Starting phenix.real_space_refine on Sat Feb 17 22:09:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euu_28617/02_2024/8euu_28617.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euu_28617/02_2024/8euu_28617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euu_28617/02_2024/8euu_28617.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euu_28617/02_2024/8euu_28617.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euu_28617/02_2024/8euu_28617.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euu_28617/02_2024/8euu_28617.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 12468 2.51 5 N 3339 2.21 5 O 3990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 211": "OE1" <-> "OE2" Residue "A ASP 325": "OD1" <-> "OD2" Residue "B GLU 584": "OE1" <-> "OE2" Residue "B ASP 624": "OD1" <-> "OD2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B GLU 657": "OE1" <-> "OE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C ASP 325": "OD1" <-> "OD2" Residue "D ASP 624": "OD1" <-> "OD2" Residue "D ASP 632": "OD1" <-> "OD2" Residue "D GLU 648": "OE1" <-> "OE2" Residue "E ASP 57": "OD1" <-> "OD2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E ASP 107": "OD1" <-> "OD2" Residue "E GLU 190": "OE1" <-> "OE2" Residue "E GLU 267": "OE1" <-> "OE2" Residue "F ASP 624": "OD1" <-> "OD2" Residue "F ASP 659": "OD1" <-> "OD2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 81": "OD1" <-> "OD2" Residue "I TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K GLU 100": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19926 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "B" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "C" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "D" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "E" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "F" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "G" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 944 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "H" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 944 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "J" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 944 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 10.84, per 1000 atoms: 0.54 Number of scatterers: 19926 At special positions: 0 Unit cell: (144.42, 151.89, 121.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 3990 8.00 N 3339 7.00 C 12468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN R 4 " - " MAN R 5 " " MAN b 4 " - " MAN b 5 " " MAN m 4 " - " MAN m 5 " ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA b 3 " - " MAN b 4 " " BMA m 3 " - " MAN m 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 602 " - " ASN A 392 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 133 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 197 " " NAG C 605 " - " ASN C 133 " " NAG E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 392 " " NAG E 603 " - " ASN E 301 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 133 " " NAG M 1 " - " ASN A 448 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 88 " " NAG P 1 " - " ASN A 276 " " NAG Q 1 " - " ASN A 386 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN A 156 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 363 " " NAG V 1 " - " ASN C 448 " " NAG W 1 " - " ASN C 160 " " NAG X 1 " - " ASN C 88 " " NAG Y 1 " - " ASN C 276 " " NAG Z 1 " - " ASN C 386 " " NAG a 1 " - " ASN A 295 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 295 " " NAG d 1 " - " ASN C 156 " " NAG e 1 " - " ASN C 332 " " NAG f 1 " - " ASN C 363 " " NAG g 1 " - " ASN E 295 " " NAG h 1 " - " ASN E 448 " " NAG i 1 " - " ASN E 160 " " NAG j 1 " - " ASN E 88 " " NAG k 1 " - " ASN E 276 " " NAG l 1 " - " ASN E 386 " " NAG m 1 " - " ASN E 262 " " NAG n 1 " - " ASN E 156 " " NAG o 1 " - " ASN E 332 " " NAG p 1 " - " ASN E 363 " Time building additional restraints: 8.62 Conformation dependent library (CDL) restraints added in 3.3 seconds 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4434 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 45 sheets defined 20.3% alpha, 37.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 3.992A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.814A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 484 removed outlier: 4.258A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.164A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.615A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.620A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 639 through 663 removed outlier: 3.773A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.959A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.696A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 474 through 484 removed outlier: 4.251A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 4.115A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.647A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 596 removed outlier: 3.552A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 639 through 663 removed outlier: 3.782A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.974A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.658A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.913A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.529A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.716A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 639 through 663 removed outlier: 3.784A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 4.293A pdb=" N ASN G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 97 through 100A removed outlier: 3.501A pdb=" N ASN G 100 " --> pdb=" O TYR G 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.901A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 4.157A pdb=" N ASN I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 97 through 100A Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.018A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 4.256A pdb=" N ASN K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 97 through 100A Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.877A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.530A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.018A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.416A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.489A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.465A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.092A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.679A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.092A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.465A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.466A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.626A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.808A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.455A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.502A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.028A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.390A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.112A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.761A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.112A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.390A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.028A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.451A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 495 through 499 removed outlier: 5.657A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.992A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.910A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.446A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.507A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.457A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.155A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.698A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.155A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.457A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.472A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.611A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.855A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 7 removed outlier: 12.065A pdb=" N CYS H 23 " --> pdb=" O THR H 74 " (cutoff:3.500A) removed outlier: 11.050A pdb=" N THR H 74 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 12.123A pdb=" N ALA H 25 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 11.716A pdb=" N THR H 72 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 11.272A pdb=" N GLN H 27 " --> pdb=" O HIS H 70 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N HIS H 70 " --> pdb=" O GLN H 27 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.883A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.861A pdb=" N THR H 97 " --> pdb=" O HIS H 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.650A pdb=" N LEU I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TRP I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.797A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 7 removed outlier: 5.596A pdb=" N THR J 69 " --> pdb=" O ALA J 25 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.880A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.860A pdb=" N THR J 97 " --> pdb=" O HIS J 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.201A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.816A pdb=" N VAL K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 4 through 7 removed outlier: 12.071A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 12.172A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 11.773A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 11.319A pdb=" N GLN L 27 " --> pdb=" O HIS L 70 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N HIS L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.913A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.870A pdb=" N THR L 97 " --> pdb=" O HIS L 90 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 2025 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: 7.90 Time building geometry restraints manager: 9.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6290 1.35 - 1.47: 5225 1.47 - 1.60: 8633 1.60 - 1.72: 0 1.72 - 1.85: 174 Bond restraints: 20322 Sorted by residual: bond pdb=" N GLN I 1 " pdb=" CA GLN I 1 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.67e+00 bond pdb=" C1 NAG f 1 " pdb=" O5 NAG f 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.58e+00 bond pdb=" N GLN K 1 " pdb=" CA GLN K 1 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.56e+00 bond pdb=" N GLN G 1 " pdb=" CA GLN G 1 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.53e+00 bond pdb=" N ALA B 512 " pdb=" CA ALA B 512 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 ... (remaining 20317 not shown) Histogram of bond angle deviations from ideal: 99.54 - 106.45: 499 106.45 - 113.36: 11662 113.36 - 120.26: 6652 120.26 - 127.17: 8508 127.17 - 134.08: 267 Bond angle restraints: 27588 Sorted by residual: angle pdb=" CB MET F 535 " pdb=" CG MET F 535 " pdb=" SD MET F 535 " ideal model delta sigma weight residual 112.70 121.63 -8.93 3.00e+00 1.11e-01 8.86e+00 angle pdb=" CA ILE B 635 " pdb=" CB ILE B 635 " pdb=" CG2 ILE B 635 " ideal model delta sigma weight residual 110.50 114.72 -4.22 1.70e+00 3.46e-01 6.16e+00 angle pdb=" CA GLN A 114 " pdb=" CB GLN A 114 " pdb=" CG GLN A 114 " ideal model delta sigma weight residual 114.10 118.87 -4.77 2.00e+00 2.50e-01 5.69e+00 angle pdb=" CA ILE F 635 " pdb=" CB ILE F 635 " pdb=" CG2 ILE F 635 " ideal model delta sigma weight residual 110.50 114.54 -4.04 1.70e+00 3.46e-01 5.66e+00 angle pdb=" CA ILE D 635 " pdb=" CB ILE D 635 " pdb=" CG2 ILE D 635 " ideal model delta sigma weight residual 110.50 114.44 -3.94 1.70e+00 3.46e-01 5.38e+00 ... (remaining 27583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.51: 11930 21.51 - 43.02: 985 43.02 - 64.52: 272 64.52 - 86.03: 57 86.03 - 107.54: 28 Dihedral angle restraints: 13272 sinusoidal: 6387 harmonic: 6885 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -152.23 66.23 1 1.00e+01 1.00e-02 5.73e+01 dihedral pdb=" CB CYS C 201 " pdb=" SG CYS C 201 " pdb=" SG CYS C 433 " pdb=" CB CYS C 433 " ideal model delta sinusoidal sigma weight residual -86.00 -148.31 62.31 1 1.00e+01 1.00e-02 5.14e+01 dihedral pdb=" CB CYS E 201 " pdb=" SG CYS E 201 " pdb=" SG CYS E 433 " pdb=" CB CYS E 433 " ideal model delta sinusoidal sigma weight residual -86.00 -147.00 61.00 1 1.00e+01 1.00e-02 4.95e+01 ... (remaining 13269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2796 0.055 - 0.111: 405 0.111 - 0.166: 141 0.166 - 0.222: 3 0.222 - 0.277: 9 Chirality restraints: 3354 Sorted by residual: chirality pdb=" C5 BMA X 3 " pdb=" C4 BMA X 3 " pdb=" C6 BMA X 3 " pdb=" O5 BMA X 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C5 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C6 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 3351 not shown) Planarity restraints: 3447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 24 " -0.138 9.50e-02 1.11e+02 6.22e-02 2.69e+00 pdb=" NE ARG J 24 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG J 24 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG J 24 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG J 24 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 635 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C ILE D 635 " -0.027 2.00e-02 2.50e+03 pdb=" O ILE D 635 " 0.010 2.00e-02 2.50e+03 pdb=" N SER D 636 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 444 " 0.127 9.50e-02 1.11e+02 5.73e-02 2.15e+00 pdb=" NE ARG A 444 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 444 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 444 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 444 " 0.002 2.00e-02 2.50e+03 ... (remaining 3444 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 161 2.59 - 3.17: 15684 3.17 - 3.74: 29963 3.74 - 4.32: 44876 4.32 - 4.90: 73331 Nonbonded interactions: 164015 Sorted by model distance: nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.012 2.440 nonbonded pdb=" O7 NAG Z 2 " pdb=" O6 NAG f 1 " model vdw 2.101 2.440 nonbonded pdb=" OG1 THR E 37 " pdb=" OG1 THR E 499 " model vdw 2.158 2.440 nonbonded pdb=" OG SER C 56 " pdb=" OG1 THR C 71 " model vdw 2.200 2.440 nonbonded pdb=" OG SER A 56 " pdb=" OG1 THR A 71 " model vdw 2.203 2.440 ... (remaining 164010 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'O' selection = chain 'X' selection = chain 'j' } ncs_group { reference = chain 'R' selection = chain 'b' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 19.410 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 54.670 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.380 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:14.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20322 Z= 0.286 Angle : 0.675 8.930 27588 Z= 0.316 Chirality : 0.049 0.277 3354 Planarity : 0.003 0.062 3402 Dihedral : 17.088 107.540 8712 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.48 % Allowed : 15.83 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.18), residues: 2352 helix: 1.87 (0.29), residues: 393 sheet: 0.93 (0.18), residues: 819 loop : 0.43 (0.20), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 47 HIS 0.002 0.001 HIS E 105 PHE 0.023 0.001 PHE C 53 TYR 0.014 0.001 TYR J 36 ARG 0.010 0.001 ARG J 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 252 time to evaluate : 2.253 Fit side-chains revert: symmetry clash REVERT: A 475 MET cc_start: 0.9058 (mmp) cc_final: 0.8585 (mmp) REVERT: D 635 ILE cc_start: 0.7335 (mp) cc_final: 0.7128 (mm) REVERT: E 95 MET cc_start: 0.8576 (ptm) cc_final: 0.8314 (ptm) REVERT: F 530 MET cc_start: 0.8384 (mtp) cc_final: 0.7904 (mtp) REVERT: F 655 LYS cc_start: 0.6671 (mtpt) cc_final: 0.5742 (pttm) REVERT: I 34 LEU cc_start: 0.8530 (tp) cc_final: 0.8161 (mt) REVERT: K 34 LEU cc_start: 0.8484 (tp) cc_final: 0.8144 (mt) REVERT: K 77 THR cc_start: 0.6727 (p) cc_final: 0.6504 (p) outliers start: 10 outliers final: 9 residues processed: 262 average time/residue: 1.2764 time to fit residues: 379.3233 Evaluate side-chains 233 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 224 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 201 CYS Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain L residue 56 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 6.9990 chunk 179 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 185 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN D 630 GLN E 137 ASN F 630 GLN H 90 HIS I 32 ASN I 105 GLN K 32 ASN L 6 GLN L 79 GLN ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20322 Z= 0.341 Angle : 0.628 8.828 27588 Z= 0.321 Chirality : 0.047 0.269 3354 Planarity : 0.004 0.034 3402 Dihedral : 9.941 70.395 4366 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.97 % Allowed : 15.49 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.18), residues: 2352 helix: 1.34 (0.28), residues: 414 sheet: 0.93 (0.18), residues: 783 loop : 0.62 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 103 HIS 0.006 0.002 HIS E 85 PHE 0.015 0.002 PHE E 383 TYR 0.021 0.002 TYR H 49 ARG 0.004 0.001 ARG I 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 218 time to evaluate : 2.066 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.6636 (tm-30) REVERT: A 327 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7895 (ptt-90) REVERT: A 444 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7283 (tpt90) REVERT: C 91 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7021 (tm-30) REVERT: C 92 GLU cc_start: 0.7409 (tp30) cc_final: 0.7091 (tp30) REVERT: C 151 ARG cc_start: 0.7754 (mtp85) cc_final: 0.7424 (mtt-85) REVERT: C 189 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7784 (tttm) REVERT: C 444 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7354 (tmm-80) REVERT: E 91 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7136 (tm-30) REVERT: E 95 MET cc_start: 0.8976 (ptm) cc_final: 0.8729 (ptm) REVERT: E 327 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7838 (ptt-90) REVERT: F 530 MET cc_start: 0.8467 (mtp) cc_final: 0.8095 (mtp) REVERT: F 617 ARG cc_start: 0.6094 (OUTLIER) cc_final: 0.5680 (ttm170) REVERT: I 34 LEU cc_start: 0.8421 (tp) cc_final: 0.8021 (mt) REVERT: J 32 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6811 (mm-30) REVERT: K 62 LYS cc_start: 0.6410 (OUTLIER) cc_final: 0.6081 (pptt) REVERT: K 69 MET cc_start: 0.7377 (mtm) cc_final: 0.6997 (mtm) REVERT: K 77 THR cc_start: 0.7005 (p) cc_final: 0.6798 (p) REVERT: L 46 LEU cc_start: 0.7592 (tt) cc_final: 0.7237 (tt) outliers start: 62 outliers final: 18 residues processed: 257 average time/residue: 1.3879 time to fit residues: 400.6246 Evaluate side-chains 236 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 207 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 617 ARG Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain K residue 62 LYS Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 119 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 179 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 232 optimal weight: 0.1980 chunk 192 optimal weight: 0.0570 chunk 213 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 172 optimal weight: 0.0970 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN C 67 ASN D 630 GLN E 137 ASN G 32 ASN I 32 ASN I 105 GLN K 32 ASN ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20322 Z= 0.133 Angle : 0.478 6.818 27588 Z= 0.246 Chirality : 0.042 0.250 3354 Planarity : 0.003 0.035 3402 Dihedral : 7.619 59.989 4356 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.25 % Allowed : 16.50 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.18), residues: 2352 helix: 1.60 (0.28), residues: 414 sheet: 1.04 (0.19), residues: 783 loop : 0.60 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 427 HIS 0.002 0.000 HIS H 90 PHE 0.013 0.001 PHE C 53 TYR 0.019 0.001 TYR A 173 ARG 0.003 0.000 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 223 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.7718 (mtp85) cc_final: 0.7388 (mtt-85) REVERT: C 327 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7781 (ptt-90) REVERT: C 444 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7130 (tmm-80) REVERT: D 658 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7573 (tt0) REVERT: E 103 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: E 327 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7777 (ptt-90) REVERT: F 530 MET cc_start: 0.8460 (mtp) cc_final: 0.8242 (mtp) REVERT: F 626 MET cc_start: 0.7149 (ttp) cc_final: 0.6913 (ttp) REVERT: F 660 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7326 (tp) REVERT: I 34 LEU cc_start: 0.8235 (tp) cc_final: 0.7915 (mt) REVERT: J 53 THR cc_start: 0.6538 (m) cc_final: 0.6268 (m) REVERT: K 34 LEU cc_start: 0.8414 (tp) cc_final: 0.8036 (mt) REVERT: K 69 MET cc_start: 0.7354 (mtm) cc_final: 0.6948 (mtm) outliers start: 47 outliers final: 14 residues processed: 255 average time/residue: 1.3275 time to fit residues: 383.4954 Evaluate side-chains 234 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 214 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain L residue 14 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 7.9990 chunk 162 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 216 optimal weight: 6.9990 chunk 229 optimal weight: 20.0000 chunk 113 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN B 543 ASN C 80 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN F 543 ASN F 658 GLN I 32 ASN I 105 GLN J 90 HIS K 32 ASN L 90 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.090 20322 Z= 0.738 Angle : 0.874 11.227 27588 Z= 0.439 Chirality : 0.059 0.314 3354 Planarity : 0.006 0.074 3402 Dihedral : 8.364 59.479 4356 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 5.04 % Allowed : 15.11 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.17), residues: 2352 helix: 0.47 (0.26), residues: 396 sheet: 0.62 (0.18), residues: 786 loop : 0.29 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP G 50 HIS 0.012 0.003 HIS I 35 PHE 0.019 0.003 PHE E 353 TYR 0.037 0.003 TYR C 384 ARG 0.006 0.001 ARG D 542 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 197 time to evaluate : 2.285 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.6490 (tm-30) REVERT: B 584 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7369 (mt-10) REVERT: C 91 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.6807 (tm-30) REVERT: C 327 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7896 (ptt-90) REVERT: C 444 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7952 (mmm-85) REVERT: D 635 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7636 (mm) REVERT: E 91 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.6730 (tm-30) REVERT: E 327 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7730 (ptt-90) REVERT: I 23 ARG cc_start: 0.7394 (ttt90) cc_final: 0.7043 (ttt90) REVERT: I 34 LEU cc_start: 0.8453 (tp) cc_final: 0.8228 (tp) REVERT: J 32 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6766 (mm-30) REVERT: K 62 LYS cc_start: 0.6394 (OUTLIER) cc_final: 0.6024 (pttt) REVERT: K 75 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7492 (pt) outliers start: 105 outliers final: 45 residues processed: 270 average time/residue: 1.4277 time to fit residues: 431.1106 Evaluate side-chains 243 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 188 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 62 LYS Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 30.0000 chunk 130 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 195 optimal weight: 0.7980 chunk 158 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 205 optimal weight: 20.0000 chunk 57 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 355 ASN G 76 ASN I 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20322 Z= 0.201 Angle : 0.551 8.686 27588 Z= 0.284 Chirality : 0.043 0.256 3354 Planarity : 0.004 0.034 3402 Dihedral : 6.701 59.356 4356 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.45 % Allowed : 18.13 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.18), residues: 2352 helix: 1.05 (0.27), residues: 414 sheet: 0.76 (0.18), residues: 765 loop : 0.36 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 427 HIS 0.004 0.001 HIS H 70 PHE 0.015 0.001 PHE A 383 TYR 0.017 0.002 TYR A 173 ARG 0.003 0.000 ARG E 444 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 208 time to evaluate : 2.221 Fit side-chains REVERT: A 103 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: C 444 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7336 (tmm-80) REVERT: D 635 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7456 (mm) REVERT: E 103 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: E 327 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7710 (ptt-90) REVERT: F 660 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7454 (tp) REVERT: I 34 LEU cc_start: 0.8316 (tp) cc_final: 0.7955 (mt) REVERT: J 32 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6649 (mm-30) outliers start: 51 outliers final: 20 residues processed: 243 average time/residue: 1.3983 time to fit residues: 382.0384 Evaluate side-chains 226 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 199 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 542 ARG Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain J residue 1 ASP Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 33 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 134 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 229 optimal weight: 20.0000 chunk 190 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN G 76 ASN I 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20322 Z= 0.270 Angle : 0.576 8.552 27588 Z= 0.296 Chirality : 0.044 0.263 3354 Planarity : 0.004 0.035 3402 Dihedral : 6.408 59.948 4356 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.69 % Allowed : 18.08 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.18), residues: 2352 helix: 1.13 (0.27), residues: 414 sheet: 0.71 (0.18), residues: 759 loop : 0.37 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 35 HIS 0.005 0.001 HIS I 35 PHE 0.014 0.002 PHE A 383 TYR 0.020 0.002 TYR A 173 ARG 0.004 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 201 time to evaluate : 2.062 Fit side-chains REVERT: A 103 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.8002 (tt0) REVERT: C 103 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: C 151 ARG cc_start: 0.7797 (mtp85) cc_final: 0.7461 (mtt-85) REVERT: C 444 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7243 (tmm-80) REVERT: D 635 ILE cc_start: 0.7681 (mp) cc_final: 0.7426 (mm) REVERT: D 658 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: E 103 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7951 (tt0) REVERT: E 327 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7741 (ptt-90) REVERT: E 444 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7237 (tpt90) REVERT: F 660 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7432 (tp) REVERT: G 75 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7343 (pt) REVERT: I 23 ARG cc_start: 0.7337 (ttt90) cc_final: 0.7133 (tpt170) REVERT: I 34 LEU cc_start: 0.8350 (tp) cc_final: 0.7982 (mt) REVERT: J 32 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6727 (mm-30) outliers start: 56 outliers final: 21 residues processed: 241 average time/residue: 1.3928 time to fit residues: 376.7286 Evaluate side-chains 229 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 198 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain J residue 1 ASP Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain L residue 14 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 193 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 228 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN D 616 ASN E 80 ASN I 39 GLN I 105 GLN J 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20322 Z= 0.225 Angle : 0.540 8.626 27588 Z= 0.278 Chirality : 0.043 0.256 3354 Planarity : 0.004 0.035 3402 Dihedral : 5.838 59.004 4356 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.78 % Allowed : 18.23 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.18), residues: 2352 helix: 1.26 (0.27), residues: 414 sheet: 0.70 (0.18), residues: 759 loop : 0.39 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 35 HIS 0.004 0.001 HIS E 85 PHE 0.014 0.001 PHE A 383 TYR 0.022 0.002 TYR A 173 ARG 0.004 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 203 time to evaluate : 2.134 Fit side-chains REVERT: A 103 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: C 151 ARG cc_start: 0.7769 (mtp85) cc_final: 0.7440 (mtt-85) REVERT: C 444 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7229 (tmm-80) REVERT: D 635 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7537 (mm) REVERT: D 658 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7611 (tt0) REVERT: E 103 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7928 (tt0) REVERT: E 455 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8370 (t) REVERT: F 660 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7437 (tp) REVERT: G 75 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7363 (pt) REVERT: I 34 LEU cc_start: 0.8308 (tp) cc_final: 0.7945 (mt) REVERT: J 32 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6716 (mm-30) outliers start: 58 outliers final: 22 residues processed: 243 average time/residue: 1.4122 time to fit residues: 386.3655 Evaluate side-chains 230 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 199 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain J residue 1 ASP Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain L residue 14 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 0.1980 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 462 ASN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 462 ASN F 658 GLN I 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20322 Z= 0.334 Angle : 0.615 9.245 27588 Z= 0.314 Chirality : 0.046 0.267 3354 Planarity : 0.004 0.035 3402 Dihedral : 6.086 58.757 4356 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.88 % Allowed : 18.18 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.18), residues: 2352 helix: 1.04 (0.27), residues: 414 sheet: 0.68 (0.18), residues: 744 loop : 0.34 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 35 HIS 0.005 0.001 HIS C 85 PHE 0.014 0.002 PHE A 383 TYR 0.022 0.002 TYR A 173 ARG 0.005 0.000 ARG E 444 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 198 time to evaluate : 2.228 Fit side-chains REVERT: C 444 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7282 (tmm-80) REVERT: D 635 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7524 (mm) REVERT: D 658 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7641 (tt0) REVERT: E 103 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: E 117 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7751 (ttmt) REVERT: E 455 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8378 (t) REVERT: F 660 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7482 (tp) REVERT: G 75 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7438 (pt) REVERT: I 23 ARG cc_start: 0.7332 (ttt90) cc_final: 0.7124 (tpt170) REVERT: I 34 LEU cc_start: 0.8369 (tp) cc_final: 0.7990 (mt) REVERT: J 32 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6719 (mm-30) outliers start: 60 outliers final: 27 residues processed: 240 average time/residue: 1.4393 time to fit residues: 388.9608 Evaluate side-chains 234 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 198 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain E residue 432 GLN Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain J residue 1 ASP Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 32 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 chunk 212 optimal weight: 20.0000 chunk 128 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 167 optimal weight: 0.1980 chunk 65 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 225 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN F 658 GLN I 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20322 Z= 0.177 Angle : 0.516 8.653 27588 Z= 0.266 Chirality : 0.042 0.250 3354 Planarity : 0.003 0.036 3402 Dihedral : 5.404 54.534 4356 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.21 % Allowed : 19.04 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.18), residues: 2352 helix: 1.34 (0.27), residues: 414 sheet: 0.80 (0.18), residues: 741 loop : 0.37 (0.19), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 35 HIS 0.003 0.001 HIS E 85 PHE 0.013 0.001 PHE E 383 TYR 0.022 0.001 TYR A 173 ARG 0.005 0.000 ARG E 444 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 200 time to evaluate : 2.102 Fit side-chains REVERT: A 103 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: C 151 ARG cc_start: 0.7769 (mtp85) cc_final: 0.7435 (mtt-85) REVERT: C 444 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7210 (tmm-80) REVERT: D 635 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7499 (mm) REVERT: D 658 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7648 (tt0) REVERT: E 103 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: E 455 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8361 (t) REVERT: F 658 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: F 660 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7408 (tp) REVERT: G 75 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7431 (pt) REVERT: I 23 ARG cc_start: 0.7355 (ttt90) cc_final: 0.7135 (tpt170) REVERT: I 34 LEU cc_start: 0.8330 (tp) cc_final: 0.7961 (mt) REVERT: I 77 THR cc_start: 0.6982 (p) cc_final: 0.6766 (p) REVERT: J 32 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6683 (mm-30) outliers start: 46 outliers final: 23 residues processed: 234 average time/residue: 1.3658 time to fit residues: 359.8499 Evaluate side-chains 231 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 198 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain E residue 432 GLN Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain L residue 14 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 236 optimal weight: 8.9990 chunk 217 optimal weight: 0.7980 chunk 188 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN F 658 GLN I 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20322 Z= 0.201 Angle : 0.527 8.738 27588 Z= 0.271 Chirality : 0.043 0.252 3354 Planarity : 0.003 0.036 3402 Dihedral : 5.316 54.830 4356 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.87 % Allowed : 19.47 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.18), residues: 2352 helix: 1.36 (0.27), residues: 414 sheet: 0.78 (0.18), residues: 762 loop : 0.36 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 35 HIS 0.003 0.001 HIS I 35 PHE 0.013 0.001 PHE A 383 TYR 0.024 0.001 TYR A 173 ARG 0.004 0.000 ARG E 444 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 199 time to evaluate : 2.378 Fit side-chains REVERT: A 103 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: B 635 ILE cc_start: 0.7594 (mp) cc_final: 0.7367 (mm) REVERT: C 151 ARG cc_start: 0.7753 (mtp85) cc_final: 0.7415 (mtt-85) REVERT: C 444 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7175 (tmm-80) REVERT: D 635 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7468 (mm) REVERT: D 658 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7631 (tt0) REVERT: E 103 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: E 455 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8358 (t) REVERT: F 660 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7357 (tp) REVERT: G 75 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7429 (pt) REVERT: I 34 LEU cc_start: 0.8333 (tp) cc_final: 0.7971 (mt) REVERT: J 32 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6710 (mm-30) REVERT: J 79 GLN cc_start: 0.7017 (OUTLIER) cc_final: 0.6813 (mm-40) outliers start: 39 outliers final: 23 residues processed: 228 average time/residue: 1.4817 time to fit residues: 380.5304 Evaluate side-chains 229 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 196 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain E residue 432 GLN Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain K residue 62 LYS Chi-restraints excluded: chain L residue 14 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 188 optimal weight: 0.0020 chunk 78 optimal weight: 2.9990 chunk 193 optimal weight: 0.0070 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 165 optimal weight: 4.9990 chunk 10 optimal weight: 0.0050 overall best weight: 0.2820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN F 658 GLN I 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.199149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.144885 restraints weight = 21052.811| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.15 r_work: 0.3367 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20322 Z= 0.130 Angle : 0.474 8.670 27588 Z= 0.244 Chirality : 0.041 0.240 3354 Planarity : 0.003 0.038 3402 Dihedral : 4.664 51.670 4356 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.44 % Allowed : 20.00 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.18), residues: 2352 helix: 1.55 (0.28), residues: 414 sheet: 0.80 (0.18), residues: 792 loop : 0.42 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 427 HIS 0.002 0.001 HIS I 35 PHE 0.012 0.001 PHE C 53 TYR 0.027 0.001 TYR A 173 ARG 0.005 0.000 ARG E 444 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7057.27 seconds wall clock time: 126 minutes 56.66 seconds (7616.66 seconds total)