Starting phenix.real_space_refine on Sun Mar 17 12:32:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6te0_10473/03_2024/6te0_10473_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6te0_10473/03_2024/6te0_10473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6te0_10473/03_2024/6te0_10473.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6te0_10473/03_2024/6te0_10473.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6te0_10473/03_2024/6te0_10473_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6te0_10473/03_2024/6te0_10473_trim_updated.pdb" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 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: 7 Type Number sf(0) Gaussians P 14 5.49 5 Mg 5 5.21 5 S 233 5.16 5 C 25085 2.51 5 N 6559 2.21 5 O 7457 1.98 5 H 39835 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 176": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 176": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 179": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 176": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 81": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 491": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 418": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 202": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 223": "OD1" <-> "OD2" Residue "M ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 11": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 126": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 156": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 79188 Number of models: 1 Model: "" Number of chains: 29 Chain: "C" Number of atoms: 8317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 8317 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 506} Chain breaks: 1 Chain: "A" Number of atoms: 8292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 8292 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 504} Chain breaks: 1 Chain: "B" Number of atoms: 8336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 8336 Classifications: {'peptide': 529} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 508} Chain breaks: 1 Chain: "F" Number of atoms: 7408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 7408 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 465} Chain: "D" Number of atoms: 7408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 7408 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 466} Chain: "E" Number of atoms: 7407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 7407 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 465} Chain: "L" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2596 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "J" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2596 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "K" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2596 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "M" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 3778 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 14, 'TRANS': 228} Chain: "G" Number of atoms: 4898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 4898 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 5, 'TRANS': 297} Chain: "H" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 2448 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "I" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1077 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "O" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "P" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "Q" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "R" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "S" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "T" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "U" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "V" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "W" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "X" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'TRT': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 25.83, per 1000 atoms: 0.33 Number of scatterers: 79188 At special positions: 0 Unit cell: (165.9, 166.95, 233.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 233 16.00 P 14 15.00 Mg 5 11.99 O 7457 8.00 N 6559 7.00 C 25085 6.00 H 39835 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 48.96 Conformation dependent library (CDL) restraints added in 6.1 seconds 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9466 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 212 helices and 27 sheets defined 47.7% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.78 Creating SS restraints... Processing helix chain 'C' and resid 166 through 171 Processing helix chain 'C' and resid 190 through 201 removed outlier: 3.723A pdb=" N ALA C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 207 removed outlier: 3.856A pdb=" N GLU C 207 " --> pdb=" O LYS C 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 203 through 207' Processing helix chain 'C' and resid 225 through 237 Processing helix chain 'C' and resid 241 through 243 No H-bonds generated for 'chain 'C' and resid 241 through 243' Processing helix chain 'C' and resid 255 through 258 No H-bonds generated for 'chain 'C' and resid 255 through 258' Processing helix chain 'C' and resid 261 through 274 removed outlier: 3.774A pdb=" N PHE C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 313 through 323 removed outlier: 3.970A pdb=" N LEU C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ARG C 323 " --> pdb=" O ARG C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 352 through 360 removed outlier: 3.645A pdb=" N SER C 359 " --> pdb=" O THR C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 399 through 418 removed outlier: 3.698A pdb=" N ALA C 404 " --> pdb=" O LYS C 400 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLU C 411 " --> pdb=" O MET C 407 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS C 414 " --> pdb=" O GLY C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 440 removed outlier: 3.801A pdb=" N ALA C 434 " --> pdb=" O MET C 430 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 439 " --> pdb=" O ARG C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 459 removed outlier: 3.681A pdb=" N VAL C 458 " --> pdb=" O ALA C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 479 Processing helix chain 'C' and resid 483 through 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' Processing helix chain 'C' and resid 503 through 509 removed outlier: 3.960A pdb=" N TYR C 508 " --> pdb=" O TYR C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 541 Proline residue: C 518 - end of helix removed outlier: 4.394A pdb=" N GLN C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER C 537 " --> pdb=" O ASP C 533 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG C 538 " --> pdb=" O ASN C 534 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN C 540 " --> pdb=" O GLN C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.568A pdb=" N LEU C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG C 560 " --> pdb=" O TYR C 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 166 through 171 Processing helix chain 'A' and resid 190 through 205 removed outlier: 3.920A pdb=" N ALA A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A 204 " --> pdb=" O ASN A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 237 Processing helix chain 'A' and resid 255 through 274 removed outlier: 3.640A pdb=" N LEU A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Proline residue: A 262 - end of helix removed outlier: 3.760A pdb=" N PHE A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 299 removed outlier: 3.780A pdb=" N VAL A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.726A pdb=" N LEU A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ARG A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'A' and resid 396 through 415 removed outlier: 4.088A pdb=" N VAL A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 440 removed outlier: 3.595A pdb=" N ALA A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 439 " --> pdb=" O ARG A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.787A pdb=" N VAL A 453 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 469 through 479 removed outlier: 4.029A pdb=" N LYS A 472 " --> pdb=" O GLN A 469 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE A 473 " --> pdb=" O TYR A 470 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 479 " --> pdb=" O PHE A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 501 through 509 removed outlier: 3.557A pdb=" N TYR A 504 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG A 507 " --> pdb=" O TYR A 504 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 509 " --> pdb=" O ILE A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 534 Proline residue: A 518 - end of helix Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 545 through 561 removed outlier: 3.663A pdb=" N LEU A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 151 through 153 No H-bonds generated for 'chain 'B' and resid 151 through 153' Processing helix chain 'B' and resid 166 through 170 Processing helix chain 'B' and resid 192 through 199 Processing helix chain 'B' and resid 202 through 205 No H-bonds generated for 'chain 'B' and resid 202 through 205' Processing helix chain 'B' and resid 225 through 237 Processing helix chain 'B' and resid 255 through 258 No H-bonds generated for 'chain 'B' and resid 255 through 258' Processing helix chain 'B' and resid 261 through 274 removed outlier: 3.668A pdb=" N GLU B 271 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 removed outlier: 3.561A pdb=" N TYR B 293 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 299 " --> pdb=" O GLN B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 313 through 323 removed outlier: 4.280A pdb=" N ARG B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 352 through 358 Processing helix chain 'B' and resid 369 through 372 No H-bonds generated for 'chain 'B' and resid 369 through 372' Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 396 through 415 removed outlier: 4.231A pdb=" N LYS B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU B 411 " --> pdb=" O MET B 407 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 440 removed outlier: 3.854A pdb=" N ALA B 434 " --> pdb=" O MET B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 459 removed outlier: 3.741A pdb=" N VAL B 453 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ALA B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 458 " --> pdb=" O ALA B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 464 No H-bonds generated for 'chain 'B' and resid 462 through 464' Processing helix chain 'B' and resid 469 through 480 removed outlier: 4.286A pdb=" N LYS B 472 " --> pdb=" O GLN B 469 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 473 " --> pdb=" O TYR B 470 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR B 474 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 477 " --> pdb=" O TYR B 474 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 479 " --> pdb=" O PHE B 476 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN B 480 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 487 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 517 through 534 removed outlier: 5.460A pdb=" N ILE B 526 " --> pdb=" O LYS B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 539 No H-bonds generated for 'chain 'B' and resid 536 through 539' Processing helix chain 'B' and resid 545 through 561 removed outlier: 3.529A pdb=" N GLN B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 154 No H-bonds generated for 'chain 'F' and resid 151 through 154' Processing helix chain 'F' and resid 173 through 187 removed outlier: 3.814A pdb=" N MET F 178 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS F 186 " --> pdb=" O ASN F 182 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY F 187 " --> pdb=" O ASN F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 213 removed outlier: 3.678A pdb=" N THR F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 240 Processing helix chain 'F' and resid 243 through 255 removed outlier: 3.876A pdb=" N TYR F 252 " --> pdb=" O THR F 248 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE F 253 " --> pdb=" O MET F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 282 removed outlier: 3.573A pdb=" N ASN F 275 " --> pdb=" O PHE F 271 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL F 278 " --> pdb=" O ALA F 274 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA F 280 " --> pdb=" O SER F 276 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LEU F 281 " --> pdb=" O GLU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 303 Processing helix chain 'F' and resid 323 through 325 No H-bonds generated for 'chain 'F' and resid 323 through 325' Processing helix chain 'F' and resid 330 through 335 removed outlier: 3.626A pdb=" N THR F 335 " --> pdb=" O ALA F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 351 Processing helix chain 'F' and resid 375 through 398 removed outlier: 3.849A pdb=" N GLU F 393 " --> pdb=" O THR F 389 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE F 397 " --> pdb=" O GLU F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 405 No H-bonds generated for 'chain 'F' and resid 403 through 405' Processing helix chain 'F' and resid 408 through 423 removed outlier: 3.606A pdb=" N ILE F 413 " --> pdb=" O GLU F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 435 removed outlier: 4.105A pdb=" N VAL F 433 " --> pdb=" O VAL F 430 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR F 435 " --> pdb=" O GLU F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 447 No H-bonds generated for 'chain 'F' and resid 445 through 447' Processing helix chain 'F' and resid 451 through 456 Processing helix chain 'F' and resid 473 through 500 removed outlier: 3.511A pdb=" N LYS F 482 " --> pdb=" O GLU F 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 52 No H-bonds generated for 'chain 'D' and resid 49 through 52' Processing helix chain 'D' and resid 99 through 101 No H-bonds generated for 'chain 'D' and resid 99 through 101' Processing helix chain 'D' and resid 149 through 154 Processing helix chain 'D' and resid 173 through 184 removed outlier: 3.682A pdb=" N ILE D 177 " --> pdb=" O LYS D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 213 removed outlier: 3.559A pdb=" N THR D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU D 210 " --> pdb=" O ASP D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 255 removed outlier: 4.380A pdb=" N ARG D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA D 243 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLN D 244 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE D 253 " --> pdb=" O MET D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 281 Processing helix chain 'D' and resid 295 through 303 removed outlier: 3.564A pdb=" N LEU D 302 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 325 No H-bonds generated for 'chain 'D' and resid 323 through 325' Processing helix chain 'D' and resid 330 through 338 removed outlier: 4.145A pdb=" N HIS D 338 " --> pdb=" O THR D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 375 through 398 Processing helix chain 'D' and resid 403 through 405 No H-bonds generated for 'chain 'D' and resid 403 through 405' Processing helix chain 'D' and resid 408 through 423 removed outlier: 3.666A pdb=" N LYS D 422 " --> pdb=" O ARG D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 435 No H-bonds generated for 'chain 'D' and resid 432 through 435' Processing helix chain 'D' and resid 444 through 456 Processing helix chain 'D' and resid 465 through 467 No H-bonds generated for 'chain 'D' and resid 465 through 467' Processing helix chain 'D' and resid 473 through 500 removed outlier: 3.931A pdb=" N LYS D 477 " --> pdb=" O LEU D 473 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU D 478 " --> pdb=" O ASP D 474 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS D 479 " --> pdb=" O SER D 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 101 No H-bonds generated for 'chain 'E' and resid 99 through 101' Processing helix chain 'E' and resid 134 through 136 No H-bonds generated for 'chain 'E' and resid 134 through 136' Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 173 through 184 Processing helix chain 'E' and resid 201 through 213 Processing helix chain 'E' and resid 236 through 239 No H-bonds generated for 'chain 'E' and resid 236 through 239' Processing helix chain 'E' and resid 242 through 255 removed outlier: 3.828A pdb=" N PHE E 253 " --> pdb=" O MET E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 279 Processing helix chain 'E' and resid 295 through 303 removed outlier: 3.747A pdb=" N LEU E 302 " --> pdb=" O ASP E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 325 No H-bonds generated for 'chain 'E' and resid 323 through 325' Processing helix chain 'E' and resid 330 through 335 Processing helix chain 'E' and resid 348 through 352 Processing helix chain 'E' and resid 375 through 398 removed outlier: 3.624A pdb=" N ASP E 383 " --> pdb=" O ASN E 379 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP E 396 " --> pdb=" O LYS E 392 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE E 397 " --> pdb=" O GLU E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 405 No H-bonds generated for 'chain 'E' and resid 403 through 405' Processing helix chain 'E' and resid 408 through 423 removed outlier: 3.624A pdb=" N LYS E 419 " --> pdb=" O ASP E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 435 removed outlier: 4.230A pdb=" N VAL E 433 " --> pdb=" O VAL E 430 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR E 435 " --> pdb=" O GLU E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 455 Processing helix chain 'E' and resid 465 through 467 No H-bonds generated for 'chain 'E' and resid 465 through 467' Processing helix chain 'E' and resid 473 through 500 Processing helix chain 'L' and resid 40 through 47 Processing helix chain 'L' and resid 56 through 65 removed outlier: 3.935A pdb=" N VAL L 60 " --> pdb=" O GLY L 56 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS L 61 " --> pdb=" O GLU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 83 Processing helix chain 'L' and resid 97 through 109 Processing helix chain 'L' and resid 118 through 131 removed outlier: 4.141A pdb=" N TYR L 123 " --> pdb=" O GLU L 119 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL L 124 " --> pdb=" O SER L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 147 Processing helix chain 'L' and resid 153 through 168 removed outlier: 3.548A pdb=" N ALA L 158 " --> pdb=" O ALA L 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 48 Processing helix chain 'J' and resid 52 through 63 removed outlier: 4.011A pdb=" N GLY J 56 " --> pdb=" O TYR J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 83 Processing helix chain 'J' and resid 97 through 109 removed outlier: 3.885A pdb=" N ILE J 104 " --> pdb=" O ALA J 100 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU J 105 " --> pdb=" O MET J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 130 removed outlier: 3.512A pdb=" N VAL J 124 " --> pdb=" O SER J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 147 removed outlier: 3.545A pdb=" N VAL J 139 " --> pdb=" O ARG J 135 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU J 147 " --> pdb=" O GLY J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 168 removed outlier: 3.866A pdb=" N ALA J 158 " --> pdb=" O ALA J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 178 No H-bonds generated for 'chain 'J' and resid 175 through 178' Processing helix chain 'K' and resid 40 through 47 removed outlier: 3.521A pdb=" N GLU K 45 " --> pdb=" O PRO K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 64 Processing helix chain 'K' and resid 71 through 83 Processing helix chain 'K' and resid 97 through 109 removed outlier: 3.871A pdb=" N MET K 101 " --> pdb=" O LYS K 97 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU K 105 " --> pdb=" O MET K 101 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU K 106 " --> pdb=" O MET K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 131 removed outlier: 3.524A pdb=" N LYS K 126 " --> pdb=" O GLY K 122 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU K 127 " --> pdb=" O TYR K 123 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU K 128 " --> pdb=" O VAL K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 147 Processing helix chain 'K' and resid 153 through 168 removed outlier: 3.627A pdb=" N ALA K 158 " --> pdb=" O ALA K 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 32 Processing helix chain 'M' and resid 49 through 62 removed outlier: 3.845A pdb=" N ALA M 53 " --> pdb=" O HIS M 49 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU M 56 " --> pdb=" O PHE M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 68 through 84 removed outlier: 3.602A pdb=" N PHE M 75 " --> pdb=" O VAL M 72 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP M 79 " --> pdb=" O LYS M 76 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE M 82 " --> pdb=" O ASP M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 102 No H-bonds generated for 'chain 'M' and resid 100 through 102' Processing helix chain 'M' and resid 105 through 117 Processing helix chain 'M' and resid 120 through 122 No H-bonds generated for 'chain 'M' and resid 120 through 122' Processing helix chain 'M' and resid 124 through 137 removed outlier: 3.886A pdb=" N ALA M 129 " --> pdb=" O ASN M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 158 Processing helix chain 'M' and resid 160 through 169 removed outlier: 3.654A pdb=" N GLU M 165 " --> pdb=" O LYS M 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 204 through 221 removed outlier: 3.541A pdb=" N ALA M 209 " --> pdb=" O ALA M 205 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR M 211 " --> pdb=" O ALA M 207 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA M 219 " --> pdb=" O ALA M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 240 through 245 Processing helix chain 'M' and resid 249 through 262 Processing helix chain 'G' and resid 4 through 43 removed outlier: 3.793A pdb=" N ARG G 8 " --> pdb=" O GLY G 4 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN G 22 " --> pdb=" O LYS G 18 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS G 34 " --> pdb=" O VAL G 30 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL G 40 " --> pdb=" O ARG G 36 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ARG G 41 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG G 43 " --> pdb=" O VAL G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 56 No H-bonds generated for 'chain 'G' and resid 53 through 56' Processing helix chain 'G' and resid 63 through 69 removed outlier: 3.579A pdb=" N ILE G 67 " --> pdb=" O ASP G 63 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU G 68 " --> pdb=" O GLN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 98 removed outlier: 3.517A pdb=" N LEU G 96 " --> pdb=" O MET G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 120 removed outlier: 3.576A pdb=" N MET G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR G 118 " --> pdb=" O LEU G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 151 removed outlier: 4.098A pdb=" N THR G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 192 removed outlier: 3.737A pdb=" N ALA G 192 " --> pdb=" O GLU G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 214 Processing helix chain 'G' and resid 217 through 246 Processing helix chain 'G' and resid 249 through 294 removed outlier: 4.380A pdb=" N GLN G 254 " --> pdb=" O ALA G 250 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY G 260 " --> pdb=" O GLY G 256 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS G 274 " --> pdb=" O ASN G 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 30 Processing helix chain 'H' and resid 131 through 133 No H-bonds generated for 'chain 'H' and resid 131 through 133' Processing helix chain 'H' and resid 136 through 151 removed outlier: 3.739A pdb=" N LYS H 141 " --> pdb=" O GLU H 137 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA H 142 " --> pdb=" O LYS H 138 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU H 144 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 175 removed outlier: 3.992A pdb=" N ILE H 159 " --> pdb=" O GLU H 155 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLN H 160 " --> pdb=" O ALA H 156 " (cutoff:3.500A) Proline residue: H 170 - end of helix Processing helix chain 'I' and resid 10 through 24 removed outlier: 3.871A pdb=" N GLU I 23 " --> pdb=" O ARG I 19 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL I 24 " --> pdb=" O CYS I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 37 removed outlier: 5.056A pdb=" N ARG I 36 " --> pdb=" O THR I 32 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE I 37 " --> pdb=" O LYS I 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 33 through 35 No H-bonds generated for 'chain 'O' and resid 33 through 35' Processing helix chain 'O' and resid 37 through 45 removed outlier: 3.897A pdb=" N GLY O 45 " --> pdb=" O MET O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 66 removed outlier: 3.861A pdb=" N GLY O 52 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 100 Proline residue: O 76 - end of helix removed outlier: 3.707A pdb=" N PHE O 82 " --> pdb=" O CYS O 78 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU O 88 " --> pdb=" O LEU O 84 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA O 96 " --> pdb=" O THR O 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 33 through 35 No H-bonds generated for 'chain 'P' and resid 33 through 35' Processing helix chain 'P' and resid 37 through 46 removed outlier: 3.581A pdb=" N SER P 44 " --> pdb=" O GLY P 40 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY P 45 " --> pdb=" O MET P 41 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL P 46 " --> pdb=" O ALA P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 66 removed outlier: 3.910A pdb=" N GLY P 52 " --> pdb=" O VAL P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 98 removed outlier: 4.143A pdb=" N ALA P 72 " --> pdb=" O ASN P 69 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS P 73 " --> pdb=" O MET P 70 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU P 74 " --> pdb=" O SER P 71 " (cutoff:3.500A) Proline residue: P 76 - end of helix removed outlier: 3.764A pdb=" N LEU P 80 " --> pdb=" O TYR P 77 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE P 82 " --> pdb=" O ILE P 79 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA P 87 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU P 88 " --> pdb=" O SER P 85 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE P 95 " --> pdb=" O THR P 92 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU P 98 " --> pdb=" O ILE P 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 45 removed outlier: 3.901A pdb=" N ILE Q 37 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLY Q 38 " --> pdb=" O ASN Q 35 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA Q 39 " --> pdb=" O LEU Q 36 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA Q 42 " --> pdb=" O ALA Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 66 removed outlier: 4.243A pdb=" N ALA Q 54 " --> pdb=" O ILE Q 51 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER Q 58 " --> pdb=" O MET Q 55 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER Q 59 " --> pdb=" O CYS Q 56 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA Q 63 " --> pdb=" O TYR Q 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 70 No H-bonds generated for 'chain 'Q' and resid 68 through 70' Processing helix chain 'Q' and resid 75 through 101 removed outlier: 3.828A pdb=" N PHE Q 82 " --> pdb=" O CYS Q 78 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER Q 85 " --> pdb=" O GLY Q 81 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU Q 88 " --> pdb=" O LEU Q 84 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA Q 89 " --> pdb=" O SER Q 85 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 46 removed outlier: 3.763A pdb=" N ILE R 37 " --> pdb=" O ALA R 34 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLY R 38 " --> pdb=" O ASN R 35 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA R 39 " --> pdb=" O LEU R 36 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA R 43 " --> pdb=" O GLY R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 66 Processing helix chain 'R' and resid 69 through 98 removed outlier: 4.091A pdb=" N ALA R 72 " --> pdb=" O ASN R 69 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU R 74 " --> pdb=" O SER R 71 " (cutoff:3.500A) Proline residue: R 76 - end of helix removed outlier: 3.581A pdb=" N ILE R 79 " --> pdb=" O PRO R 76 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU R 84 " --> pdb=" O GLY R 81 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU R 88 " --> pdb=" O SER R 85 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA R 96 " --> pdb=" O LEU R 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 33 through 35 No H-bonds generated for 'chain 'S' and resid 33 through 35' Processing helix chain 'S' and resid 37 through 45 removed outlier: 3.957A pdb=" N SER S 44 " --> pdb=" O GLY S 40 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY S 45 " --> pdb=" O MET S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 66 removed outlier: 3.537A pdb=" N CYS S 56 " --> pdb=" O GLY S 52 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE S 57 " --> pdb=" O VAL S 53 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU S 62 " --> pdb=" O SER S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 68 through 74 removed outlier: 4.410A pdb=" N ALA S 72 " --> pdb=" O ASN S 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 98 removed outlier: 3.762A pdb=" N LEU S 80 " --> pdb=" O PRO S 76 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLY S 81 " --> pdb=" O TYR S 77 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU S 88 " --> pdb=" O LEU S 84 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA S 89 " --> pdb=" O SER S 85 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE S 95 " --> pdb=" O PHE S 91 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA S 96 " --> pdb=" O THR S 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 32 through 35 Processing helix chain 'T' and resid 37 through 45 removed outlier: 3.878A pdb=" N MET T 41 " --> pdb=" O ILE T 37 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY T 45 " --> pdb=" O MET T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 66 removed outlier: 4.331A pdb=" N ALA T 54 " --> pdb=" O ILE T 51 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET T 55 " --> pdb=" O GLY T 52 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER T 58 " --> pdb=" O MET T 55 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER T 59 " --> pdb=" O CYS T 56 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU T 62 " --> pdb=" O SER T 59 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA T 64 " --> pdb=" O MET T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 68 through 98 removed outlier: 4.354A pdb=" N ALA T 72 " --> pdb=" O ASN T 69 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU T 74 " --> pdb=" O SER T 71 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU T 75 " --> pdb=" O ALA T 72 " (cutoff:3.500A) Proline residue: T 76 - end of helix removed outlier: 3.601A pdb=" N GLY T 81 " --> pdb=" O CYS T 78 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU T 84 " --> pdb=" O GLY T 81 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA T 87 " --> pdb=" O LEU T 84 " (cutoff:3.500A) Processing helix chain 'U' and resid 33 through 35 No H-bonds generated for 'chain 'U' and resid 33 through 35' Processing helix chain 'U' and resid 38 through 45 removed outlier: 4.112A pdb=" N GLY U 45 " --> pdb=" O MET U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 66 removed outlier: 3.629A pdb=" N TYR U 60 " --> pdb=" O CYS U 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 98 removed outlier: 4.208A pdb=" N ALA U 72 " --> pdb=" O ASN U 69 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU U 74 " --> pdb=" O SER U 71 " (cutoff:3.500A) Proline residue: U 76 - end of helix removed outlier: 3.838A pdb=" N ILE U 79 " --> pdb=" O PRO U 76 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU U 80 " --> pdb=" O TYR U 77 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA U 83 " --> pdb=" O LEU U 80 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU U 84 " --> pdb=" O GLY U 81 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE U 95 " --> pdb=" O THR U 92 " (cutoff:3.500A) Processing helix chain 'V' and resid 33 through 45 removed outlier: 3.810A pdb=" N ILE V 37 " --> pdb=" O ALA V 34 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLY V 38 " --> pdb=" O ASN V 35 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA V 42 " --> pdb=" O ALA V 39 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA V 43 " --> pdb=" O GLY V 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 66 removed outlier: 3.522A pdb=" N SER V 59 " --> pdb=" O MET V 55 " (cutoff:3.500A) Processing helix chain 'V' and resid 68 through 98 removed outlier: 4.226A pdb=" N ALA V 72 " --> pdb=" O ASN V 69 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU V 74 " --> pdb=" O SER V 71 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU V 75 " --> pdb=" O ALA V 72 " (cutoff:3.500A) Proline residue: V 76 - end of helix removed outlier: 4.189A pdb=" N ILE V 79 " --> pdb=" O PRO V 76 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU V 80 " --> pdb=" O TYR V 77 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU V 84 " --> pdb=" O GLY V 81 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA V 87 " --> pdb=" O LEU V 84 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE V 95 " --> pdb=" O THR V 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 33 through 35 No H-bonds generated for 'chain 'W' and resid 33 through 35' Processing helix chain 'W' and resid 37 through 46 removed outlier: 4.280A pdb=" N MET W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL W 46 " --> pdb=" O ALA W 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 66 removed outlier: 3.771A pdb=" N MET W 55 " --> pdb=" O GLY W 52 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER W 58 " --> pdb=" O MET W 55 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER W 59 " --> pdb=" O CYS W 56 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA W 63 " --> pdb=" O TYR W 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 101 removed outlier: 4.686A pdb=" N ALA W 72 " --> pdb=" O ASN W 69 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU W 75 " --> pdb=" O ALA W 72 " (cutoff:3.500A) Proline residue: W 76 - end of helix removed outlier: 3.849A pdb=" N ILE W 79 " --> pdb=" O PRO W 76 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU W 80 " --> pdb=" O TYR W 77 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY W 81 " --> pdb=" O CYS W 78 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE W 82 " --> pdb=" O ILE W 79 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU W 84 " --> pdb=" O GLY W 81 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU W 88 " --> pdb=" O SER W 85 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU W 90 " --> pdb=" O ALA W 87 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR W 92 " --> pdb=" O ALA W 89 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE W 95 " --> pdb=" O THR W 92 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA W 96 " --> pdb=" O LEU W 93 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU W 100 " --> pdb=" O LEU W 97 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE W 101 " --> pdb=" O LEU W 98 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 46 removed outlier: 3.885A pdb=" N ILE X 37 " --> pdb=" O ALA X 34 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLY X 38 " --> pdb=" O ASN X 35 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY X 40 " --> pdb=" O ILE X 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET X 41 " --> pdb=" O GLY X 38 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY X 45 " --> pdb=" O ALA X 42 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 66 removed outlier: 3.534A pdb=" N PHE X 57 " --> pdb=" O ALA X 54 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG X 66 " --> pdb=" O ALA X 63 " (cutoff:3.500A) Processing helix chain 'X' and resid 68 through 70 No H-bonds generated for 'chain 'X' and resid 68 through 70' Processing helix chain 'X' and resid 75 through 100 removed outlier: 3.861A pdb=" N GLY X 81 " --> pdb=" O TYR X 77 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE X 82 " --> pdb=" O CYS X 78 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU X 88 " --> pdb=" O LEU X 84 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA X 96 " --> pdb=" O THR X 92 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU X 100 " --> pdb=" O ALA X 96 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 97 through 99 removed outlier: 6.770A pdb=" N GLY C 81 " --> pdb=" O PHE C 72 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 105 through 107 Processing sheet with id= C, first strand: chain 'C' and resid 245 through 249 removed outlier: 3.519A pdb=" N LEU C 215 " --> pdb=" O HIS C 278 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N SER C 335 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU C 281 " --> pdb=" O SER C 335 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR C 337 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N TYR C 283 " --> pdb=" O THR C 337 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU C 339 " --> pdb=" O TYR C 283 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 30 through 36 removed outlier: 6.767A pdb=" N THR C 41 " --> pdb=" O HIS C 33 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 39 " --> pdb=" O ILE C 35 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 30 through 36 removed outlier: 6.721A pdb=" N THR A 41 " --> pdb=" O HIS A 33 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ILE A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE A 39 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN A 73 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE A 83 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL A 71 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 57 through 59 Processing sheet with id= G, first strand: chain 'A' and resid 105 through 107 Processing sheet with id= H, first strand: chain 'A' and resid 116 through 118 removed outlier: 6.464A pdb=" N ILE A 246 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TYR A 218 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ALA A 249 " --> pdb=" O TYR A 218 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N SER A 220 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL A 282 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE A 221 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ASP A 284 " --> pdb=" O ILE A 221 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 57 through 59 removed outlier: 3.950A pdb=" N GLY B 30 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA B 99 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS B 28 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR B 41 " --> pdb=" O HIS B 33 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 80 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE B 83 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL B 71 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.499A pdb=" N ILE B 246 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 21 through 26 removed outlier: 3.509A pdb=" N TYR F 21 " --> pdb=" O THR F 33 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP F 31 " --> pdb=" O GLN F 23 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE F 25 " --> pdb=" O VAL F 29 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL F 29 " --> pdb=" O ILE F 25 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN F 62 " --> pdb=" O ARG F 70 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE F 72 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ILE F 60 " --> pdb=" O ILE F 72 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 163 through 166 removed outlier: 6.689A pdb=" N ALA F 341 " --> pdb=" O GLY F 164 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N PHE F 166 " --> pdb=" O ALA F 341 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR F 343 " --> pdb=" O PHE F 166 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'F' and resid 226 through 230 removed outlier: 8.105A pdb=" N VAL F 193 " --> pdb=" O ASP F 260 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU F 262 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ALA F 195 " --> pdb=" O LEU F 262 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE F 264 " --> pdb=" O ALA F 195 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL F 197 " --> pdb=" O PHE F 264 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASP F 266 " --> pdb=" O VAL F 197 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER F 313 " --> pdb=" O VAL F 261 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU F 263 " --> pdb=" O SER F 313 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR F 315 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL F 265 " --> pdb=" O THR F 315 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL F 317 " --> pdb=" O VAL F 265 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 85 through 87 removed outlier: 6.829A pdb=" N ASP D 31 " --> pdb=" O GLN D 23 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ILE D 25 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL D 29 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE D 72 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE D 60 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 56 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 94 through 96 Processing sheet with id= P, first strand: chain 'D' and resid 316 through 319 removed outlier: 6.508A pdb=" N ALA D 341 " --> pdb=" O GLY D 164 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N PHE D 166 " --> pdb=" O ALA D 341 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR D 343 " --> pdb=" O PHE D 166 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 262 through 265 Processing sheet with id= R, first strand: chain 'E' and resid 19 through 21 Processing sheet with id= S, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.589A pdb=" N GLN E 62 " --> pdb=" O ARG E 70 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE E 72 " --> pdb=" O ILE E 60 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ILE E 60 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 56 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 94 through 96 Processing sheet with id= U, first strand: chain 'E' and resid 342 through 344 removed outlier: 8.352A pdb=" N THR E 343 " --> pdb=" O LYS E 162 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLY E 164 " --> pdb=" O THR E 343 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ILE E 163 " --> pdb=" O ILE E 314 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER E 316 " --> pdb=" O ILE E 163 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N LEU E 165 " --> pdb=" O SER E 316 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLN E 318 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL E 261 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL E 317 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU E 263 " --> pdb=" O VAL E 317 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA E 319 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL E 265 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'M' and resid 140 through 146 removed outlier: 5.694A pdb=" N LYS M 176 " --> pdb=" O THR M 141 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ALA M 143 " --> pdb=" O LYS M 176 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL M 178 " --> pdb=" O ALA M 143 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL M 145 " --> pdb=" O VAL M 178 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLU M 180 " --> pdb=" O VAL M 145 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'M' and resid 190 through 194 Processing sheet with id= X, first strand: chain 'G' and resid 74 through 77 removed outlier: 6.322A pdb=" N SER G 169 " --> pdb=" O HIS G 165 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 106 through 109 removed outlier: 7.701A pdb=" N SER G 108 " --> pdb=" O ARG G 126 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR G 128 " --> pdb=" O SER G 108 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 85 through 88 removed outlier: 7.200A pdb=" N LEU H 51 " --> pdb=" O LYS H 60 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LYS H 60 " --> pdb=" O LEU H 51 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'H' and resid 75 through 78 removed outlier: 4.231A pdb=" N ARG H 70 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE H 93 " --> pdb=" O ARG H 70 " (cutoff:3.500A) 1505 hydrogen bonds defined for protein. 3867 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: 28.82 Time building geometry restraints manager: 51.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 39771 1.02 - 1.22: 66 1.22 - 1.42: 16072 1.42 - 1.62: 23546 1.62 - 1.82: 402 Bond restraints: 79857 Sorted by residual: bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.18e+01 bond pdb=" C4 ATP E 601 " pdb=" C5 ATP E 601 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.46e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.45e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.38e+01 bond pdb=" C5 ATP C 601 " pdb=" C6 ATP C 601 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.27e+01 ... (remaining 79852 not shown) Histogram of bond angle deviations from ideal: 97.72 - 105.44: 888 105.44 - 113.15: 96396 113.15 - 120.87: 29849 120.87 - 128.59: 17389 128.59 - 136.30: 268 Bond angle restraints: 144790 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 115.96 23.91 1.00e+00 1.00e+00 5.72e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 117.31 22.56 1.00e+00 1.00e+00 5.09e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 117.57 22.30 1.00e+00 1.00e+00 4.97e+02 angle pdb=" PB ATP E 601 " pdb=" O3B ATP E 601 " pdb=" PG ATP E 601 " ideal model delta sigma weight residual 139.87 118.09 21.78 1.00e+00 1.00e+00 4.74e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 118.93 17.90 1.00e+00 1.00e+00 3.20e+02 ... (remaining 144785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 34367 17.78 - 35.56: 2394 35.56 - 53.35: 585 53.35 - 71.13: 166 71.13 - 88.91: 8 Dihedral angle restraints: 37520 sinusoidal: 20701 harmonic: 16819 Sorted by residual: dihedral pdb=" CA ILE A 117 " pdb=" C ILE A 117 " pdb=" N ASN A 118 " pdb=" CA ASN A 118 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA ALA D 287 " pdb=" C ALA D 287 " pdb=" N ALA D 288 " pdb=" CA ALA D 288 " ideal model delta harmonic sigma weight residual 180.00 -156.76 -23.24 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA ASP B 284 " pdb=" C ASP B 284 " pdb=" N ASP B 285 " pdb=" CA ASP B 285 " ideal model delta harmonic sigma weight residual 180.00 -160.12 -19.88 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 37517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 6030 0.098 - 0.197: 275 0.197 - 0.295: 2 0.295 - 0.394: 0 0.394 - 0.492: 1 Chirality restraints: 6308 Sorted by residual: chirality pdb=" CG LEU F 82 " pdb=" CB LEU F 82 " pdb=" CD1 LEU F 82 " pdb=" CD2 LEU F 82 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 6.05e+00 chirality pdb=" CA ARG F 83 " pdb=" N ARG F 83 " pdb=" C ARG F 83 " pdb=" CB ARG F 83 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA ILE M 146 " pdb=" N ILE M 146 " pdb=" C ILE M 146 " pdb=" CB ILE M 146 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 6305 not shown) Planarity restraints: 11833 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 385 " -0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C VAL F 385 " 0.072 2.00e-02 2.50e+03 pdb=" O VAL F 385 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU F 386 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 318 " -0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C SER A 318 " 0.069 2.00e-02 2.50e+03 pdb=" O SER A 318 " -0.026 2.00e-02 2.50e+03 pdb=" N ARG A 319 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 315 " -0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C TYR A 315 " 0.068 2.00e-02 2.50e+03 pdb=" O TYR A 315 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU A 316 " -0.023 2.00e-02 2.50e+03 ... (remaining 11830 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.07: 865 2.07 - 2.70: 134124 2.70 - 3.33: 232307 3.33 - 3.97: 294729 3.97 - 4.60: 477605 Nonbonded interactions: 1139630 Sorted by model distance: nonbonded pdb=" PB ATP A 601 " pdb="MG MG A 602 " model vdw 1.432 2.450 nonbonded pdb=" O2B ATP A 601 " pdb="MG MG A 602 " model vdw 1.443 2.050 nonbonded pdb="HG21 THR F 174 " pdb="MG MG F 602 " model vdw 1.496 1.870 nonbonded pdb=" O ASP F 450 " pdb=" HG SER F 453 " model vdw 1.636 1.850 nonbonded pdb=" O ALA T 54 " pdb=" H SER T 58 " model vdw 1.652 1.850 ... (remaining 1139625 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and ((resid 26 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name H \ Z1 or name HZ2 or name HZ3)) or resid 27 through 562 or resid 601 through 602)) selection = (chain 'C' and ((resid 26 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name H \ Z1 or name HZ2 or name HZ3)) or resid 27 through 562 or resid 601 through 602)) } ncs_group { reference = (chain 'D' and (resid 15 through 173 or (resid 174 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 175 through 501)) selection = (chain 'E' and resid 15 through 501) selection = (chain 'F' and (resid 15 through 173 or (resid 174 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 175 through 501)) } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.990 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: 0.890 Extract box with map and model: 18.520 Check model and map are aligned: 0.850 Set scattering table: 0.570 Process input model: 195.390 Find NCS groups from input model: 2.820 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 226.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 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 : 0.007 0.086 40022 Z= 0.474 Angle : 0.811 23.911 54248 Z= 0.493 Chirality : 0.046 0.492 6308 Planarity : 0.006 0.070 6928 Dihedral : 11.704 88.912 14811 Min Nonbonded Distance : 1.432 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.03 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % 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: -3.76 (0.10), residues: 5084 helix: -2.58 (0.07), residues: 2437 sheet: -3.22 (0.17), residues: 572 loop : -1.89 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 113 HIS 0.009 0.002 HIS E 377 PHE 0.023 0.002 PHE E 336 TYR 0.025 0.002 TYR F 391 ARG 0.017 0.001 ARG J 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 904 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 904 time to evaluate : 4.624 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: 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: 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: 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: C 297 SER cc_start: 0.9523 (m) cc_final: 0.9255 (p) REVERT: C 430 MET cc_start: 0.7601 (mmm) cc_final: 0.7303 (tpt) REVERT: A 263 TYR cc_start: 0.8949 (m-10) cc_final: 0.8712 (m-80) REVERT: A 281 LEU cc_start: 0.9109 (tp) cc_final: 0.8820 (tp) REVERT: B 64 THR cc_start: 0.8164 (p) cc_final: 0.7930 (t) REVERT: B 350 THR cc_start: 0.8255 (p) cc_final: 0.8035 (m) REVERT: F 145 VAL cc_start: 0.8736 (t) cc_final: 0.8507 (p) REVERT: F 261 VAL cc_start: 0.8867 (t) cc_final: 0.8666 (m) REVERT: F 315 THR cc_start: 0.8354 (m) cc_final: 0.8082 (p) REVERT: F 325 ASP cc_start: 0.8082 (m-30) cc_final: 0.6963 (t70) REVERT: E 179 GLU cc_start: 0.6453 (tp30) cc_final: 0.6114 (tp30) REVERT: E 491 ARG cc_start: 0.8384 (mtt180) cc_final: 0.8168 (mtm180) REVERT: L 153 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8126 (mm-40) REVERT: K 53 ASP cc_start: 0.7435 (t70) cc_final: 0.6770 (t0) REVERT: K 141 ILE cc_start: 0.8714 (mm) cc_final: 0.8386 (mm) REVERT: M 48 SER cc_start: 0.7875 (m) cc_final: 0.7477 (t) REVERT: G 300 LYS cc_start: 0.7655 (tttt) cc_final: 0.7375 (mmtm) REVERT: H 172 GLU cc_start: 0.9047 (tt0) cc_final: 0.8562 (tp30) REVERT: O 41 MET cc_start: 0.8063 (mtp) cc_final: 0.7759 (mtp) REVERT: O 95 ILE cc_start: 0.8999 (mt) cc_final: 0.8654 (tt) REVERT: P 56 CYS cc_start: 0.8919 (t) cc_final: 0.8613 (p) REVERT: Q 82 PHE cc_start: 0.8190 (t80) cc_final: 0.7714 (t80) REVERT: R 86 GLU cc_start: 0.8821 (tp30) cc_final: 0.8435 (tp30) REVERT: T 56 CYS cc_start: 0.8644 (t) cc_final: 0.8421 (t) REVERT: U 37 ILE cc_start: 0.8916 (mt) cc_final: 0.8598 (tt) REVERT: U 51 ILE cc_start: 0.9352 (mt) cc_final: 0.9143 (tp) REVERT: U 56 CYS cc_start: 0.9038 (t) cc_final: 0.8780 (t) REVERT: U 61 MET cc_start: 0.9300 (mtt) cc_final: 0.8986 (mtp) REVERT: U 92 THR cc_start: 0.9016 (m) cc_final: 0.8811 (p) REVERT: W 29 VAL cc_start: 0.9462 (m) cc_final: 0.9091 (p) REVERT: W 55 MET cc_start: 0.8863 (ttm) cc_final: 0.8312 (ttm) REVERT: X 55 MET cc_start: 0.8614 (ttm) cc_final: 0.8042 (tpp) REVERT: X 90 LEU cc_start: 0.9014 (tt) cc_final: 0.8803 (tt) outliers start: 0 outliers final: 0 residues processed: 904 average time/residue: 1.1437 time to fit residues: 1651.9438 Evaluate side-chains 533 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 533 time to evaluate : 4.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 428 optimal weight: 8.9990 chunk 384 optimal weight: 6.9990 chunk 213 optimal weight: 0.6980 chunk 131 optimal weight: 0.1980 chunk 259 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 397 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 241 optimal weight: 2.9990 chunk 295 optimal weight: 4.9990 chunk 460 optimal weight: 10.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN C 395 ASN ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 ASN B 441 ASN B 469 GLN B 550 GLN F 188 HIS D 62 GLN D 115 GLN D 128 HIS D 231 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 ASN ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 40022 Z= 0.230 Angle : 0.554 6.448 54248 Z= 0.294 Chirality : 0.040 0.161 6308 Planarity : 0.004 0.056 6928 Dihedral : 6.126 85.538 5686 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.42 % Favored : 96.56 % Rotamer: Outliers : 1.17 % Allowed : 8.72 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % 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: -2.24 (0.11), residues: 5084 helix: -1.08 (0.09), residues: 2502 sheet: -2.76 (0.18), residues: 585 loop : -1.37 (0.14), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 224 HIS 0.008 0.001 HIS A 513 PHE 0.028 0.001 PHE S 82 TYR 0.016 0.001 TYR G 267 ARG 0.009 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 623 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 574 time to evaluate : 4.786 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: 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: 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: C 281 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.8822 (mp) REVERT: C 297 SER cc_start: 0.9511 (m) cc_final: 0.9236 (p) REVERT: A 281 LEU cc_start: 0.9154 (tp) cc_final: 0.8815 (tp) REVERT: A 449 MET cc_start: 0.8074 (ttp) cc_final: 0.7795 (ttp) REVERT: A 497 MET cc_start: 0.8793 (mmm) cc_final: 0.8509 (mmt) REVERT: B 64 THR cc_start: 0.8220 (p) cc_final: 0.7959 (t) REVERT: F 74 MET cc_start: 0.7251 (mtm) cc_final: 0.7048 (mtm) REVERT: F 266 ASP cc_start: 0.7698 (t0) cc_final: 0.7482 (m-30) REVERT: F 368 MET cc_start: 0.8100 (tpp) cc_final: 0.7890 (ttm) REVERT: D 410 ASP cc_start: 0.8221 (m-30) cc_final: 0.7921 (m-30) REVERT: E 179 GLU cc_start: 0.6286 (tp30) cc_final: 0.5992 (tp30) REVERT: K 102 MET cc_start: 0.7785 (tpt) cc_final: 0.7494 (tpt) REVERT: G 300 LYS cc_start: 0.7654 (tttt) cc_final: 0.7433 (mmtm) REVERT: H 172 GLU cc_start: 0.9031 (tt0) cc_final: 0.8591 (tp30) REVERT: O 61 MET cc_start: 0.8515 (mtt) cc_final: 0.8296 (mtp) REVERT: O 95 ILE cc_start: 0.8988 (mt) cc_final: 0.8608 (tt) REVERT: P 56 CYS cc_start: 0.8920 (t) cc_final: 0.8651 (p) REVERT: P 61 MET cc_start: 0.9148 (mtt) cc_final: 0.8303 (mtp) REVERT: P 73 LYS cc_start: 0.9021 (mtpt) cc_final: 0.8289 (tmtt) REVERT: Q 82 PHE cc_start: 0.8097 (t80) cc_final: 0.7663 (t80) REVERT: R 86 GLU cc_start: 0.8839 (tp30) cc_final: 0.8483 (tp30) REVERT: T 56 CYS cc_start: 0.8844 (t) cc_final: 0.8585 (t) REVERT: U 51 ILE cc_start: 0.9244 (mt) cc_final: 0.8981 (tp) REVERT: U 61 MET cc_start: 0.8980 (mtt) cc_final: 0.8633 (mtp) REVERT: V 82 PHE cc_start: 0.8913 (t80) cc_final: 0.8345 (t80) REVERT: W 35 ASN cc_start: 0.8958 (p0) cc_final: 0.8683 (p0) outliers start: 49 outliers final: 33 residues processed: 605 average time/residue: 1.0333 time to fit residues: 1023.2541 Evaluate side-chains 526 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 492 time to evaluate : 5.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 377 HIS Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain K residue 103 ASP Chi-restraints excluded: chain K residue 130 GLN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain V residue 35 ASN Chi-restraints excluded: chain W residue 69 ASN Chi-restraints excluded: chain X residue 56 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 255 optimal weight: 4.9990 chunk 142 optimal weight: 0.1980 chunk 383 optimal weight: 6.9990 chunk 313 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 461 optimal weight: 0.0970 chunk 498 optimal weight: 9.9990 chunk 410 optimal weight: 7.9990 chunk 457 optimal weight: 9.9990 chunk 157 optimal weight: 2.9990 chunk 370 optimal weight: 9.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN B 534 ASN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 40022 Z= 0.251 Angle : 0.534 6.623 54248 Z= 0.281 Chirality : 0.040 0.157 6308 Planarity : 0.004 0.060 6928 Dihedral : 5.891 77.631 5686 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.07 % Favored : 95.91 % Rotamer: Outliers : 1.32 % Allowed : 10.26 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % 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: -1.62 (0.12), residues: 5084 helix: -0.47 (0.10), residues: 2506 sheet: -2.57 (0.19), residues: 586 loop : -1.17 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 10 HIS 0.005 0.001 HIS E 377 PHE 0.024 0.001 PHE P 82 TYR 0.014 0.001 TYR I 13 ARG 0.005 0.000 ARG G 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 563 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 508 time to evaluate : 4.798 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: 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: 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: C 281 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.8893 (mp) REVERT: A 281 LEU cc_start: 0.9185 (tp) cc_final: 0.8829 (tp) REVERT: A 497 MET cc_start: 0.8819 (mmm) cc_final: 0.8526 (mmt) REVERT: F 206 ASP cc_start: 0.8198 (m-30) cc_final: 0.7961 (t0) REVERT: F 266 ASP cc_start: 0.7902 (t0) cc_final: 0.7631 (m-30) REVERT: F 368 MET cc_start: 0.8115 (tpp) cc_final: 0.7883 (ttp) REVERT: D 410 ASP cc_start: 0.8235 (m-30) cc_final: 0.7830 (m-30) REVERT: E 109 MET cc_start: 0.8110 (mpp) cc_final: 0.7478 (mpp) REVERT: E 179 GLU cc_start: 0.6699 (tp30) cc_final: 0.6286 (tp30) REVERT: K 102 MET cc_start: 0.8044 (tpt) cc_final: 0.7731 (tpt) REVERT: K 144 MET cc_start: 0.9211 (mtt) cc_final: 0.8609 (mtt) REVERT: G 300 LYS cc_start: 0.7699 (tttt) cc_final: 0.7448 (mmtm) REVERT: H 172 GLU cc_start: 0.9050 (tt0) cc_final: 0.8572 (tp30) REVERT: O 61 MET cc_start: 0.8636 (mtt) cc_final: 0.8396 (mtp) REVERT: O 95 ILE cc_start: 0.8976 (mt) cc_final: 0.8568 (tt) REVERT: P 56 CYS cc_start: 0.8901 (t) cc_final: 0.8620 (p) REVERT: P 61 MET cc_start: 0.9142 (mtt) cc_final: 0.8297 (mtp) REVERT: P 73 LYS cc_start: 0.9127 (mtpt) cc_final: 0.8384 (tmtt) REVERT: Q 82 PHE cc_start: 0.8032 (t80) cc_final: 0.7752 (t80) REVERT: R 86 GLU cc_start: 0.8896 (tp30) cc_final: 0.8539 (tp30) REVERT: T 56 CYS cc_start: 0.8917 (t) cc_final: 0.8687 (t) REVERT: U 61 MET cc_start: 0.8988 (mtt) cc_final: 0.8558 (mtp) REVERT: V 82 PHE cc_start: 0.8804 (t80) cc_final: 0.8224 (t80) REVERT: W 35 ASN cc_start: 0.8924 (p0) cc_final: 0.8628 (p0) REVERT: W 55 MET cc_start: 0.8742 (ttt) cc_final: 0.8152 (ttm) outliers start: 55 outliers final: 43 residues processed: 547 average time/residue: 1.0423 time to fit residues: 938.7626 Evaluate side-chains 517 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 473 time to evaluate : 4.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 512 ASN Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 158 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 103 ASP Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 130 GLN Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain P residue 90 LEU Chi-restraints excluded: chain V residue 35 ASN Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain X residue 56 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 455 optimal weight: 10.0000 chunk 346 optimal weight: 4.9990 chunk 239 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 220 optimal weight: 1.9990 chunk 309 optimal weight: 1.9990 chunk 462 optimal weight: 10.0000 chunk 490 optimal weight: 0.5980 chunk 241 optimal weight: 3.9990 chunk 438 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 ASN B 356 ASN B 512 ASN D 275 ASN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 40022 Z= 0.209 Angle : 0.506 8.047 54248 Z= 0.264 Chirality : 0.039 0.146 6308 Planarity : 0.004 0.069 6928 Dihedral : 5.695 75.887 5686 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.76 % Favored : 96.22 % Rotamer: Outliers : 1.25 % Allowed : 10.91 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % 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: -1.22 (0.12), residues: 5084 helix: -0.12 (0.10), residues: 2517 sheet: -2.39 (0.20), residues: 584 loop : -1.02 (0.15), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP G 10 HIS 0.015 0.001 HIS B 513 PHE 0.031 0.001 PHE P 82 TYR 0.015 0.001 TYR I 13 ARG 0.005 0.000 ARG K 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 555 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 503 time to evaluate : 4.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 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: 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: C 281 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.8908 (mp) REVERT: A 281 LEU cc_start: 0.9182 (tp) cc_final: 0.8859 (tp) REVERT: A 497 MET cc_start: 0.8838 (mmm) cc_final: 0.8548 (mmt) REVERT: F 266 ASP cc_start: 0.7948 (t0) cc_final: 0.7628 (m-30) REVERT: F 368 MET cc_start: 0.8126 (tpp) cc_final: 0.7879 (ttp) REVERT: F 483 MET cc_start: 0.8743 (mtp) cc_final: 0.8528 (mtp) REVERT: D 410 ASP cc_start: 0.8201 (m-30) cc_final: 0.7817 (m-30) REVERT: E 74 MET cc_start: 0.8499 (mmt) cc_final: 0.8027 (mmt) REVERT: E 109 MET cc_start: 0.8082 (mpp) cc_final: 0.7462 (mpp) REVERT: E 179 GLU cc_start: 0.6886 (tp30) cc_final: 0.6381 (tp30) REVERT: K 102 MET cc_start: 0.8145 (tpt) cc_final: 0.7833 (tpt) REVERT: G 300 LYS cc_start: 0.7683 (tttt) cc_final: 0.7401 (mmtm) REVERT: H 172 GLU cc_start: 0.9069 (tt0) cc_final: 0.8548 (tp30) REVERT: O 61 MET cc_start: 0.8705 (mtt) cc_final: 0.8439 (mtp) REVERT: O 95 ILE cc_start: 0.8949 (mt) cc_final: 0.8561 (tt) REVERT: P 56 CYS cc_start: 0.8925 (t) cc_final: 0.8642 (p) REVERT: P 61 MET cc_start: 0.9120 (mtt) cc_final: 0.8255 (mtp) REVERT: P 73 LYS cc_start: 0.9132 (mtpt) cc_final: 0.8381 (tmtt) REVERT: Q 82 PHE cc_start: 0.8107 (t80) cc_final: 0.7895 (t80) REVERT: R 55 MET cc_start: 0.8899 (ttp) cc_final: 0.8623 (ttp) REVERT: R 86 GLU cc_start: 0.8909 (tp30) cc_final: 0.8534 (tp30) REVERT: U 61 MET cc_start: 0.8993 (mtt) cc_final: 0.8609 (mtt) REVERT: V 51 ILE cc_start: 0.9211 (tt) cc_final: 0.8721 (tt) REVERT: W 35 ASN cc_start: 0.8958 (p0) cc_final: 0.8684 (p0) REVERT: W 55 MET cc_start: 0.8712 (ttt) cc_final: 0.8143 (ttm) outliers start: 52 outliers final: 43 residues processed: 538 average time/residue: 0.9817 time to fit residues: 868.9652 Evaluate side-chains 518 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 474 time to evaluate : 4.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 103 ASP Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 130 GLN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 56 CYS Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain S residue 98 LEU Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain W residue 69 ASN Chi-restraints excluded: chain W residue 74 LEU Chi-restraints excluded: chain X residue 56 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 408 optimal weight: 10.0000 chunk 278 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 364 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 418 optimal weight: 8.9990 chunk 338 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 439 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 GLN B 501 ASN B 512 ASN ** B 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 395 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 40022 Z= 0.379 Angle : 0.599 7.285 54248 Z= 0.318 Chirality : 0.041 0.178 6308 Planarity : 0.004 0.071 6928 Dihedral : 6.113 86.214 5686 Min Nonbonded Distance : 1.630 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.82 % Favored : 94.14 % Rotamer: Outliers : 1.94 % Allowed : 11.79 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.12), residues: 5084 helix: -0.14 (0.10), residues: 2508 sheet: -2.46 (0.20), residues: 590 loop : -1.08 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 224 HIS 0.008 0.002 HIS B 278 PHE 0.019 0.002 PHE F 166 TYR 0.017 0.002 TYR A 165 ARG 0.006 0.001 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 562 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 481 time to evaluate : 4.756 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: 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: 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: C 281 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.8934 (mp) REVERT: A 169 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.8074 (t0) REVERT: A 281 LEU cc_start: 0.9281 (tp) cc_final: 0.8913 (tp) REVERT: F 151 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7669 (mt) REVERT: F 266 ASP cc_start: 0.8237 (t0) cc_final: 0.7988 (t0) REVERT: F 382 MET cc_start: 0.8166 (mmp) cc_final: 0.7594 (mmp) REVERT: F 395 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8235 (mt0) REVERT: F 483 MET cc_start: 0.8752 (mtp) cc_final: 0.8509 (mtp) REVERT: E 109 MET cc_start: 0.8215 (mpp) cc_final: 0.7966 (mtp) REVERT: K 102 MET cc_start: 0.8298 (tpt) cc_final: 0.7954 (tpt) REVERT: G 300 LYS cc_start: 0.7769 (tttt) cc_final: 0.7404 (mmtm) REVERT: H 172 GLU cc_start: 0.9119 (tt0) cc_final: 0.8635 (tp30) REVERT: O 61 MET cc_start: 0.8809 (mtt) cc_final: 0.8496 (mtp) REVERT: O 95 ILE cc_start: 0.8959 (mt) cc_final: 0.8577 (tt) REVERT: P 56 CYS cc_start: 0.8988 (t) cc_final: 0.8717 (p) REVERT: P 61 MET cc_start: 0.9149 (mtt) cc_final: 0.8307 (mtp) REVERT: P 73 LYS cc_start: 0.9024 (mtpt) cc_final: 0.8305 (tmtt) REVERT: R 55 MET cc_start: 0.9022 (ttp) cc_final: 0.8544 (tmm) REVERT: R 73 LYS cc_start: 0.9040 (mtmm) cc_final: 0.8817 (mmmt) REVERT: R 86 GLU cc_start: 0.8935 (tp30) cc_final: 0.8561 (tp30) REVERT: U 61 MET cc_start: 0.9019 (mtt) cc_final: 0.8614 (mtt) REVERT: V 55 MET cc_start: 0.8861 (ttm) cc_final: 0.8571 (ttm) REVERT: W 35 ASN cc_start: 0.8908 (p0) cc_final: 0.8579 (p0) REVERT: W 55 MET cc_start: 0.8778 (ttt) cc_final: 0.8205 (ttm) outliers start: 81 outliers final: 64 residues processed: 535 average time/residue: 1.0261 time to fit residues: 909.3244 Evaluate side-chains 521 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 453 time to evaluate : 4.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain F residue 395 GLN Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 158 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 103 ASP Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 130 GLN Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 56 CYS Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain T residue 56 CYS Chi-restraints excluded: chain T residue 86 GLU Chi-restraints excluded: chain U residue 41 MET Chi-restraints excluded: chain V residue 35 ASN Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain X residue 56 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 164 optimal weight: 0.9980 chunk 441 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 490 optimal weight: 1.9990 chunk 407 optimal weight: 10.0000 chunk 227 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 257 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 ASN ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 395 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 40022 Z= 0.280 Angle : 0.533 7.345 54248 Z= 0.279 Chirality : 0.040 0.160 6308 Planarity : 0.004 0.054 6928 Dihedral : 5.961 89.660 5686 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.46 % Favored : 95.52 % Rotamer: Outliers : 1.70 % Allowed : 12.75 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.12), residues: 5084 helix: 0.01 (0.10), residues: 2511 sheet: -2.39 (0.20), residues: 584 loop : -0.92 (0.14), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 224 HIS 0.005 0.001 HIS G 227 PHE 0.026 0.001 PHE F 166 TYR 0.015 0.001 TYR J 52 ARG 0.004 0.000 ARG C 277 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 540 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 469 time to evaluate : 4.777 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: 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: 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: C 281 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.8941 (mp) REVERT: C 439 LEU cc_start: 0.8738 (mt) cc_final: 0.8334 (mp) REVERT: A 281 LEU cc_start: 0.9253 (tp) cc_final: 0.8900 (tp) REVERT: F 483 MET cc_start: 0.8748 (mtp) cc_final: 0.8501 (mtp) REVERT: E 109 MET cc_start: 0.8039 (mpp) cc_final: 0.7835 (mtp) REVERT: E 151 ILE cc_start: 0.8967 (mp) cc_final: 0.8700 (mt) REVERT: K 102 MET cc_start: 0.8323 (tpt) cc_final: 0.7922 (tpt) REVERT: M 216 LYS cc_start: 0.6958 (mtmt) cc_final: 0.6448 (mmmt) REVERT: M 258 LYS cc_start: 0.5710 (mmtt) cc_final: 0.5416 (mptt) REVERT: G 115 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8228 (p0) REVERT: G 300 LYS cc_start: 0.7760 (tttt) cc_final: 0.7398 (mmtm) REVERT: H 172 GLU cc_start: 0.9102 (tt0) cc_final: 0.8600 (tp30) REVERT: O 61 MET cc_start: 0.8829 (mtt) cc_final: 0.8550 (mtp) REVERT: O 95 ILE cc_start: 0.8950 (mt) cc_final: 0.8583 (tt) REVERT: P 56 CYS cc_start: 0.8968 (t) cc_final: 0.8706 (p) REVERT: P 61 MET cc_start: 0.9175 (mtt) cc_final: 0.8486 (mtp) REVERT: P 73 LYS cc_start: 0.9035 (mtpt) cc_final: 0.8319 (tmtt) REVERT: R 55 MET cc_start: 0.8949 (ttp) cc_final: 0.8513 (tmm) REVERT: R 86 GLU cc_start: 0.8933 (tp30) cc_final: 0.8569 (tp30) REVERT: U 61 MET cc_start: 0.8994 (mtt) cc_final: 0.8593 (mtt) REVERT: V 55 MET cc_start: 0.8871 (ttm) cc_final: 0.8535 (ttm) REVERT: W 35 ASN cc_start: 0.8867 (p0) cc_final: 0.8527 (p0) REVERT: W 55 MET cc_start: 0.8775 (ttt) cc_final: 0.8215 (ttm) outliers start: 71 outliers final: 60 residues processed: 516 average time/residue: 0.9792 time to fit residues: 831.0627 Evaluate side-chains 525 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 463 time to evaluate : 4.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 158 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 103 ASP Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 130 GLN Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain Q residue 56 CYS Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain T residue 56 CYS Chi-restraints excluded: chain U residue 41 MET Chi-restraints excluded: chain V residue 35 ASN Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 69 ASN Chi-restraints excluded: chain X residue 56 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 472 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 279 optimal weight: 0.7980 chunk 358 optimal weight: 5.9990 chunk 277 optimal weight: 1.9990 chunk 412 optimal weight: 5.9990 chunk 273 optimal weight: 2.9990 chunk 488 optimal weight: 9.9990 chunk 305 optimal weight: 3.9990 chunk 297 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 501 ASN ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 ASN ** M 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 40022 Z= 0.300 Angle : 0.539 7.299 54248 Z= 0.284 Chirality : 0.040 0.164 6308 Planarity : 0.004 0.054 6928 Dihedral : 5.910 88.553 5686 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.66 % Favored : 94.32 % Rotamer: Outliers : 1.89 % Allowed : 12.73 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % 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: -1.02 (0.12), residues: 5084 helix: 0.06 (0.10), residues: 2519 sheet: -2.40 (0.20), residues: 591 loop : -0.89 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 224 HIS 0.005 0.001 HIS G 227 PHE 0.020 0.001 PHE F 166 TYR 0.014 0.001 TYR J 52 ARG 0.003 0.000 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 546 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 467 time to evaluate : 4.740 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: 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: 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: C 281 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.8939 (mp) REVERT: A 281 LEU cc_start: 0.9263 (tp) cc_final: 0.8912 (tp) REVERT: F 151 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7692 (mt) REVERT: D 450 ASP cc_start: 0.7709 (m-30) cc_final: 0.7403 (m-30) REVERT: K 102 MET cc_start: 0.8344 (tpt) cc_final: 0.7951 (tpt) REVERT: M 216 LYS cc_start: 0.6987 (mtmt) cc_final: 0.6560 (mmmt) REVERT: G 300 LYS cc_start: 0.7818 (tttt) cc_final: 0.7421 (mmtm) REVERT: H 102 LYS cc_start: 0.8420 (ptpp) cc_final: 0.8008 (pttm) REVERT: H 172 GLU cc_start: 0.9081 (tt0) cc_final: 0.8618 (tp30) REVERT: O 41 MET cc_start: 0.8142 (mtp) cc_final: 0.7898 (mtm) REVERT: O 61 MET cc_start: 0.8854 (mtt) cc_final: 0.8561 (mtp) REVERT: O 95 ILE cc_start: 0.8958 (mt) cc_final: 0.8598 (tt) REVERT: P 61 MET cc_start: 0.9182 (mtt) cc_final: 0.8309 (mtp) REVERT: P 73 LYS cc_start: 0.9041 (mtpt) cc_final: 0.8334 (tmtt) REVERT: R 55 MET cc_start: 0.8955 (ttp) cc_final: 0.8528 (tmm) REVERT: R 86 GLU cc_start: 0.8932 (tp30) cc_final: 0.8580 (tp30) REVERT: U 61 MET cc_start: 0.9015 (mtt) cc_final: 0.8624 (mtp) REVERT: V 55 MET cc_start: 0.8898 (ttm) cc_final: 0.8650 (ttm) REVERT: W 35 ASN cc_start: 0.8871 (p0) cc_final: 0.8507 (p0) REVERT: W 55 MET cc_start: 0.8702 (ttt) cc_final: 0.8173 (ttm) outliers start: 79 outliers final: 69 residues processed: 519 average time/residue: 0.9966 time to fit residues: 856.2863 Evaluate side-chains 524 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 453 time to evaluate : 4.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 73 CYS Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 103 ASP Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 130 GLN Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain M residue 226 SER Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain Q residue 56 CYS Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain T residue 56 CYS Chi-restraints excluded: chain T residue 86 GLU Chi-restraints excluded: chain U residue 41 MET Chi-restraints excluded: chain V residue 35 ASN Chi-restraints excluded: chain V residue 41 MET Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 69 ASN Chi-restraints excluded: chain W residue 94 LEU Chi-restraints excluded: chain X residue 56 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 302 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 291 optimal weight: 0.3980 chunk 147 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 310 optimal weight: 1.9990 chunk 332 optimal weight: 4.9990 chunk 241 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 384 optimal weight: 0.9980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN B 356 ASN ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40022 Z= 0.222 Angle : 0.506 7.175 54248 Z= 0.263 Chirality : 0.039 0.153 6308 Planarity : 0.004 0.045 6928 Dihedral : 5.687 89.890 5686 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.97 % Favored : 96.01 % Rotamer: Outliers : 1.70 % Allowed : 13.30 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % 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: -0.77 (0.12), residues: 5084 helix: 0.26 (0.11), residues: 2510 sheet: -2.28 (0.20), residues: 591 loop : -0.77 (0.15), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 224 HIS 0.005 0.001 HIS G 227 PHE 0.014 0.001 PHE F 166 TYR 0.017 0.001 TYR E 468 ARG 0.003 0.000 ARG D 366 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 547 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 476 time to evaluate : 4.653 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: 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: 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: C 281 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.8946 (mp) REVERT: A 281 LEU cc_start: 0.9250 (tp) cc_final: 0.8916 (tp) REVERT: B 320 LEU cc_start: 0.9040 (tt) cc_final: 0.8835 (tt) REVERT: F 151 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7606 (mt) REVERT: D 363 CYS cc_start: 0.7999 (m) cc_final: 0.7791 (m) REVERT: K 102 MET cc_start: 0.8301 (tpt) cc_final: 0.7957 (tpt) REVERT: M 216 LYS cc_start: 0.7082 (mtmt) cc_final: 0.6646 (mmmt) REVERT: G 300 LYS cc_start: 0.7902 (tttt) cc_final: 0.7458 (mmtm) REVERT: H 102 LYS cc_start: 0.8458 (ptpp) cc_final: 0.8060 (pttm) REVERT: H 172 GLU cc_start: 0.9117 (tt0) cc_final: 0.8634 (tp30) REVERT: O 61 MET cc_start: 0.8810 (mtt) cc_final: 0.8529 (mtp) REVERT: O 95 ILE cc_start: 0.8967 (mt) cc_final: 0.8612 (tt) REVERT: P 41 MET cc_start: 0.6699 (tpt) cc_final: 0.6241 (tpp) REVERT: P 61 MET cc_start: 0.9170 (mtt) cc_final: 0.8440 (mtp) REVERT: P 73 LYS cc_start: 0.9045 (mtpt) cc_final: 0.8369 (tmtt) REVERT: R 55 MET cc_start: 0.8936 (ttp) cc_final: 0.8545 (tmm) REVERT: R 86 GLU cc_start: 0.8958 (tp30) cc_final: 0.8582 (tp30) REVERT: S 41 MET cc_start: 0.8838 (mtp) cc_final: 0.8624 (mmp) REVERT: U 61 MET cc_start: 0.9004 (mtt) cc_final: 0.8633 (mtp) REVERT: V 55 MET cc_start: 0.8876 (ttm) cc_final: 0.8620 (ttm) REVERT: W 35 ASN cc_start: 0.8819 (p0) cc_final: 0.8442 (p0) REVERT: W 55 MET cc_start: 0.8699 (ttt) cc_final: 0.8152 (ttm) outliers start: 71 outliers final: 61 residues processed: 521 average time/residue: 0.9978 time to fit residues: 866.1098 Evaluate side-chains 524 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 461 time to evaluate : 4.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain F residue 73 CYS Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 103 ASP Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 130 GLN Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain M residue 226 SER Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain Q residue 56 CYS Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain T residue 56 CYS Chi-restraints excluded: chain T residue 86 GLU Chi-restraints excluded: chain U residue 41 MET Chi-restraints excluded: chain V residue 35 ASN Chi-restraints excluded: chain V residue 41 MET Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 69 ASN Chi-restraints excluded: chain W residue 74 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 444 optimal weight: 10.0000 chunk 468 optimal weight: 20.0000 chunk 427 optimal weight: 8.9990 chunk 455 optimal weight: 9.9990 chunk 274 optimal weight: 0.9990 chunk 198 optimal weight: 5.9990 chunk 357 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 chunk 411 optimal weight: 7.9990 chunk 430 optimal weight: 10.0000 chunk 453 optimal weight: 10.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 HIS ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 40022 Z= 0.508 Angle : 0.656 7.879 54248 Z= 0.351 Chirality : 0.043 0.191 6308 Planarity : 0.005 0.069 6928 Dihedral : 6.334 87.358 5686 Min Nonbonded Distance : 1.595 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.28 % Favored : 92.68 % Rotamer: Outliers : 2.04 % Allowed : 13.47 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % 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: -1.37 (0.12), residues: 5084 helix: -0.21 (0.10), residues: 2548 sheet: -2.54 (0.20), residues: 591 loop : -1.12 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 224 HIS 0.010 0.002 HIS B 278 PHE 0.028 0.002 PHE F 166 TYR 0.023 0.002 TYR A 165 ARG 0.006 0.001 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 545 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 460 time to evaluate : 4.671 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: 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: 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: C 281 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.8919 (mp) REVERT: A 281 LEU cc_start: 0.9338 (tp) cc_final: 0.8976 (tp) REVERT: B 409 MET cc_start: 0.8202 (mmp) cc_final: 0.7996 (mmp) REVERT: F 151 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7736 (mt) REVERT: K 102 MET cc_start: 0.8441 (tpt) cc_final: 0.8144 (tpt) REVERT: M 216 LYS cc_start: 0.7085 (mtmt) cc_final: 0.6636 (mmmt) REVERT: G 300 LYS cc_start: 0.7965 (tttt) cc_final: 0.7491 (mmtm) REVERT: H 102 LYS cc_start: 0.8510 (ptpp) cc_final: 0.8101 (pttm) REVERT: H 172 GLU cc_start: 0.9164 (tt0) cc_final: 0.8723 (tp30) REVERT: O 41 MET cc_start: 0.8234 (mtp) cc_final: 0.7958 (mtm) REVERT: O 61 MET cc_start: 0.8869 (mtt) cc_final: 0.8593 (mtp) REVERT: O 95 ILE cc_start: 0.9036 (mt) cc_final: 0.8697 (tt) REVERT: P 61 MET cc_start: 0.9214 (mtt) cc_final: 0.8360 (mtp) REVERT: P 73 LYS cc_start: 0.9070 (mtpt) cc_final: 0.8398 (tmtt) REVERT: Q 82 PHE cc_start: 0.8369 (t80) cc_final: 0.8107 (t80) REVERT: Q 95 ILE cc_start: 0.9266 (mt) cc_final: 0.8956 (tp) REVERT: R 55 MET cc_start: 0.9019 (ttp) cc_final: 0.8647 (tmm) REVERT: R 86 GLU cc_start: 0.8964 (tp30) cc_final: 0.8591 (tp30) REVERT: U 61 MET cc_start: 0.9013 (mtt) cc_final: 0.8684 (mtp) REVERT: U 92 THR cc_start: 0.8961 (m) cc_final: 0.8708 (p) REVERT: V 55 MET cc_start: 0.8949 (ttm) cc_final: 0.8711 (ttm) REVERT: W 35 ASN cc_start: 0.8903 (p0) cc_final: 0.8554 (p0) REVERT: W 55 MET cc_start: 0.8725 (ttt) cc_final: 0.8208 (ttm) outliers start: 85 outliers final: 74 residues processed: 516 average time/residue: 0.9648 time to fit residues: 825.7464 Evaluate side-chains 521 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 445 time to evaluate : 4.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 103 ASP Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 130 GLN Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain M residue 226 SER Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 56 CYS Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain T residue 56 CYS Chi-restraints excluded: chain T residue 86 GLU Chi-restraints excluded: chain U residue 41 MET Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain U residue 82 PHE Chi-restraints excluded: chain V residue 41 MET Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 69 ASN Chi-restraints excluded: chain W residue 94 LEU Chi-restraints excluded: chain X residue 56 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 299 optimal weight: 5.9990 chunk 481 optimal weight: 10.0000 chunk 293 optimal weight: 0.7980 chunk 228 optimal weight: 1.9990 chunk 334 optimal weight: 3.9990 chunk 505 optimal weight: 0.9980 chunk 464 optimal weight: 0.9990 chunk 402 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 310 optimal weight: 0.9990 chunk 246 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 HIS ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 40022 Z= 0.178 Angle : 0.516 11.131 54248 Z= 0.265 Chirality : 0.040 0.148 6308 Planarity : 0.004 0.050 6928 Dihedral : 5.769 86.006 5686 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.62 % Favored : 96.36 % Rotamer: Outliers : 1.37 % Allowed : 14.26 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % 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: -0.80 (0.12), residues: 5084 helix: 0.21 (0.10), residues: 2534 sheet: -2.31 (0.20), residues: 591 loop : -0.74 (0.15), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 138 HIS 0.005 0.001 HIS G 227 PHE 0.016 0.001 PHE F 166 TYR 0.015 0.001 TYR E 468 ARG 0.004 0.000 ARG B 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 523 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 466 time to evaluate : 4.765 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: 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: 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: C 281 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.8905 (mp) REVERT: A 281 LEU cc_start: 0.9216 (tp) cc_final: 0.8859 (tp) REVERT: K 102 MET cc_start: 0.8298 (tpt) cc_final: 0.7988 (tpt) REVERT: M 216 LYS cc_start: 0.7041 (mtmt) cc_final: 0.6596 (mmmt) REVERT: G 300 LYS cc_start: 0.7918 (tttt) cc_final: 0.7447 (mmtm) REVERT: H 102 LYS cc_start: 0.8509 (ptpp) cc_final: 0.8101 (pttm) REVERT: H 172 GLU cc_start: 0.9104 (tt0) cc_final: 0.8645 (tp30) REVERT: O 61 MET cc_start: 0.8827 (mtt) cc_final: 0.8550 (mtp) REVERT: O 95 ILE cc_start: 0.8976 (mt) cc_final: 0.8637 (tt) REVERT: P 61 MET cc_start: 0.9212 (mtt) cc_final: 0.8470 (mtp) REVERT: P 73 LYS cc_start: 0.9068 (mtpt) cc_final: 0.8376 (tmtt) REVERT: Q 95 ILE cc_start: 0.9238 (mt) cc_final: 0.8931 (tp) REVERT: R 55 MET cc_start: 0.8957 (ttp) cc_final: 0.8571 (tmm) REVERT: R 86 GLU cc_start: 0.8974 (tp30) cc_final: 0.8611 (tp30) REVERT: U 61 MET cc_start: 0.8928 (mtt) cc_final: 0.8481 (mtp) REVERT: U 92 THR cc_start: 0.8925 (m) cc_final: 0.8668 (p) REVERT: V 55 MET cc_start: 0.8868 (ttm) cc_final: 0.8618 (ttm) REVERT: W 35 ASN cc_start: 0.8851 (p0) cc_final: 0.8464 (p0) REVERT: W 55 MET cc_start: 0.8661 (ttt) cc_final: 0.8132 (ttm) outliers start: 57 outliers final: 53 residues processed: 502 average time/residue: 1.0284 time to fit residues: 861.1855 Evaluate side-chains 513 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 459 time to evaluate : 5.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 130 GLN Chi-restraints excluded: chain M residue 226 SER Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 56 CYS Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain T residue 56 CYS Chi-restraints excluded: chain T residue 86 GLU Chi-restraints excluded: chain U residue 41 MET Chi-restraints excluded: chain V residue 41 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 319 optimal weight: 2.9990 chunk 428 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 370 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 402 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 413 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 ASN ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.094328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.067025 restraints weight = 326329.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.068199 restraints weight = 154957.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.068334 restraints weight = 100380.296| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 40022 Z= 0.240 Angle : 0.611 59.199 54248 Z= 0.341 Chirality : 0.040 0.304 6308 Planarity : 0.004 0.049 6928 Dihedral : 5.760 85.820 5686 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.82 % Favored : 96.16 % Rotamer: Outliers : 1.51 % Allowed : 14.26 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % 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: -0.78 (0.12), residues: 5084 helix: 0.22 (0.10), residues: 2534 sheet: -2.30 (0.20), residues: 591 loop : -0.73 (0.15), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 138 HIS 0.005 0.001 HIS G 227 PHE 0.015 0.001 PHE F 166 TYR 0.014 0.001 TYR J 52 ARG 0.003 0.000 ARG D 366 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15404.18 seconds wall clock time: 268 minutes 26.89 seconds (16106.89 seconds total)