00e+01 2.50e-03 4.23e+01 ... (remaining 40675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.216: 10580 0.216 - 0.432: 6 0.432 - 0.648: 2 0.648 - 0.864: 3 0.864 - 1.080: 1 Chirality restraints: 10592 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 2.92e+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 1.69 0.84 2.00e-01 2.50e+01 1.76e+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 1.66e+01 ... (remaining 10589 not shown) Planarity restraints: 11328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY O 93 " 0.039 2.00e-02 2.50e+03 8.10e-02 6.56e+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 6.81e-02 4.63e+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 6.10e-02 3.72e+01 pdb=" C THR P 101 " -0.106 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 11325 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.79: 45 1.79 - 2.57: 766 2.57 - 3.35: 75323 3.35 - 4.12: 157206 4.12 - 4.90: 288393 Nonbonded interactions: 521733 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 1.071 2.390 nonbonded pdb=" OG1 THR G 95 " pdb=" F3 AF3 G 603 " model vdw 1.098 2.390 ... (remaining 521728 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: 0.740 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: 0.050 Extract box with map and model: 6.340 Check model and map are aligned: 0.730 Set scattering table: 0.460 Process input model: 141.990 Find NCS groups from input model: 5.880 Set up NCS constraints: 0.570 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 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 : 0.005 0.261 65732 Z= 0.310 Angle : 0.610 16.380 88764 Z= 0.337 Chirality : 0.047 1.080 10592 Planarity : 0.005 0.081 11328 Dihedral : 10.889 139.846 24942 Min Nonbonded Distance : 1.018 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.88 % Favored : 95.10 % Rotamer: Outliers : 3.50 % Allowed : 5.51 % Favored : 90.99 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.42 % 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: -5.90 (0.06), residues: 8408 helix: -4.90 (0.02), residues: 4004 sheet: -2.17 (0.14), residues: 1024 loop : -2.92 (0.08), residues: 3380 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 0.015 0.001 PHE a 239 TYR 0.008 0.001 TYR G 437 ARG 0.013 0.000 ARG z 157 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2953 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 2707 time to evaluate : 5.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 44 MET cc_start: 0.8132 (mmm) cc_final: 0.7703 (mmt) REVERT: K 63 LEU cc_start: 0.8158 (mt) cc_final: 0.7948 (mp) REVERT: K 157 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7861 (mtt180) REVERT: K 250 TYR cc_start: 0.8371 (p90) cc_final: 0.8086 (p90) REVERT: J 321 LEU cc_start: 0.8742 (tp) cc_final: 0.8527 (tp) REVERT: J 418 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7427 (mm-30) REVERT: J 426 TYR cc_start: 0.6019 (m-80) cc_final: 0.5818 (m-80) REVERT: J 463 VAL cc_start: 0.8458 (t) cc_final: 0.8215 (t) REVERT: H 16 SER cc_start: 0.7510 (t) cc_final: 0.7193 (m) REVERT: H 29 CYS cc_start: 0.6893 (m) cc_final: 0.6689 (m) REVERT: H 279 GLU cc_start: 0.6592 (mm-30) cc_final: 0.6367 (mm-30) REVERT: H 323 MET cc_start: 0.7843 (ttp) cc_final: 0.7638 (ttm) REVERT: H 481 ASN cc_start: 0.6669 (m-40) cc_final: 0.6262 (m-40) REVERT: G 130 LEU cc_start: 0.8977 (tp) cc_final: 0.8766 (tp) REVERT: G 278 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7964 (mt) REVERT: G 331 ILE cc_start: 0.8575 (mt) cc_final: 0.8075 (mt) REVERT: G 416 MET cc_start: 0.8047 (mmp) cc_final: 0.7653 (mmm) REVERT: E 360 ILE cc_start: 0.7417 (mm) cc_final: 0.7153 (tp) REVERT: E 369 MET cc_start: 0.5659 (mmm) cc_final: 0.5382 (mmt) REVERT: E 392 ILE cc_start: 0.8932 (tp) cc_final: 0.8662 (tp) REVERT: E 447 ARG cc_start: 0.7739 (mtt-85) cc_final: 0.7524 (mtt-85) REVERT: I 28 ASP cc_start: 0.4827 (OUTLIER) cc_final: 0.4626 (t70) REVERT: I 42 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7036 (mmmt) REVERT: I 67 ASP cc_start: 0.6974 (t70) cc_final: 0.6739 (t70) REVERT: I 397 VAL cc_start: 0.8890 (t) cc_final: 0.8663 (p) REVERT: B 50 LYS cc_start: 0.8320 (mttm) cc_final: 0.7921 (mttp) REVERT: B 208 SER cc_start: 0.8263 (p) cc_final: 0.8046 (p) REVERT: B 415 MET cc_start: 0.8650 (mmm) cc_final: 0.8383 (mmm) REVERT: B 445 MET cc_start: 0.8053 (mmm) cc_final: 0.7805 (mmt) REVERT: A 54 ILE cc_start: 0.8455 (mt) cc_final: 0.8140 (mt) REVERT: A 55 THR cc_start: 0.8704 (t) cc_final: 0.8245 (p) REVERT: z 79 LYS cc_start: 0.7777 (mttt) cc_final: 0.7544 (mmtm) REVERT: z 385 THR cc_start: 0.6983 (p) cc_final: 0.6698 (p) REVERT: z 389 ASP cc_start: 0.6567 (m-30) cc_final: 0.6348 (m-30) REVERT: z 520 GLU cc_start: 0.5997 (OUTLIER) cc_final: 0.5678 (tt0) REVERT: P 71 THR cc_start: 0.8426 (p) cc_final: 0.7638 (m) REVERT: P 117 GLU cc_start: 0.6055 (mt-10) cc_final: 0.5836 (mt-10) REVERT: P 173 TYR cc_start: 0.8370 (t80) cc_final: 0.7734 (t80) REVERT: P 311 MET cc_start: 0.7866 (ttp) cc_final: 0.7461 (ttm) REVERT: P 461 ASN cc_start: 0.7002 (m-40) cc_final: 0.6696 (m110) REVERT: P 506 TRP cc_start: 0.8177 (m100) cc_final: 0.7975 (m100) REVERT: O 382 MET cc_start: 0.7929 (mtm) cc_final: 0.7535 (mtm) REVERT: N 50 LEU cc_start: 0.8942 (mt) cc_final: 0.8613 (mp) REVERT: N 88 ASP cc_start: 0.6188 (t70) cc_final: 0.5969 (t0) REVERT: N 460 ILE cc_start: 0.7906 (mm) cc_final: 0.7446 (mm) REVERT: a 20 GLN cc_start: 0.7716 (mt0) cc_final: 0.7508 (mt0) REVERT: a 30 ASN cc_start: 0.8334 (m-40) cc_final: 0.8067 (m-40) REVERT: a 244 THR cc_start: 0.7441 (m) cc_final: 0.7094 (t) REVERT: a 534 HIS cc_start: 0.7340 (m-70) cc_final: 0.7002 (m-70) REVERT: M 312 LEU cc_start: 0.8214 (tp) cc_final: 0.7895 (tt) REVERT: L 365 VAL cc_start: 0.8379 (m) cc_final: 0.7946 (m) outliers start: 246 outliers final: 47 residues processed: 2850 average time/residue: 0.6603 time to fit residues: 3057.2028 Evaluate side-chains 1427 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 1375 time to evaluate : 5.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 157 ARG Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain G residue 12 GLN Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 42 LYS Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 535 VAL Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain z residue 62 VAL Chi-restraints excluded: chain z residue 292 ILE Chi-restraints excluded: chain z residue 477 VAL Chi-restraints excluded: chain z residue 520 GLU Chi-restraints excluded: chain P residue 11 PHE Chi-restraints excluded: chain P residue 123 LEU 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 498 LEU Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 389 LEU Chi-restraints excluded: chain O residue 516 VAL Chi-restraints excluded: chain N residue 12 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 522 VAL Chi-restraints excluded: chain a residue 352 VAL Chi-restraints excluded: chain M residue 42 LYS 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 535 VAL Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 64 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 705 optimal weight: 0.8980 chunk 633 optimal weight: 1.9990 chunk 351 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 427 optimal weight: 0.8980 chunk 338 optimal weight: 0.7980 chunk 655 optimal weight: 6.9990 chunk 253 optimal weight: 3.9990 chunk 398 optimal weight: 0.4980 chunk 487 optimal weight: 6.9990 chunk 759 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 214 HIS K 368 ASN ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN J 79 GLN J 219 HIS J 279 GLN J 303 HIS J 306 ASN ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 523 GLN H 25 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 GLN H 201 GLN H 234 ASN H 283 HIS H 331 GLN ** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 448 GLN H 470 GLN G 64 ASN ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS G 390 ASN G 442 GLN G 454 ASN E 20 GLN E 137 GLN ** E 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN E 377 ASN E 501 GLN I 125 GLN I 263 GLN I 301 GLN I 394 ASN I 486 GLN ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN A 201 HIS A 251 GLN A 284 ASN ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 ASN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 37 ASN ** z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 293 ASN z 294 GLN z 346 HIS ** P 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN P 41 GLN P 303 HIS P 422 GLN ** P 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 GLN O 21 GLN O 117 HIS O 264 GLN ** O 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 501 ASN N 64 ASN N 73 GLN ** N 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 GLN N 390 ASN ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 262 HIS ** e 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 251 GLN a 381 ASN a 455 ASN ** a 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 GLN M 98 GLN M 301 GLN M 347 HIS M 486 GLN ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 148 HIS L 298 ASN L 502 GLN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 65732 Z= 0.197 Angle : 0.648 15.552 88764 Z= 0.320 Chirality : 0.043 0.237 10592 Planarity : 0.005 0.067 11328 Dihedral : 7.839 169.892 9230 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.30 % Allowed : 14.44 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.51 (0.08), residues: 8408 helix: -2.34 (0.06), residues: 3980 sheet: -1.61 (0.16), residues: 990 loop : -2.34 (0.09), residues: 3438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 319 HIS 0.016 0.001 HIS H 283 PHE 0.019 0.001 PHE P 103 TYR 0.024 0.001 TYR z 353 ARG 0.007 0.001 ARG P 450 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1683 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1451 time to evaluate : 5.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 399 LYS cc_start: 0.8728 (tmmt) cc_final: 0.8299 (tttm) REVERT: K 520 GLU cc_start: 0.7165 (tp30) cc_final: 0.6899 (tp30) REVERT: H 16 SER cc_start: 0.8040 (t) cc_final: 0.7642 (m) REVERT: H 207 ASP cc_start: 0.6708 (OUTLIER) cc_final: 0.6418 (m-30) REVERT: H 414 MET cc_start: 0.8285 (tpt) cc_final: 0.7963 (mmm) REVERT: G 168 TRP cc_start: 0.8303 (m-90) cc_final: 0.7973 (m-90) REVERT: E 119 GLU cc_start: 0.6299 (tt0) cc_final: 0.5973 (tt0) REVERT: E 237 MET cc_start: 0.7730 (tpp) cc_final: 0.6495 (mmt) REVERT: I 42 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7213 (tptm) REVERT: I 323 MET cc_start: 0.8078 (ttm) cc_final: 0.7852 (mtp) REVERT: B 62 MET cc_start: 0.7780 (tmm) cc_final: 0.7310 (ppp) REVERT: B 415 MET cc_start: 0.8600 (mmm) cc_final: 0.8361 (mmm) REVERT: A 201 HIS cc_start: 0.7271 (p-80) cc_final: 0.6443 (p90) REVERT: z 44 MET cc_start: 0.7454 (mmm) cc_final: 0.7042 (mtp) REVERT: z 56 LEU cc_start: 0.8594 (tp) cc_final: 0.8218 (tp) REVERT: z 385 THR cc_start: 0.7368 (p) cc_final: 0.6965 (p) REVERT: P 173 TYR cc_start: 0.8487 (t80) cc_final: 0.7725 (t80) REVERT: P 311 MET cc_start: 0.7803 (ttp) cc_final: 0.7484 (ttm) REVERT: O 1 MET cc_start: 0.4656 (mtm) cc_final: 0.3481 (tpt) REVERT: O 78 THR cc_start: 0.8912 (m) cc_final: 0.8633 (m) REVERT: O 226 GLU cc_start: 0.6028 (mm-30) cc_final: 0.5653 (mm-30) REVERT: N 88 ASP cc_start: 0.7094 (t70) cc_final: 0.6857 (t0) REVERT: N 395 MET cc_start: 0.8227 (mtm) cc_final: 0.8001 (mtm) REVERT: e 123 ASP cc_start: 0.7237 (p0) cc_final: 0.6999 (p0) REVERT: e 292 GLU cc_start: 0.7067 (pp20) cc_final: 0.6839 (pp20) REVERT: e 418 TYR cc_start: 0.7840 (m-80) cc_final: 0.7572 (m-80) REVERT: a 534 HIS cc_start: 0.7263 (m-70) cc_final: 0.7030 (m-70) REVERT: M 35 PHE cc_start: 0.8732 (m-80) cc_final: 0.8487 (m-80) REVERT: M 42 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7695 (tttm) REVERT: M 530 LEU cc_start: 0.8584 (mt) cc_final: 0.8290 (mt) REVERT: L 215 ASP cc_start: 0.6766 (t0) cc_final: 0.6510 (t0) REVERT: L 452 ASP cc_start: 0.7489 (p0) cc_final: 0.7281 (p0) REVERT: L 481 ARG cc_start: 0.6931 (OUTLIER) cc_final: 0.6436 (ptp-110) REVERT: L 526 ARG cc_start: 0.7135 (ptp90) cc_final: 0.6916 (ptp-170) outliers start: 232 outliers final: 126 residues processed: 1606 average time/residue: 0.6276 time to fit residues: 1699.4528 Evaluate side-chains 1243 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1113 time to evaluate : 5.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 205 SER Chi-restraints excluded: chain K residue 324 LEU Chi-restraints excluded: chain K residue 435 LEU Chi-restraints excluded: chain K residue 483 THR Chi-restraints excluded: chain K residue 506 HIS Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain J residue 156 ASP Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain J residue 359 GLN Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 243 GLU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 345 CYS Chi-restraints excluded: chain H residue 382 MET Chi-restraints excluded: chain H residue 395 ILE Chi-restraints excluded: chain G residue 226 HIS Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 263 ASP Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain I residue 42 LYS Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 406 HIS Chi-restraints excluded: chain I residue 447 GLU Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 535 VAL Chi-restraints excluded: chain B residue 11 ILE 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 261 THR Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain z residue 63 LEU Chi-restraints excluded: chain z residue 176 ILE Chi-restraints excluded: chain z residue 265 LYS Chi-restraints excluded: chain z residue 414 VAL Chi-restraints excluded: chain z residue 435 LEU Chi-restraints excluded: chain z residue 506 HIS Chi-restraints excluded: chain P residue 11 PHE Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 191 PHE Chi-restraints excluded: chain P residue 212 ILE 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 302 LEU Chi-restraints excluded: chain P residue 380 SER Chi-restraints excluded: chain P residue 381 THR Chi-restraints excluded: chain P residue 415 THR Chi-restraints excluded: chain P residue 463 VAL Chi-restraints excluded: chain P residue 498 LEU Chi-restraints excluded: chain O residue 17 GLN Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 178 MET Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 364 CYS Chi-restraints excluded: chain O residue 400 ILE Chi-restraints excluded: chain O residue 479 ILE Chi-restraints excluded: chain O residue 516 VAL Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain N residue 57 ILE Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain N residue 195 ILE Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 388 GLU Chi-restraints excluded: chain N residue 459 THR Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 163 LEU Chi-restraints excluded: chain e residue 179 CYS Chi-restraints excluded: chain e residue 217 LEU Chi-restraints excluded: chain e residue 226 VAL Chi-restraints excluded: chain e residue 250 THR Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain e residue 399 SER Chi-restraints excluded: chain a residue 352 VAL Chi-restraints excluded: chain a residue 355 ARG Chi-restraints excluded: chain a residue 359 ASP Chi-restraints excluded: chain a residue 447 VAL Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 125 GLN Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 336 ILE Chi-restraints excluded: chain M residue 374 LEU Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain L residue 313 GLU Chi-restraints excluded: chain L residue 371 CYS Chi-restraints excluded: chain L residue 481 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 421 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 631 optimal weight: 6.9990 chunk 516 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 760 optimal weight: 6.9990 chunk 821 optimal weight: 3.9990 chunk 677 optimal weight: 2.9990 chunk 754 optimal weight: 4.9990 chunk 259 optimal weight: 0.8980 chunk 610 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 382 HIS ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 201 GLN H 359 ASN ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 ASN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN E 433 GLN ** I 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 ASN A 500 GLN z 65 HIS ** z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 245 ASN z 320 ASN ** P 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN P 346 HIS ** P 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 30 GLN ** O 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 501 ASN N 302 HIS ** e 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 180 HIS ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 377 ASN ** e 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 251 GLN a 284 ASN a 366 ASN a 475 GLN ** a 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 172 ASN M 301 GLN M 484 HIS L 73 ASN L 298 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 65732 Z= 0.319 Angle : 0.670 27.014 88764 Z= 0.328 Chirality : 0.045 0.338 10592 Planarity : 0.004 0.055 11328 Dihedral : 7.598 173.585 9185 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.27 % Favored : 94.72 % Rotamer: Outliers : 4.01 % Allowed : 16.03 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.16 (0.08), residues: 8408 helix: -0.78 (0.08), residues: 4058 sheet: -1.45 (0.15), residues: 1058 loop : -2.13 (0.10), residues: 3292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 506 HIS 0.013 0.001 HIS E 262 PHE 0.019 0.002 PHE e 232 TYR 0.019 0.002 TYR N 303 ARG 0.008 0.001 ARG M 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1386 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 1104 time to evaluate : 5.932 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: K 399 LYS cc_start: 0.8702 (tmmt) cc_final: 0.8485 (tttp) REVERT: J 302 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8624 (tt) REVERT: H 451 ASP cc_start: 0.6978 (m-30) cc_final: 0.6737 (m-30) REVERT: G 23 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7796 (mt0) REVERT: G 342 ASP cc_start: 0.6792 (m-30) cc_final: 0.6466 (m-30) REVERT: G 463 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8673 (mm) REVERT: E 462 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7709 (tm-30) REVERT: I 323 MET cc_start: 0.8204 (ttm) cc_final: 0.7781 (mtp) REVERT: B 196 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7350 (mm) REVERT: B 414 GLU cc_start: 0.7235 (mp0) cc_final: 0.6978 (mp0) REVERT: B 432 GLU cc_start: 0.6578 (mp0) cc_final: 0.6239 (mp0) REVERT: A 388 MET cc_start: 0.8704 (mtp) cc_final: 0.8495 (mtm) REVERT: z 44 MET cc_start: 0.7695 (mmm) cc_final: 0.7153 (mtp) REVERT: z 442 ASP cc_start: 0.7452 (m-30) cc_final: 0.7098 (m-30) REVERT: P 311 MET cc_start: 0.7870 (ttp) cc_final: 0.7660 (ttm) REVERT: P 521 VAL cc_start: 0.8897 (t) cc_final: 0.8674 (m) REVERT: O 1 MET cc_start: 0.5275 (mtm) cc_final: 0.3795 (tpp) REVERT: O 78 THR cc_start: 0.9126 (m) cc_final: 0.8876 (m) REVERT: O 382 MET cc_start: 0.8247 (mtm) cc_final: 0.8031 (mtp) REVERT: O 442 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8739 (mp) REVERT: N 47 MET cc_start: 0.7994 (mmm) cc_final: 0.7758 (mmm) REVERT: N 88 ASP cc_start: 0.7497 (t70) cc_final: 0.7239 (t0) REVERT: N 305 MET cc_start: 0.7528 (mmm) cc_final: 0.7090 (tpp) REVERT: N 362 PHE cc_start: 0.8422 (m-80) cc_final: 0.8157 (m-10) REVERT: e 46 MET cc_start: 0.8319 (mmm) cc_final: 0.8107 (mmm) REVERT: a 271 THR cc_start: 0.7284 (m) cc_final: 0.6688 (p) REVERT: a 534 HIS cc_start: 0.7317 (m-70) cc_final: 0.7112 (m-70) REVERT: M 42 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7959 (tttm) REVERT: L 48 MET cc_start: 0.8388 (mmp) cc_final: 0.8155 (mmp) REVERT: L 60 SER cc_start: 0.8037 (m) cc_final: 0.7700 (p) outliers start: 282 outliers final: 179 residues processed: 1313 average time/residue: 0.5896 time to fit residues: 1333.3635 Evaluate side-chains 1154 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 969 time to evaluate : 6.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 205 SER Chi-restraints excluded: chain K residue 324 LEU Chi-restraints excluded: chain K residue 342 ASP Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain J residue 156 ASP Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain H residue 382 MET Chi-restraints excluded: chain H residue 395 ILE Chi-restraints excluded: chain H residue 481 ASN Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 191 LYS Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 263 ASP Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 235 ASN Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 503 ILE Chi-restraints excluded: chain I residue 535 VAL Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain z residue 63 LEU Chi-restraints excluded: chain z residue 65 HIS Chi-restraints excluded: chain z residue 108 LEU Chi-restraints excluded: chain z residue 114 LEU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 176 ILE Chi-restraints excluded: chain z residue 333 LEU Chi-restraints excluded: chain z residue 391 VAL Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 414 VAL Chi-restraints excluded: chain z residue 435 LEU Chi-restraints excluded: chain z residue 506 HIS Chi-restraints excluded: chain P residue 11 PHE Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 67 ASN Chi-restraints excluded: chain P residue 101 THR Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 169 MET Chi-restraints excluded: chain P residue 212 ILE 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 297 VAL Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 380 SER Chi-restraints excluded: chain P residue 381 THR Chi-restraints excluded: chain P residue 415 THR Chi-restraints excluded: chain P residue 463 VAL Chi-restraints excluded: chain P residue 498 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 259 THR Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 273 ILE Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain O residue 364 CYS Chi-restraints excluded: chain O residue 395 ILE Chi-restraints excluded: chain O residue 400 ILE Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain O residue 479 ILE Chi-restraints excluded: chain O residue 501 ASN Chi-restraints excluded: chain O residue 516 VAL Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 57 ILE Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain N residue 195 ILE Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 298 ASP Chi-restraints excluded: chain N residue 383 ILE Chi-restraints excluded: chain N residue 388 GLU Chi-restraints excluded: chain N residue 459 THR Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain N residue 521 ASP Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 45 THR Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 170 THR Chi-restraints excluded: chain e residue 179 CYS Chi-restraints excluded: chain e residue 226 VAL Chi-restraints excluded: chain e residue 250 THR Chi-restraints excluded: chain e residue 251 CYS Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain e residue 330 LEU Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain e residue 462 GLU Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 48 ASP Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 149 ILE Chi-restraints excluded: chain a residue 352 VAL Chi-restraints excluded: chain a residue 523 THR Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 125 GLN Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 336 ILE Chi-restraints excluded: chain M residue 503 ILE Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 88 SER Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain L residue 313 GLU Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 346 CYS Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 379 THR Chi-restraints excluded: chain L residue 480 MET Chi-restraints excluded: chain L residue 514 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 751 optimal weight: 6.9990 chunk 571 optimal weight: 4.9990 chunk 394 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 362 optimal weight: 1.9990 chunk 510 optimal weight: 6.9990 chunk 763 optimal weight: 0.2980 chunk 808 optimal weight: 2.9990 chunk 398 optimal weight: 0.0470 chunk 723 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 overall best weight: 1.6684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 386 GLN ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 503 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 ASN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 504 GLN E 53 ASN ** E 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 276 GLN ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS z 161 HIS P 472 GLN ** P 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 GLN O 233 HIS ** O 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 501 ASN O 522 ASN ** N 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 377 ASN ** e 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 30 ASN ** a 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 25 GLN M 172 ASN L 73 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 65732 Z= 0.224 Angle : 0.612 28.617 88764 Z= 0.295 Chirality : 0.043 0.218 10592 Planarity : 0.003 0.046 11328 Dihedral : 7.457 179.164 9179 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.44 % Allowed : 17.19 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.42 (0.09), residues: 8408 helix: -0.03 (0.08), residues: 4046 sheet: -1.18 (0.16), residues: 1010 loop : -1.95 (0.10), residues: 3352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 435 HIS 0.012 0.001 HIS z 65 PHE 0.022 0.001 PHE H 360 TYR 0.016 0.001 TYR z 351 ARG 0.006 0.000 ARG J 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1274 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1032 time to evaluate : 5.999 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: K 44 MET cc_start: 0.7891 (mtt) cc_final: 0.7602 (mtt) REVERT: K 399 LYS cc_start: 0.8668 (tmmt) cc_final: 0.8234 (tttp) REVERT: J 302 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8649 (tt) REVERT: J 357 ASP cc_start: 0.6630 (t0) cc_final: 0.6354 (t0) REVERT: J 443 GLU cc_start: 0.7102 (tp30) cc_final: 0.6646 (tp30) REVERT: H 451 ASP cc_start: 0.6961 (m-30) cc_final: 0.6724 (m-30) REVERT: G 17 GLU cc_start: 0.7167 (tt0) cc_final: 0.6712 (tt0) REVERT: G 342 ASP cc_start: 0.6662 (m-30) cc_final: 0.6383 (m-30) REVERT: E 288 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.7067 (tm-30) REVERT: E 400 LEU cc_start: 0.9091 (tp) cc_final: 0.8846 (mp) REVERT: E 462 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7722 (tm-30) REVERT: I 323 MET cc_start: 0.8211 (ttm) cc_final: 0.7880 (mtp) REVERT: B 182 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8726 (tt) REVERT: B 196 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7394 (mm) REVERT: B 414 GLU cc_start: 0.7009 (mp0) cc_final: 0.6767 (mp0) REVERT: B 432 GLU cc_start: 0.6552 (mp0) cc_final: 0.6232 (mp0) REVERT: z 44 MET cc_start: 0.7718 (mmm) cc_final: 0.7126 (mtp) REVERT: z 56 LEU cc_start: 0.8572 (tp) cc_final: 0.8346 (tp) REVERT: z 442 ASP cc_start: 0.7390 (m-30) cc_final: 0.7022 (m-30) REVERT: P 296 LYS cc_start: 0.8040 (tppt) cc_final: 0.7807 (tptt) REVERT: P 418 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6827 (mm-30) REVERT: P 521 VAL cc_start: 0.8870 (t) cc_final: 0.8582 (m) REVERT: O 78 THR cc_start: 0.9121 (m) cc_final: 0.8885 (m) REVERT: O 114 GLU cc_start: 0.7209 (pp20) cc_final: 0.7005 (pp20) REVERT: O 382 MET cc_start: 0.8197 (mtm) cc_final: 0.7978 (mtp) REVERT: N 47 MET cc_start: 0.7943 (mmm) cc_final: 0.7732 (mmm) REVERT: e 533 LYS cc_start: 0.8584 (pttm) cc_final: 0.8304 (pttm) REVERT: a 271 THR cc_start: 0.7327 (m) cc_final: 0.6691 (p) REVERT: M 42 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7976 (tttm) REVERT: M 399 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6815 (mm-30) REVERT: L 48 MET cc_start: 0.8332 (mmp) cc_final: 0.8119 (mmp) REVERT: L 60 SER cc_start: 0.8235 (m) cc_final: 0.7967 (p) outliers start: 242 outliers final: 169 residues processed: 1207 average time/residue: 0.5708 time to fit residues: 1192.0806 Evaluate side-chains 1121 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 947 time to evaluate : 5.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 324 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain J residue 156 ASP Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 499 ASP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 382 MET Chi-restraints excluded: chain H residue 395 ILE Chi-restraints excluded: chain H residue 481 ASN Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 235 ASN Chi-restraints excluded: chain I residue 269 TYR Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 503 ILE Chi-restraints excluded: chain I residue 535 VAL 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 182 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain z residue 63 LEU Chi-restraints excluded: chain z residue 65 HIS Chi-restraints excluded: chain z residue 108 LEU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 176 ILE Chi-restraints excluded: chain z residue 333 LEU Chi-restraints excluded: chain z residue 367 ASN Chi-restraints excluded: chain z residue 414 VAL Chi-restraints excluded: chain z residue 435 LEU Chi-restraints excluded: chain z residue 506 HIS Chi-restraints excluded: chain P residue 11 PHE Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 94 GLU Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 148 CYS Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 221 MET 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 297 VAL Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 380 SER Chi-restraints excluded: chain P residue 415 THR Chi-restraints excluded: chain P residue 462 GLU Chi-restraints excluded: chain P residue 498 LEU Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 259 THR Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain O residue 364 CYS Chi-restraints excluded: chain O residue 371 THR Chi-restraints excluded: chain O residue 395 ILE Chi-restraints excluded: chain O residue 400 ILE Chi-restraints excluded: chain O residue 432 GLN Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain O residue 479 ILE Chi-restraints excluded: chain O residue 516 VAL Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 57 ILE Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 383 ILE Chi-restraints excluded: chain N residue 388 GLU Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 459 THR Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain N residue 521 ASP Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 45 THR Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 179 CYS Chi-restraints excluded: chain e residue 226 VAL Chi-restraints excluded: chain e residue 250 THR Chi-restraints excluded: chain e residue 251 CYS Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain e residue 312 LEU Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain e residue 471 THR Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 352 VAL Chi-restraints excluded: chain a residue 523 THR Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 118 ASP Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 336 ILE Chi-restraints excluded: chain M residue 503 ILE Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 224 ILE Chi-restraints excluded: chain L residue 244 MET Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain L residue 313 GLU Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 346 CYS Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 379 THR Chi-restraints excluded: chain L residue 480 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 673 optimal weight: 0.9980 chunk 458 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 601 optimal weight: 2.9990 chunk 333 optimal weight: 10.0000 chunk 689 optimal weight: 3.9990 chunk 558 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 412 optimal weight: 9.9990 chunk 725 optimal weight: 7.9990 chunk 203 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 61 ASN ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS J 306 ASN ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 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 314 GLN ** I 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 484 HIS B 234 ASN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 ASN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS ** P 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 233 HIS O 448 GLN N 111 HIS ** N 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 377 ASN e 409 ASN ** e 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 520 GLN a 455 ASN ** a 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 534 HIS M 172 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 65732 Z= 0.338 Angle : 0.663 27.953 88764 Z= 0.323 Chirality : 0.045 0.220 10592 Planarity : 0.004 0.044 11328 Dihedral : 7.703 174.028 9177 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.89 % Favored : 94.10 % Rotamer: Outliers : 4.26 % Allowed : 17.06 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.01 (0.09), residues: 8408 helix: 0.36 (0.08), residues: 4086 sheet: -1.07 (0.16), residues: 1024 loop : -1.82 (0.10), residues: 3298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 435 HIS 0.035 0.001 HIS z 65 PHE 0.021 0.002 PHE e 232 TYR 0.024 0.002 TYR N 303 ARG 0.013 0.001 ARG H 375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1289 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 989 time to evaluate : 5.952 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: K 393 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7470 (t0) REVERT: K 399 LYS cc_start: 0.8693 (tmmt) cc_final: 0.8492 (tttp) REVERT: J 121 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7678 (tp) REVERT: J 357 ASP cc_start: 0.6912 (t0) cc_final: 0.6704 (t0) REVERT: H 359 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.8146 (m-40) REVERT: H 451 ASP cc_start: 0.7090 (m-30) cc_final: 0.6813 (m-30) REVERT: G 23 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7945 (mt0) REVERT: G 31 LYS cc_start: 0.7714 (mttt) cc_final: 0.7449 (mtpp) REVERT: G 342 ASP cc_start: 0.6761 (m-30) cc_final: 0.6531 (m-30) REVERT: G 511 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6944 (mp0) REVERT: E 288 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.7090 (tm-30) REVERT: E 370 LEU cc_start: 0.5586 (tp) cc_final: 0.5385 (tp) REVERT: E 462 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7594 (tm-30) REVERT: I 70 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8518 (mp) REVERT: I 323 MET cc_start: 0.8185 (ttm) cc_final: 0.7841 (mtp) REVERT: B 196 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7625 (mm) REVERT: B 297 TYR cc_start: 0.8026 (m-10) cc_final: 0.7785 (m-80) REVERT: A 51 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7515 (m-30) REVERT: A 368 LYS cc_start: 0.8376 (tmtt) cc_final: 0.7996 (tptp) REVERT: z 442 ASP cc_start: 0.7360 (m-30) cc_final: 0.7089 (m-30) REVERT: P 196 HIS cc_start: 0.6273 (m-70) cc_final: 0.6067 (m170) REVERT: P 521 VAL cc_start: 0.8995 (t) cc_final: 0.8723 (m) REVERT: O 114 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6960 (pp20) REVERT: O 382 MET cc_start: 0.8243 (mtm) cc_final: 0.8039 (mtp) REVERT: O 414 MET cc_start: 0.7957 (mmm) cc_final: 0.7753 (mmm) REVERT: O 442 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8760 (mp) REVERT: N 95 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.7681 (m) REVERT: N 305 MET cc_start: 0.7889 (mmm) cc_final: 0.7671 (mmm) REVERT: N 429 MET cc_start: 0.8032 (mmm) cc_final: 0.7718 (mmt) REVERT: e 10 TYR cc_start: 0.8203 (m-80) cc_final: 0.7965 (m-80) REVERT: e 171 LEU cc_start: 0.9187 (mt) cc_final: 0.8972 (mt) REVERT: e 262 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.7345 (m90) REVERT: e 520 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7718 (mp-120) REVERT: M 42 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7942 (tptm) outliers start: 300 outliers final: 207 residues processed: 1209 average time/residue: 0.5988 time to fit residues: 1254.3312 Evaluate side-chains 1125 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 903 time to evaluate : 6.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 205 SER Chi-restraints excluded: chain K residue 322 GLU Chi-restraints excluded: chain K residue 324 LEU Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain K residue 499 CYS Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 113 GLU Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain J residue 156 ASP Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 499 ASP Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain H residue 382 MET Chi-restraints excluded: chain H residue 395 ILE Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 481 ASN Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 191 LYS Chi-restraints excluded: chain G residue 263 ASP Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 452 ILE Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 511 GLU Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 235 ASN Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain I residue 269 TYR Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 503 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain z residue 63 LEU Chi-restraints excluded: chain z residue 65 HIS Chi-restraints excluded: chain z residue 114 LEU Chi-restraints excluded: chain z residue 134 LEU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 274 ILE Chi-restraints excluded: chain z residue 333 LEU Chi-restraints excluded: chain z residue 367 ASN Chi-restraints excluded: chain z residue 391 VAL Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 414 VAL Chi-restraints excluded: chain z residue 429 VAL Chi-restraints excluded: chain z residue 435 LEU Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain z residue 499 CYS Chi-restraints excluded: chain z residue 518 VAL Chi-restraints excluded: chain P residue 11 PHE Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 101 THR Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 148 CYS Chi-restraints excluded: chain P residue 212 ILE 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 297 VAL Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 347 CYS Chi-restraints excluded: chain P residue 380 SER Chi-restraints excluded: chain P residue 381 THR Chi-restraints excluded: chain P residue 415 THR Chi-restraints excluded: chain P residue 462 GLU Chi-restraints excluded: chain P residue 463 VAL Chi-restraints excluded: chain P residue 498 LEU Chi-restraints excluded: chain P residue 499 ASP Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain O residue 193 LYS Chi-restraints excluded: chain O residue 242 VAL Chi-restraints excluded: chain O residue 259 THR Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 273 ILE Chi-restraints excluded: chain O residue 347 VAL Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain O residue 364 CYS Chi-restraints excluded: chain O residue 371 THR Chi-restraints excluded: chain O residue 395 ILE Chi-restraints excluded: chain O residue 400 ILE Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 516 VAL Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 57 ILE Chi-restraints excluded: chain N residue 90 GLU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 111 HIS Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 383 ILE Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 459 THR Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain N residue 521 ASP Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 45 THR Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 170 THR Chi-restraints excluded: chain e residue 179 CYS Chi-restraints excluded: chain e residue 226 VAL Chi-restraints excluded: chain e residue 250 THR Chi-restraints excluded: chain e residue 251 CYS Chi-restraints excluded: chain e residue 262 HIS Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain e residue 312 LEU Chi-restraints excluded: chain e residue 330 LEU Chi-restraints excluded: chain e residue 360 ILE Chi-restraints excluded: chain e residue 371 VAL Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain e residue 471 THR Chi-restraints excluded: chain e residue 520 GLN Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 48 ASP Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 88 ASP Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 352 VAL Chi-restraints excluded: chain a residue 523 THR Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 118 ASP Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 252 CYS Chi-restraints excluded: chain M residue 336 ILE Chi-restraints excluded: chain M residue 374 LEU Chi-restraints excluded: chain M residue 503 ILE Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain L residue 18 GLU 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 88 SER Chi-restraints excluded: chain L residue 158 ASP Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 244 MET Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain L residue 313 GLU Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 349 ILE Chi-restraints excluded: chain L residue 379 THR Chi-restraints excluded: chain L residue 480 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 271 optimal weight: 3.9990 chunk 727 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 474 optimal weight: 6.9990 chunk 199 optimal weight: 0.7980 chunk 808 optimal weight: 7.9990 chunk 671 optimal weight: 0.6980 chunk 374 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 267 optimal weight: 0.9990 chunk 424 optimal weight: 6.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 8 ASN ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 ASN ** G 390 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** I 301 GLN B 65 ASN B 234 ASN B 298 ASN z 65 HIS z 105 GLN P 34 GLN ** P 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 233 HIS N 276 GLN ** N 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 377 ASN ** e 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 514 GLN ** a 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 172 ASN L 241 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 65732 Z= 0.164 Angle : 0.588 25.902 88764 Z= 0.282 Chirality : 0.042 0.244 10592 Planarity : 0.003 0.042 11328 Dihedral : 7.383 179.052 9176 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.96 % Allowed : 18.83 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.58 (0.09), residues: 8408 helix: 0.81 (0.08), residues: 4038 sheet: -0.95 (0.16), residues: 1022 loop : -1.66 (0.10), residues: 3348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 506 HIS 0.026 0.001 HIS N 111 PHE 0.016 0.001 PHE O 216 TYR 0.020 0.001 TYR z 351 ARG 0.006 0.000 ARG M 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1232 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1024 time to evaluate : 6.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 44 MET cc_start: 0.7898 (mtt) cc_final: 0.7669 (mtt) REVERT: J 121 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7577 (tp) REVERT: G 23 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7924 (mt0) REVERT: G 31 LYS cc_start: 0.7632 (mttt) cc_final: 0.7357 (mtpp) REVERT: G 316 ARG cc_start: 0.7138 (mmp-170) cc_final: 0.6726 (mmp-170) REVERT: G 330 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7488 (mpt-90) REVERT: E 462 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7573 (tm-30) REVERT: I 323 MET cc_start: 0.8140 (ttm) cc_final: 0.7754 (mtp) REVERT: B 196 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7411 (mm) REVERT: A 368 LYS cc_start: 0.8379 (tmtt) cc_final: 0.7927 (tptp) REVERT: z 442 ASP cc_start: 0.7476 (m-30) cc_final: 0.7208 (m-30) REVERT: P 196 HIS cc_start: 0.6244 (m-70) cc_final: 0.6038 (m170) REVERT: P 296 LYS cc_start: 0.8072 (tppt) cc_final: 0.7852 (tptt) REVERT: O 358 TYR cc_start: 0.8806 (m-80) cc_final: 0.8591 (m-80) REVERT: O 382 MET cc_start: 0.8178 (mtm) cc_final: 0.7978 (mtp) REVERT: O 414 MET cc_start: 0.7875 (mmm) cc_final: 0.7668 (mmm) REVERT: O 442 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8692 (mp) REVERT: N 95 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.7786 (m) REVERT: N 219 MET cc_start: 0.7836 (tmm) cc_final: 0.7598 (ttp) REVERT: N 305 MET cc_start: 0.7795 (mmm) cc_final: 0.7412 (mmm) REVERT: N 429 MET cc_start: 0.7973 (mmm) cc_final: 0.7678 (mmt) REVERT: e 171 LEU cc_start: 0.9096 (mt) cc_final: 0.8874 (mt) REVERT: e 262 HIS cc_start: 0.7667 (OUTLIER) cc_final: 0.7062 (m90) REVERT: e 533 LYS cc_start: 0.8517 (pttm) cc_final: 0.8274 (pttm) REVERT: M 42 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7880 (tptp) outliers start: 208 outliers final: 143 residues processed: 1173 average time/residue: 0.5910 time to fit residues: 1198.1681 Evaluate side-chains 1080 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 929 time to evaluate : 5.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 324 LEU Chi-restraints excluded: chain K residue 380 ASN Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 113 GLU Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 299 ASP Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain H residue 360 PHE Chi-restraints excluded: chain H residue 395 ILE Chi-restraints excluded: chain H residue 481 ASN Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 263 ASP Chi-restraints excluded: chain G residue 330 ARG Chi-restraints excluded: chain G residue 452 ILE Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain E residue 530 ASP Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 235 ASN Chi-restraints excluded: chain I residue 269 TYR Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 503 ILE 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 196 LEU Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain z residue 63 LEU Chi-restraints excluded: chain z residue 134 LEU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 333 LEU Chi-restraints excluded: chain z residue 391 VAL Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 414 VAL Chi-restraints excluded: chain z residue 435 LEU Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain P residue 11 PHE Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 221 MET 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 297 VAL Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 415 THR Chi-restraints excluded: chain P residue 462 GLU Chi-restraints excluded: chain P residue 463 VAL Chi-restraints excluded: chain P residue 498 LEU Chi-restraints excluded: chain P residue 522 ASP Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 242 VAL Chi-restraints excluded: chain O residue 259 THR Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain O residue 395 ILE Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 516 VAL Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 383 ILE Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 459 THR Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain N residue 521 ASP Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 250 THR Chi-restraints excluded: chain e residue 262 HIS Chi-restraints excluded: chain e residue 330 LEU Chi-restraints excluded: chain e residue 371 VAL Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain e residue 462 GLU Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 271 THR Chi-restraints excluded: chain a residue 352 VAL Chi-restraints excluded: chain a residue 382 ASP Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 336 ILE Chi-restraints excluded: chain M residue 503 ILE Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 158 ASP Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 244 MET Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 379 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 779 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 460 optimal weight: 2.9990 chunk 590 optimal weight: 0.4980 chunk 457 optimal weight: 0.9990 chunk 680 optimal weight: 2.9990 chunk 451 optimal weight: 10.0000 chunk 805 optimal weight: 6.9990 chunk 504 optimal weight: 4.9990 chunk 491 optimal weight: 9.9990 chunk 372 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 390 HIS ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 ASN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 ASN P 67 ASN ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 102 ASN ** P 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 233 HIS N 111 HIS ** N 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 481 ASN ** e 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 377 ASN ** e 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 172 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 65732 Z= 0.194 Angle : 0.590 14.102 88764 Z= 0.284 Chirality : 0.043 0.236 10592 Planarity : 0.003 0.042 11328 Dihedral : 7.330 178.762 9176 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.15 % Allowed : 18.90 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.09), residues: 8408 helix: 1.04 (0.08), residues: 4014 sheet: -0.89 (0.16), residues: 1052 loop : -1.59 (0.10), residues: 3342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 506 HIS 0.008 0.001 HIS E 262 PHE 0.019 0.001 PHE E 232 TYR 0.023 0.001 TYR K 239 ARG 0.007 0.000 ARG e 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1183 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 961 time to evaluate : 6.038 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: K 44 MET cc_start: 0.7939 (mtt) cc_final: 0.7724 (mtt) REVERT: K 393 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7472 (t0) REVERT: J 121 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7670 (tp) REVERT: H 359 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.7982 (m-40) REVERT: H 451 ASP cc_start: 0.7039 (m-30) cc_final: 0.6751 (m-30) REVERT: G 23 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7954 (mt0) REVERT: G 31 LYS cc_start: 0.7658 (mttt) cc_final: 0.7336 (mtpp) REVERT: G 330 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.8042 (mmt90) REVERT: G 511 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: I 323 MET cc_start: 0.8176 (ttm) cc_final: 0.7807 (mtp) REVERT: B 196 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7433 (mm) REVERT: B 452 ASP cc_start: 0.7557 (p0) cc_final: 0.7316 (p0) REVERT: A 51 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7625 (m-30) REVERT: A 368 LYS cc_start: 0.8347 (tmtt) cc_final: 0.7889 (tptp) REVERT: z 442 ASP cc_start: 0.7451 (m-30) cc_final: 0.7144 (m-30) REVERT: P 196 HIS cc_start: 0.6254 (m-70) cc_final: 0.6053 (m170) REVERT: P 296 LYS cc_start: 0.8073 (tppt) cc_final: 0.7860 (tptt) REVERT: O 87 ASP cc_start: 0.7347 (t0) cc_final: 0.7079 (t0) REVERT: O 358 TYR cc_start: 0.8812 (m-80) cc_final: 0.8586 (m-80) REVERT: O 382 MET cc_start: 0.8199 (mtm) cc_final: 0.7971 (mtp) REVERT: O 414 MET cc_start: 0.7920 (mmm) cc_final: 0.7702 (mmm) REVERT: O 442 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8708 (mp) REVERT: N 95 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.7818 (m) REVERT: N 219 MET cc_start: 0.7775 (tmm) cc_final: 0.7517 (ttp) REVERT: N 305 MET cc_start: 0.7821 (mmm) cc_final: 0.7330 (mmm) REVERT: N 350 LEU cc_start: 0.7893 (tt) cc_final: 0.7595 (tp) REVERT: N 429 MET cc_start: 0.7994 (mmm) cc_final: 0.7777 (mmt) REVERT: e 171 LEU cc_start: 0.9117 (mt) cc_final: 0.8864 (mt) REVERT: e 176 VAL cc_start: 0.9155 (m) cc_final: 0.8853 (t) REVERT: e 262 HIS cc_start: 0.7772 (OUTLIER) cc_final: 0.7169 (m90) REVERT: M 42 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7886 (tptp) outliers start: 222 outliers final: 162 residues processed: 1121 average time/residue: 0.5934 time to fit residues: 1157.6916 Evaluate side-chains 1096 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 922 time to evaluate : 5.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 324 LEU Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 299 ASP Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 499 ASP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 324 MET Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain H residue 360 PHE Chi-restraints excluded: chain H residue 395 ILE Chi-restraints excluded: chain H residue 481 ASN Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 263 ASP Chi-restraints excluded: chain G residue 330 ARG Chi-restraints excluded: chain G residue 452 ILE Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 511 GLU Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain E residue 530 ASP Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 269 TYR Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 503 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 63 LEU Chi-restraints excluded: chain z residue 134 LEU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 176 ILE Chi-restraints excluded: chain z residue 333 LEU Chi-restraints excluded: chain z residue 391 VAL Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 414 VAL Chi-restraints excluded: chain z residue 418 MET Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain z residue 520 GLU Chi-restraints excluded: chain P residue 11 PHE Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 148 CYS 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 297 VAL Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 415 THR Chi-restraints excluded: chain P residue 462 GLU Chi-restraints excluded: chain P residue 463 VAL Chi-restraints excluded: chain P residue 498 LEU Chi-restraints excluded: chain P residue 499 ASP Chi-restraints excluded: chain O residue 16 SER Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 259 THR Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain O residue 364 CYS Chi-restraints excluded: chain O residue 371 THR Chi-restraints excluded: chain O residue 395 ILE Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 516 VAL Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain N residue 57 ILE Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 111 HIS Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain N residue 225 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 383 ILE Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 459 THR Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain N residue 521 ASP Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 45 THR Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 226 VAL Chi-restraints excluded: chain e residue 250 THR Chi-restraints excluded: chain e residue 262 HIS Chi-restraints excluded: chain e residue 312 LEU Chi-restraints excluded: chain e residue 330 LEU Chi-restraints excluded: chain e residue 360 ILE Chi-restraints excluded: chain e residue 371 VAL Chi-restraints excluded: chain e residue 375 CYS Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain e residue 471 THR Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain a residue 382 ASP Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 336 ILE Chi-restraints excluded: chain M residue 503 ILE Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 158 ASP Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 224 ILE Chi-restraints excluded: chain L residue 244 MET Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain L residue 284 LYS Chi-restraints excluded: chain L residue 313 GLU Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 349 ILE Chi-restraints excluded: chain L residue 379 THR Chi-restraints excluded: chain L residue 434 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 498 optimal weight: 2.9990 chunk 321 optimal weight: 7.9990 chunk 481 optimal weight: 6.9990 chunk 242 optimal weight: 0.0970 chunk 158 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 512 optimal weight: 2.9990 chunk 548 optimal weight: 2.9990 chunk 398 optimal weight: 3.9990 chunk 75 optimal weight: 0.3980 chunk 633 optimal weight: 0.9980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN ** z 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 21 GLN O 233 HIS ** N 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 377 ASN e 389 ASN ** a 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.5981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 65732 Z= 0.208 Angle : 0.604 27.046 88764 Z= 0.289 Chirality : 0.043 0.226 10592 Planarity : 0.003 0.044 11328 Dihedral : 7.287 178.230 9175 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.13 % Allowed : 19.11 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.09), residues: 8408 helix: 1.15 (0.08), residues: 4012 sheet: -0.83 (0.16), residues: 1052 loop : -1.54 (0.10), residues: 3344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 168 HIS 0.016 0.001 HIS N 111 PHE 0.015 0.001 PHE O 360 TYR 0.022 0.001 TYR K 239 ARG 0.007 0.000 ARG M 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1172 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 952 time to evaluate : 6.109 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 44 MET cc_start: 0.7956 (mtt) cc_final: 0.7725 (mtt) REVERT: K 393 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7426 (t0) REVERT: J 121 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7641 (tp) REVERT: H 359 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.8023 (m-40) REVERT: H 451 ASP cc_start: 0.7006 (m-30) cc_final: 0.6738 (m-30) REVERT: G 23 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7980 (mt0) REVERT: G 31 LYS cc_start: 0.7668 (mttt) cc_final: 0.7337 (mtpp) REVERT: G 511 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: I 323 MET cc_start: 0.8169 (ttm) cc_final: 0.7815 (mtp) REVERT: B 196 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7583 (mm) REVERT: A 51 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7617 (m-30) REVERT: A 225 MET cc_start: 0.8466 (ptp) cc_final: 0.8197 (mtm) REVERT: A 368 LYS cc_start: 0.8215 (tmtt) cc_final: 0.7953 (tptp) REVERT: z 101 GLU cc_start: 0.7288 (tp30) cc_final: 0.7009 (tp30) REVERT: z 442 ASP cc_start: 0.7418 (m-30) cc_final: 0.7168 (m-30) REVERT: P 196 HIS cc_start: 0.6273 (m-70) cc_final: 0.6072 (m170) REVERT: P 296 LYS cc_start: 0.8095 (tppt) cc_final: 0.7881 (tptt) REVERT: O 87 ASP cc_start: 0.7358 (t0) cc_final: 0.7095 (t0) REVERT: O 358 TYR cc_start: 0.8834 (m-80) cc_final: 0.8611 (m-80) REVERT: O 382 MET cc_start: 0.8205 (mtm) cc_final: 0.7978 (mtp) REVERT: O 414 MET cc_start: 0.7930 (mmm) cc_final: 0.7698 (mmm) REVERT: O 442 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8707 (mp) REVERT: N 95 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7790 (m) REVERT: N 219 MET cc_start: 0.7764 (tmm) cc_final: 0.7462 (ttp) REVERT: N 305 MET cc_start: 0.7819 (mmm) cc_final: 0.7376 (mmm) REVERT: N 350 LEU cc_start: 0.7969 (tt) cc_final: 0.7713 (tp) REVERT: N 429 MET cc_start: 0.8028 (mmm) cc_final: 0.7805 (mmt) REVERT: e 171 LEU cc_start: 0.9120 (mt) cc_final: 0.8880 (mt) REVERT: e 176 VAL cc_start: 0.9154 (m) cc_final: 0.8862 (t) REVERT: e 262 HIS cc_start: 0.7777 (OUTLIER) cc_final: 0.7214 (m90) REVERT: e 533 LYS cc_start: 0.8516 (pttm) cc_final: 0.8254 (pttm) REVERT: M 42 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7928 (tptp) outliers start: 220 outliers final: 180 residues processed: 1110 average time/residue: 0.5990 time to fit residues: 1157.3117 Evaluate side-chains 1107 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 916 time to evaluate : 5.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 324 LEU Chi-restraints excluded: chain K residue 352 GLU Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 399 LYS Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 299 ASP Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 292 LYS Chi-restraints excluded: chain H residue 324 MET Chi-restraints excluded: chain H residue 345 CYS Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain H residue 360 PHE Chi-restraints excluded: chain H residue 395 ILE Chi-restraints excluded: chain H residue 481 ASN Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 263 ASP Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 452 ILE Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 511 GLU Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain E residue 483 MET Chi-restraints excluded: chain E residue 530 ASP Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 235 ASN Chi-restraints excluded: chain I residue 269 TYR Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 503 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 63 LEU Chi-restraints excluded: chain z residue 114 LEU Chi-restraints excluded: chain z residue 134 LEU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 333 LEU Chi-restraints excluded: chain z residue 367 ASN Chi-restraints excluded: chain z residue 391 VAL Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 414 VAL Chi-restraints excluded: chain z residue 418 MET Chi-restraints excluded: chain z residue 435 LEU Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain z residue 520 GLU Chi-restraints excluded: chain P residue 11 PHE Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 148 CYS Chi-restraints excluded: chain P residue 221 MET 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 297 VAL Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 381 THR Chi-restraints excluded: chain P residue 415 THR Chi-restraints excluded: chain P residue 462 GLU Chi-restraints excluded: chain P residue 463 VAL Chi-restraints excluded: chain P residue 498 LEU Chi-restraints excluded: chain P residue 499 ASP Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 259 THR Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain O residue 364 CYS Chi-restraints excluded: chain O residue 371 THR Chi-restraints excluded: chain O residue 395 ILE Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 516 VAL Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 57 ILE Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain N residue 225 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 383 ILE Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 459 THR Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain N residue 521 ASP Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 45 THR Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 226 VAL Chi-restraints excluded: chain e residue 250 THR Chi-restraints excluded: chain e residue 251 CYS Chi-restraints excluded: chain e residue 262 HIS Chi-restraints excluded: chain e residue 312 LEU Chi-restraints excluded: chain e residue 330 LEU Chi-restraints excluded: chain e residue 360 ILE Chi-restraints excluded: chain e residue 371 VAL Chi-restraints excluded: chain e residue 375 CYS Chi-restraints excluded: chain e residue 389 ASN Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain e residue 471 THR Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 48 ASP Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain a residue 352 VAL Chi-restraints excluded: chain a residue 382 ASP Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 336 ILE Chi-restraints excluded: chain M residue 503 ILE Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 244 MET Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain L residue 284 LYS Chi-restraints excluded: chain L residue 313 GLU Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 349 ILE Chi-restraints excluded: chain L residue 379 THR Chi-restraints excluded: chain L residue 434 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 732 optimal weight: 7.9990 chunk 771 optimal weight: 0.9980 chunk 704 optimal weight: 0.2980 chunk 750 optimal weight: 0.4980 chunk 451 optimal weight: 0.8980 chunk 327 optimal weight: 9.9990 chunk 589 optimal weight: 6.9990 chunk 230 optimal weight: 10.0000 chunk 678 optimal weight: 3.9990 chunk 710 optimal weight: 0.7980 chunk 748 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN ** z 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 233 HIS N 111 HIS N 400 ASN ** e 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 276 GLN ** e 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 377 ASN e 389 ASN ** a 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.6008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 65732 Z= 0.157 Angle : 0.594 22.689 88764 Z= 0.283 Chirality : 0.042 0.236 10592 Planarity : 0.003 0.072 11328 Dihedral : 7.093 173.022 9175 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.76 % Allowed : 19.61 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.09 (0.09), residues: 8408 helix: 1.27 (0.08), residues: 4038 sheet: -0.78 (0.16), residues: 1060 loop : -1.48 (0.11), residues: 3310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 506 HIS 0.009 0.001 HIS z 198 PHE 0.015 0.001 PHE O 216 TYR 0.023 0.001 TYR K 239 ARG 0.007 0.000 ARG M 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1171 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 977 time to evaluate : 5.990 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: J 121 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7548 (tp) REVERT: G 23 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7943 (mt0) REVERT: G 31 LYS cc_start: 0.7612 (mttt) cc_final: 0.7314 (mtpp) REVERT: G 511 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: I 323 MET cc_start: 0.8115 (ttm) cc_final: 0.7762 (mtp) REVERT: B 196 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7474 (mm) REVERT: A 51 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7646 (m-30) REVERT: A 63 LYS cc_start: 0.8207 (ttmt) cc_final: 0.7991 (mttp) REVERT: A 225 MET cc_start: 0.8472 (ptp) cc_final: 0.8191 (mtm) REVERT: z 442 ASP cc_start: 0.7438 (m-30) cc_final: 0.7143 (m-30) REVERT: P 296 LYS cc_start: 0.8091 (tppt) cc_final: 0.7872 (tptt) REVERT: P 461 ASN cc_start: 0.8163 (m-40) cc_final: 0.7781 (m110) REVERT: O 87 ASP cc_start: 0.7353 (t0) cc_final: 0.7052 (t0) REVERT: O 358 TYR cc_start: 0.8816 (m-80) cc_final: 0.8595 (m-80) REVERT: O 382 MET cc_start: 0.8163 (mtm) cc_final: 0.7923 (mtp) REVERT: O 442 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8741 (mp) REVERT: N 95 THR cc_start: 0.8208 (OUTLIER) cc_final: 0.7744 (m) REVERT: N 219 MET cc_start: 0.7721 (tmm) cc_final: 0.7384 (ttp) REVERT: N 305 MET cc_start: 0.7758 (mmm) cc_final: 0.7287 (mmm) REVERT: N 350 LEU cc_start: 0.7864 (tt) cc_final: 0.7503 (tp) REVERT: N 429 MET cc_start: 0.8022 (mmm) cc_final: 0.7789 (mmt) REVERT: e 176 VAL cc_start: 0.9093 (m) cc_final: 0.8821 (t) REVERT: e 262 HIS cc_start: 0.7647 (OUTLIER) cc_final: 0.7099 (m90) REVERT: M 42 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7910 (tptp) outliers start: 194 outliers final: 150 residues processed: 1115 average time/residue: 0.5889 time to fit residues: 1139.7360 Evaluate side-chains 1081 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 922 time to evaluate : 6.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 352 GLU Chi-restraints excluded: chain K residue 380 ASN Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 299 ASP Chi-restraints excluded: chain J residue 359 GLN Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 324 MET Chi-restraints excluded: chain H residue 345 CYS Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain H residue 360 PHE Chi-restraints excluded: chain H residue 395 ILE Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 263 ASP Chi-restraints excluded: chain G residue 452 ILE Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 511 GLU Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain E residue 483 MET Chi-restraints excluded: chain E residue 530 ASP Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 269 TYR Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 503 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 63 LEU Chi-restraints excluded: chain z residue 114 LEU Chi-restraints excluded: chain z residue 134 LEU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 333 LEU Chi-restraints excluded: chain z residue 391 VAL Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 414 VAL Chi-restraints excluded: chain z residue 435 LEU Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain z residue 520 GLU Chi-restraints excluded: chain P residue 11 PHE Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 221 MET 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 297 VAL Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 381 THR Chi-restraints excluded: chain P residue 415 THR Chi-restraints excluded: chain P residue 463 VAL Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 259 THR Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain O residue 364 CYS Chi-restraints excluded: chain O residue 371 THR Chi-restraints excluded: chain O residue 395 ILE Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 57 ILE Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 383 ILE Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 459 THR Chi-restraints excluded: chain N residue 521 ASP Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 250 THR Chi-restraints excluded: chain e residue 251 CYS Chi-restraints excluded: chain e residue 262 HIS Chi-restraints excluded: chain e residue 312 LEU Chi-restraints excluded: chain e residue 330 LEU Chi-restraints excluded: chain e residue 371 VAL Chi-restraints excluded: chain e residue 375 CYS Chi-restraints excluded: chain e residue 392 ILE Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain e residue 471 THR Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain a residue 352 VAL Chi-restraints excluded: chain a residue 382 ASP Chi-restraints excluded: chain a residue 447 VAL Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 336 ILE Chi-restraints excluded: chain M residue 503 ILE Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 244 MET Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain L residue 284 LYS Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 349 ILE Chi-restraints excluded: chain L residue 379 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 493 optimal weight: 2.9990 chunk 794 optimal weight: 4.9990 chunk 484 optimal weight: 0.0770 chunk 376 optimal weight: 0.1980 chunk 551 optimal weight: 5.9990 chunk 832 optimal weight: 0.8980 chunk 766 optimal weight: 5.9990 chunk 663 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 512 optimal weight: 0.9990 chunk 406 optimal weight: 9.9990 overall best weight: 0.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 GLN H 25 ASN ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 ASN ** z 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 191 GLN O 233 HIS N 111 HIS ** e 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 377 ASN ** a 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.6066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 65732 Z= 0.163 Angle : 0.594 19.187 88764 Z= 0.283 Chirality : 0.042 0.229 10592 Planarity : 0.003 0.043 11328 Dihedral : 6.883 168.833 9168 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.47 % Allowed : 20.11 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.03 (0.09), residues: 8408 helix: 1.37 (0.08), residues: 4044 sheet: -0.72 (0.16), residues: 1072 loop : -1.44 (0.11), residues: 3292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 506 HIS 0.014 0.001 HIS N 111 PHE 0.020 0.001 PHE L 179 TYR 0.021 0.001 TYR K 239 ARG 0.007 0.000 ARG M 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1134 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 960 time to evaluate : 6.118 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: J 121 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7597 (tp) REVERT: J 300 MET cc_start: 0.7741 (tpp) cc_final: 0.7489 (tpt) REVERT: G 23 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7969 (mt0) REVERT: G 31 LYS cc_start: 0.7608 (mttt) cc_final: 0.7246 (mtpp) REVERT: G 511 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: I 323 MET cc_start: 0.8101 (ttm) cc_final: 0.7763 (mtp) REVERT: B 196 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7478 (mm) REVERT: A 51 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7657 (m-30) REVERT: A 225 MET cc_start: 0.8528 (ptp) cc_final: 0.8267 (mtm) REVERT: z 442 ASP cc_start: 0.7384 (m-30) cc_final: 0.7089 (m-30) REVERT: P 38 GLU cc_start: 0.6411 (pp20) cc_final: 0.6172 (pp20) REVERT: P 296 LYS cc_start: 0.8106 (tppt) cc_final: 0.7903 (tmtt) REVERT: O 87 ASP cc_start: 0.7340 (t0) cc_final: 0.7051 (t0) REVERT: O 358 TYR cc_start: 0.8826 (m-80) cc_final: 0.8626 (m-80) REVERT: O 382 MET cc_start: 0.8167 (mtm) cc_final: 0.7897 (mtp) REVERT: O 442 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8703 (mp) REVERT: N 95 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.7811 (m) REVERT: N 305 MET cc_start: 0.7602 (mmm) cc_final: 0.7154 (mmm) REVERT: N 350 LEU cc_start: 0.7933 (tt) cc_final: 0.7664 (tp) REVERT: N 429 MET cc_start: 0.8024 (mmm) cc_final: 0.7812 (mmt) REVERT: e 262 HIS cc_start: 0.7754 (OUTLIER) cc_final: 0.7262 (m90) REVERT: e 521 MET cc_start: 0.7358 (mmm) cc_final: 0.6816 (tpp) REVERT: M 42 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7891 (tptp) outliers start: 174 outliers final: 146 residues processed: 1086 average time/residue: 0.6108 time to fit residues: 1153.9122 Evaluate side-chains 1076 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 921 time to evaluate : 6.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 352 GLU Chi-restraints excluded: chain K residue 380 ASN Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 299 ASP Chi-restraints excluded: chain J residue 359 GLN Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 345 CYS Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain H residue 360 PHE Chi-restraints excluded: chain H residue 395 ILE Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 263 ASP Chi-restraints excluded: chain G residue 452 ILE Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 511 GLU Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain E residue 483 MET Chi-restraints excluded: chain E residue 530 ASP Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 269 TYR Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 503 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 63 LEU Chi-restraints excluded: chain z residue 114 LEU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 333 LEU Chi-restraints excluded: chain z residue 391 VAL Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 414 VAL Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain z residue 520 GLU Chi-restraints excluded: chain P residue 11 PHE Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 148 CYS 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 297 VAL Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 381 THR Chi-restraints excluded: chain P residue 415 THR Chi-restraints excluded: chain P residue 463 VAL Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 193 LYS Chi-restraints excluded: chain O residue 259 THR Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain O residue 364 CYS Chi-restraints excluded: chain O residue 371 THR Chi-restraints excluded: chain O residue 395 ILE Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 57 ILE Chi-restraints excluded: chain N residue 90 GLU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 111 HIS Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 383 ILE Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 459 THR Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain N residue 521 ASP Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 179 CYS Chi-restraints excluded: chain e residue 250 THR Chi-restraints excluded: chain e residue 251 CYS Chi-restraints excluded: chain e residue 262 HIS Chi-restraints excluded: chain e residue 312 LEU Chi-restraints excluded: chain e residue 330 LEU Chi-restraints excluded: chain e residue 371 VAL Chi-restraints excluded: chain e residue 375 CYS Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain e residue 471 THR Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 48 ASP Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain a residue 352 VAL Chi-restraints excluded: chain a residue 382 ASP Chi-restraints excluded: chain a residue 447 VAL Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 336 ILE Chi-restraints excluded: chain M residue 503 ILE Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 224 ILE Chi-restraints excluded: chain L residue 244 MET Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain L residue 284 LYS Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 349 ILE Chi-restraints excluded: chain L residue 379 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 526 optimal weight: 7.9990 chunk 706 optimal weight: 3.9990 chunk 203 optimal weight: 9.9990 chunk 611 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 184 optimal weight: 0.0980 chunk 664 optimal weight: 5.9990 chunk 278 optimal weight: 4.9990 chunk 682 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 8 ASN ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 461 ASN ** J 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 472 GLN ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 ASN ** E 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 140 HIS ** P 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 233 HIS N 111 HIS N 276 GLN N 392 GLN ** e 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 377 ASN a 196 ASN ** a 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.102011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.088432 restraints weight = 123737.838| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.64 r_work: 0.3019 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.6281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 65732 Z= 0.341 Angle : 0.679 17.581 88764 Z= 0.329 Chirality : 0.045 0.232 10592 Planarity : 0.004 0.045 11328 Dihedral : 7.257 172.584 9165 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.24 % Favored : 93.74 % Rotamer: Outliers : 2.84 % Allowed : 19.85 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.17 (0.09), residues: 8408 helix: 1.15 (0.08), residues: 4106 sheet: -0.86 (0.16), residues: 1118 loop : -1.51 (0.11), residues: 3184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 485 HIS 0.015 0.001 HIS N 111 PHE 0.031 0.002 PHE N 112 TYR 0.024 0.002 TYR L 456 ARG 0.008 0.001 ARG M 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20037.48 seconds wall clock time: 350 minutes 36.62 seconds (21036.62 seconds total)