Starting phenix.real_space_refine on Sat Feb 17 23:35:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euv_28618/02_2024/8euv_28618.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euv_28618/02_2024/8euv_28618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euv_28618/02_2024/8euv_28618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euv_28618/02_2024/8euv_28618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euv_28618/02_2024/8euv_28618.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euv_28618/02_2024/8euv_28618.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 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 12486 2.51 5 N 3342 2.21 5 O 4181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 107": "OD1" <-> "OD2" Residue "A ASP 412": "OD1" <-> "OD2" Residue "B GLU 634": "OE1" <-> "OE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C ASP 325": "OD1" <-> "OD2" Residue "D ASP 624": "OD1" <-> "OD2" Residue "D GLU 648": "OE1" <-> "OE2" Residue "E TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 57": "OD1" <-> "OD2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E ASP 107": "OD1" <-> "OD2" Residue "E ASP 140": "OD1" <-> "OD2" Residue "E ASP 141": "OD1" <-> "OD2" Residue "E GLU 267": "OE1" <-> "OE2" Residue "E GLU 340": "OE1" <-> "OE2" Residue "E GLU 381": "OE1" <-> "OE2" Residue "F ASP 589": "OD1" <-> "OD2" Residue "F ASP 624": "OD1" <-> "OD2" Residue "F ASP 632": "OD1" <-> "OD2" Residue "F GLU 648": "OE1" <-> "OE2" Residue "G ASP 72": "OD1" <-> "OD2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 81": "OD1" <-> "OD2" Residue "J TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 72": "OD1" <-> "OD2" Residue "K GLU 100": "OE1" <-> "OE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 20138 Number of models: 1 Model: "" Number of chains: 54 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: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 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: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 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: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 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 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 10.88, per 1000 atoms: 0.54 Number of scatterers: 20138 At special positions: 0 Unit cell: (153.55, 142.76, 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 4181 8.00 N 3342 7.00 C 12486 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=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 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=2.05 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 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=2.03 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=2.05 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=1.85 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 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=2.03 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=2.05 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=2.04 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=2.04 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=2.04 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: 8.72 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: 39 helices and 45 sheets defined 17.9% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 3.940A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.941A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.505A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.640A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 595 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 662 Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.929A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.065A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.508A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.619A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 595 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 662 Processing helix chain 'E' and resid 98 through 116 removed outlier: 3.940A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.011A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.504A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.978A 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: 3.719A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 595 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 662 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.997A 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 83 through 87 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.992A 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 83 through 87 Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.990A 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 sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.344A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.394A 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: 3.602A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.496A 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 removed outlier: 6.788A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) 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: 6.419A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.377A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.930A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.956A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.778A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.070A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.072A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.059A 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: 12.191A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 11.072A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 11.070A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.778A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.956A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.930A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.521A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.501A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.589A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.500A 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 removed outlier: 6.810A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) 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: 6.418A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.378A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.431A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.921A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.947A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.781A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.067A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.074A pdb=" N ASP C 457 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 12.195A pdb=" N ILE C 284 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.586A 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: 12.195A pdb=" N ILE C 284 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 11.074A pdb=" N ASP C 457 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 11.067A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.781A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.947A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.921A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.431A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 4.709A 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: 6.522A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.209A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.590A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.521A 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: 6.790A 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: 6.416A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.378A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.943A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.957A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.068A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.075A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 12.193A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.055A 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 273 removed outlier: 12.193A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 11.075A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 11.068A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.957A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.943A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.522A 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: 6.512A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.628A 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: 3.767A 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: 12.015A pdb=" N CYS H 23 " --> pdb=" O THR H 74 " (cutoff:3.500A) removed outlier: 10.985A pdb=" N THR H 74 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 12.093A pdb=" N ALA H 25 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 11.730A pdb=" N THR H 72 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 11.119A pdb=" N GLN H 27 " --> pdb=" O HIS H 70 " (cutoff:3.500A) removed outlier: 6.783A 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: 6.706A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.316A 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: 3.758A 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: 6.525A pdb=" N LEU I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TRP I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.651A 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: 3.749A 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: 12.005A pdb=" N CYS J 23 " --> pdb=" O THR J 74 " (cutoff:3.500A) removed outlier: 11.018A pdb=" N THR J 74 " --> pdb=" O CYS J 23 " (cutoff:3.500A) removed outlier: 12.105A pdb=" N ALA J 25 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR J 72 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 11.110A pdb=" N GLN J 27 " --> pdb=" O HIS J 70 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N HIS J 70 " --> pdb=" O GLN J 27 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.717A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.314A 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: 3.766A 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: 6.511A pdb=" N LEU K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TRP K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.759A 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: 12.055A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 12.142A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 11.762A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 11.136A pdb=" N GLN L 27 " --> pdb=" O HIS L 70 " (cutoff:3.500A) removed outlier: 6.785A 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: 6.724A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.315A 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: 3.768A pdb=" N THR L 97 " --> pdb=" O HIS L 90 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 2070 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: 7.53 Time building geometry restraints manager: 9.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.61: 20158 1.61 - 1.99: 176 1.99 - 2.37: 1 2.37 - 2.75: 0 2.75 - 3.14: 2 Bond restraints: 20337 Sorted by residual: bond pdb=" N PRO H 8 " pdb=" CD PRO H 8 " ideal model delta sigma weight residual 1.474 3.137 -1.663 1.40e-02 5.10e+03 1.41e+04 bond pdb=" N PRO J 8 " pdb=" CD PRO J 8 " ideal model delta sigma weight residual 1.474 2.946 -1.472 1.40e-02 5.10e+03 1.11e+04 bond pdb=" CB PRO H 8 " pdb=" CG PRO H 8 " ideal model delta sigma weight residual 1.506 2.053 -0.547 3.90e-02 6.57e+02 1.96e+02 bond pdb=" CB PRO J 8 " pdb=" CG PRO J 8 " ideal model delta sigma weight residual 1.506 1.933 -0.427 3.90e-02 6.57e+02 1.20e+02 bond pdb=" N PRO H 59 " pdb=" CD PRO H 59 " ideal model delta sigma weight residual 1.473 1.622 -0.149 1.40e-02 5.10e+03 1.13e+02 ... (remaining 20332 not shown) Histogram of bond angle deviations from ideal: 21.03 - 46.00: 2 46.00 - 70.97: 0 70.97 - 95.94: 7 95.94 - 120.91: 20826 120.91 - 145.87: 6768 Bond angle restraints: 27603 Sorted by residual: angle pdb=" N PRO H 8 " pdb=" CD PRO H 8 " pdb=" CG PRO H 8 " ideal model delta sigma weight residual 103.80 21.03 82.77 1.20e+00 6.94e-01 4.76e+03 angle pdb=" N PRO J 8 " pdb=" CD PRO J 8 " pdb=" CG PRO J 8 " ideal model delta sigma weight residual 103.80 36.76 67.04 1.20e+00 6.94e-01 3.12e+03 angle pdb=" CA PRO H 8 " pdb=" N PRO H 8 " pdb=" CD PRO H 8 " ideal model delta sigma weight residual 111.50 86.14 25.36 1.40e+00 5.10e-01 3.28e+02 angle pdb=" CA PRO J 8 " pdb=" N PRO J 8 " pdb=" CD PRO J 8 " ideal model delta sigma weight residual 111.50 88.42 23.08 1.40e+00 5.10e-01 2.72e+02 angle pdb=" CB PRO H 8 " pdb=" CG PRO H 8 " pdb=" CD PRO H 8 " ideal model delta sigma weight residual 105.40 78.06 27.34 2.30e+00 1.89e-01 1.41e+02 ... (remaining 27598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.29: 12499 27.29 - 54.58: 639 54.58 - 81.87: 110 81.87 - 109.17: 28 109.17 - 136.46: 2 Dihedral angle restraints: 13278 sinusoidal: 6393 harmonic: 6885 Sorted by residual: dihedral pdb=" CA ASN D 618 " pdb=" C ASN D 618 " pdb=" N LEU D 619 " pdb=" CA LEU D 619 " ideal model delta harmonic sigma weight residual -180.00 -135.65 -44.35 0 5.00e+00 4.00e-02 7.87e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 605 " pdb=" CB CYS B 605 " ideal model delta sinusoidal sigma weight residual -86.00 -6.74 -79.26 1 1.00e+01 1.00e-02 7.81e+01 dihedral pdb=" CA ASN B 618 " pdb=" C ASN B 618 " pdb=" N LEU B 619 " pdb=" CA LEU B 619 " ideal model delta harmonic sigma weight residual -180.00 -136.28 -43.72 0 5.00e+00 4.00e-02 7.64e+01 ... (remaining 13275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2729 0.060 - 0.120: 501 0.120 - 0.180: 110 0.180 - 0.240: 3 0.240 - 0.299: 8 Chirality restraints: 3351 Sorted by residual: chirality pdb=" C1 MAN R 4 " pdb=" O3 BMA R 3 " pdb=" C2 MAN R 4 " pdb=" O5 MAN R 4 " both_signs ideal model delta sigma weight residual False 2.40 2.43 -0.03 2.00e-02 2.50e+03 2.76e+00 chirality pdb=" C5 BMA m 3 " pdb=" C4 BMA m 3 " pdb=" C6 BMA m 3 " pdb=" O5 BMA m 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.24e+00 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 -2.57 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 3348 not shown) Planarity restraints: 3447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS K 13 " -0.085 5.00e-02 4.00e+02 1.28e-01 2.60e+01 pdb=" N PRO K 14 " 0.221 5.00e-02 4.00e+02 pdb=" CA PRO K 14 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO K 14 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 7 " -0.060 5.00e-02 4.00e+02 6.62e-02 7.01e+00 pdb=" N PRO H 8 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO H 8 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 8 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 75 " -0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO E 76 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO E 76 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 76 " -0.029 5.00e-02 4.00e+02 ... (remaining 3444 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 425 2.68 - 3.24: 17949 3.24 - 3.79: 31436 3.79 - 4.35: 46106 4.35 - 4.90: 73105 Nonbonded interactions: 169021 Sorted by model distance: nonbonded pdb=" OG SER C 56 " pdb=" OG1 THR C 71 " model vdw 2.127 2.440 nonbonded pdb=" OG SER A 56 " pdb=" OG1 THR A 71 " model vdw 2.130 2.440 nonbonded pdb=" OG SER E 56 " pdb=" OG1 THR E 71 " model vdw 2.131 2.440 nonbonded pdb=" O GLN E 293 " pdb=" O HOH E 701 " model vdw 2.168 2.440 nonbonded pdb=" O GLN A 293 " pdb=" O HOH A 701 " model vdw 2.181 2.440 ... (remaining 169016 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: 4.240 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: 19.660 Check model and map are aligned: 0.360 Set scattering table: 0.190 Process input model: 55.930 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.410 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:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 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 : 0.017 1.663 20337 Z= 0.952 Angle : 1.108 82.766 27603 Z= 0.700 Chirality : 0.053 0.299 3351 Planarity : 0.005 0.128 3402 Dihedral : 16.363 136.457 8718 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.62 % Allowed : 10.17 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.16 (0.17), residues: 2352 helix: 0.50 (0.27), residues: 408 sheet: 0.59 (0.18), residues: 765 loop : -0.28 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 69 HIS 0.006 0.001 HIS K 35 PHE 0.024 0.002 PHE A 53 TYR 0.010 0.002 TYR F 638 ARG 0.005 0.000 ARG L 30 *********************** 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 267 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 254 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 ARG cc_start: 0.8579 (mtp-110) cc_final: 0.7439 (mtm110) REVERT: G 75 ILE cc_start: 0.8202 (pt) cc_final: 0.7959 (pp) REVERT: I 75 ILE cc_start: 0.8316 (pt) cc_final: 0.7933 (pp) outliers start: 13 outliers final: 11 residues processed: 267 average time/residue: 1.2680 time to fit residues: 385.2610 Evaluate side-chains 246 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 235 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain K residue 11 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 0.9980 chunk 179 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 185 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 215 optimal weight: 0.0270 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 137 ASN ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN E 67 ASN E 137 ASN F 591 GLN F 651 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: 0.8355 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20337 Z= 0.221 Angle : 0.604 10.625 27603 Z= 0.308 Chirality : 0.045 0.286 3351 Planarity : 0.004 0.077 3402 Dihedral : 9.432 69.635 4370 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.59 % Allowed : 9.93 % Favored : 87.48 % 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: 0.70 (0.18), residues: 2352 helix: 1.04 (0.27), residues: 405 sheet: 0.79 (0.18), residues: 795 loop : 0.13 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 427 HIS 0.004 0.001 HIS H 90 PHE 0.015 0.002 PHE E 53 TYR 0.012 0.001 TYR J 49 ARG 0.006 0.000 ARG H 30 *********************** 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 317 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 263 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 542 ARG cc_start: 0.8593 (mtp-110) cc_final: 0.7571 (mtm110) REVERT: B 658 GLN cc_start: 0.7052 (OUTLIER) cc_final: 0.6846 (tm-30) REVERT: C 103 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: E 103 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7763 (tt0) REVERT: E 327 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.8005 (ptt-90) REVERT: I 12 LYS cc_start: 0.7012 (OUTLIER) cc_final: 0.6545 (mmtt) REVERT: L 79 GLN cc_start: 0.5482 (OUTLIER) cc_final: 0.4952 (tp40) outliers start: 54 outliers final: 23 residues processed: 296 average time/residue: 1.2717 time to fit residues: 428.2415 Evaluate side-chains 272 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 243 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 119 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 179 optimal weight: 9.9990 chunk 146 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 232 optimal weight: 8.9990 chunk 192 optimal weight: 7.9990 chunk 213 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 172 optimal weight: 20.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 137 ASN D 543 ASN D 611 ASN E 137 ASN E 315 GLN E 422 GLN G 76 ASN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN K 76 ASN ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 20337 Z= 0.377 Angle : 0.678 8.418 27603 Z= 0.344 Chirality : 0.048 0.293 3351 Planarity : 0.005 0.065 3402 Dihedral : 8.351 58.232 4361 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.60 % Allowed : 10.55 % Favored : 85.85 % 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: 0.55 (0.17), residues: 2352 helix: 0.85 (0.26), residues: 405 sheet: 0.67 (0.18), residues: 771 loop : 0.10 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 427 HIS 0.005 0.001 HIS E 72 PHE 0.016 0.002 PHE E 383 TYR 0.017 0.002 TYR E 384 ARG 0.004 0.001 ARG A 298 *********************** 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 331 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 256 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9149 (t) cc_final: 0.8932 (t) REVERT: A 66 HIS cc_start: 0.6489 (OUTLIER) cc_final: 0.6187 (m90) REVERT: A 103 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: A 178 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7881 (tpt170) REVERT: A 502 LYS cc_start: 0.8168 (ttpt) cc_final: 0.7727 (tttt) REVERT: B 530 MET cc_start: 0.8772 (mtp) cc_final: 0.8510 (mtp) REVERT: B 542 ARG cc_start: 0.8615 (mtp-110) cc_final: 0.7684 (mtt90) REVERT: C 103 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7746 (tt0) REVERT: C 173 TYR cc_start: 0.8858 (p90) cc_final: 0.8648 (p90) REVERT: E 95 MET cc_start: 0.9101 (ptm) cc_final: 0.8809 (ptm) REVERT: E 97 LYS cc_start: 0.8542 (mmpt) cc_final: 0.8078 (mptt) REVERT: E 103 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: E 178 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7887 (tpt170) REVERT: E 327 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7940 (ptt-90) REVERT: E 412 ASP cc_start: 0.8258 (p0) cc_final: 0.8023 (p0) REVERT: H 79 GLN cc_start: 0.5329 (OUTLIER) cc_final: 0.4683 (tp40) REVERT: L 79 GLN cc_start: 0.5436 (OUTLIER) cc_final: 0.5074 (tp40) outliers start: 75 outliers final: 32 residues processed: 299 average time/residue: 1.2394 time to fit residues: 422.1189 Evaluate side-chains 284 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 243 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 chunk 229 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 137 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 137 ASN C 422 GLN D 611 ASN E 136 ASN E 137 ASN E 315 GLN E 352 HIS F 611 ASN F 651 ASN G 76 ASN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN J 45 ASN K 76 ASN ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20337 Z= 0.285 Angle : 0.614 12.389 27603 Z= 0.314 Chirality : 0.046 0.292 3351 Planarity : 0.004 0.057 3402 Dihedral : 7.572 58.021 4361 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.88 % Allowed : 11.27 % Favored : 84.84 % 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: 0.65 (0.17), residues: 2352 helix: 0.93 (0.26), residues: 405 sheet: 0.74 (0.18), residues: 795 loop : 0.15 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 427 HIS 0.003 0.001 HIS A 85 PHE 0.014 0.002 PHE A 383 TYR 0.015 0.002 TYR A 318 ARG 0.003 0.000 ARG E 178 *********************** 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 336 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 255 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8917 (t) REVERT: A 103 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: A 178 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7889 (tpt170) REVERT: A 501 CYS cc_start: 0.7572 (OUTLIER) cc_final: 0.6953 (p) REVERT: A 502 LYS cc_start: 0.7765 (ttpt) cc_final: 0.7359 (tttt) REVERT: B 542 ARG cc_start: 0.8612 (mtp-110) cc_final: 0.7679 (mtt90) REVERT: C 66 HIS cc_start: 0.6495 (OUTLIER) cc_final: 0.6216 (m90) REVERT: C 103 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: C 173 TYR cc_start: 0.8851 (p90) cc_final: 0.8643 (p90) REVERT: D 632 ASP cc_start: 0.8352 (t70) cc_final: 0.8004 (t70) REVERT: D 658 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6656 (tt0) REVERT: E 95 MET cc_start: 0.9062 (ptm) cc_final: 0.8754 (ptm) REVERT: E 97 LYS cc_start: 0.8547 (mmpt) cc_final: 0.8108 (mptt) REVERT: E 103 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7726 (tt0) REVERT: E 178 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7892 (tpt170) REVERT: E 327 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7953 (ptt-90) REVERT: E 412 ASP cc_start: 0.8189 (p0) cc_final: 0.7910 (p0) REVERT: F 530 MET cc_start: 0.8720 (mtp) cc_final: 0.8515 (mtp) REVERT: F 637 ASN cc_start: 0.5904 (OUTLIER) cc_final: 0.5629 (p0) REVERT: H 79 GLN cc_start: 0.5209 (OUTLIER) cc_final: 0.4614 (tp40) REVERT: J 1 ASP cc_start: 0.5528 (OUTLIER) cc_final: 0.4656 (t0) REVERT: L 79 GLN cc_start: 0.5397 (OUTLIER) cc_final: 0.5055 (tp40) outliers start: 81 outliers final: 38 residues processed: 307 average time/residue: 1.2451 time to fit residues: 435.2791 Evaluate side-chains 296 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 244 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain J residue 1 ASP Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 195 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 57 optimal weight: 0.0970 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 137 ASN B 543 ASN B 658 GLN C 136 ASN C 137 ASN D 590 GLN D 611 ASN E 136 ASN E 137 ASN F 611 ASN F 651 ASN G 76 ASN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN L 45 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 20337 Z= 0.351 Angle : 0.657 12.782 27603 Z= 0.334 Chirality : 0.048 0.298 3351 Planarity : 0.004 0.054 3402 Dihedral : 7.443 56.901 4361 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.84 % Allowed : 12.09 % Favored : 84.08 % 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: 0.55 (0.17), residues: 2352 helix: 0.79 (0.26), residues: 408 sheet: 0.73 (0.18), residues: 771 loop : 0.07 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 427 HIS 0.006 0.001 HIS L 90 PHE 0.017 0.002 PHE E 383 TYR 0.017 0.002 TYR E 384 ARG 0.004 0.000 ARG E 178 *********************** 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 336 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 256 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8930 (t) REVERT: A 103 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: A 178 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7896 (tpt170) REVERT: A 502 LYS cc_start: 0.7960 (ttpt) cc_final: 0.7549 (tttt) REVERT: B 542 ARG cc_start: 0.8613 (mtp-110) cc_final: 0.7692 (mtm110) REVERT: B 655 LYS cc_start: 0.7245 (mtmt) cc_final: 0.5707 (pttt) REVERT: C 103 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: C 173 TYR cc_start: 0.8834 (p90) cc_final: 0.8626 (p90) REVERT: C 327 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7792 (ptt-90) REVERT: D 632 ASP cc_start: 0.8337 (t70) cc_final: 0.8063 (t70) REVERT: D 658 GLN cc_start: 0.7135 (OUTLIER) cc_final: 0.6606 (tt0) REVERT: E 95 MET cc_start: 0.9089 (ptm) cc_final: 0.8735 (ptm) REVERT: E 97 LYS cc_start: 0.8524 (mmpt) cc_final: 0.8114 (mptt) REVERT: E 103 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: E 178 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7906 (tpt170) REVERT: E 327 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7973 (ptt-90) REVERT: F 637 ASN cc_start: 0.6245 (OUTLIER) cc_final: 0.6043 (p0) REVERT: H 79 GLN cc_start: 0.5326 (OUTLIER) cc_final: 0.4692 (tp40) REVERT: J 1 ASP cc_start: 0.5556 (OUTLIER) cc_final: 0.4599 (t0) REVERT: L 79 GLN cc_start: 0.5431 (OUTLIER) cc_final: 0.5078 (tp40) outliers start: 80 outliers final: 43 residues processed: 304 average time/residue: 1.2333 time to fit residues: 427.9492 Evaluate side-chains 305 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 249 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain J residue 1 ASP Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 79 GLN 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: 0.9990 chunk 45 optimal weight: 0.8980 chunk 134 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 229 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 136 ASN A 137 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 137 ASN D 611 ASN E 136 ASN E 137 ASN E 315 GLN F 611 ASN G 76 ASN I 76 ASN J 45 ASN K 76 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20337 Z= 0.207 Angle : 0.559 10.468 27603 Z= 0.287 Chirality : 0.044 0.289 3351 Planarity : 0.004 0.051 3402 Dihedral : 6.721 55.464 4361 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.97 % Allowed : 13.81 % Favored : 83.21 % 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: 0.80 (0.18), residues: 2352 helix: 1.28 (0.27), residues: 390 sheet: 0.84 (0.18), residues: 795 loop : 0.15 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 427 HIS 0.007 0.001 HIS H 90 PHE 0.014 0.001 PHE E 383 TYR 0.012 0.001 TYR A 318 ARG 0.002 0.000 ARG H 30 *********************** 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 316 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 254 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8892 (t) REVERT: A 103 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: A 444 ARG cc_start: 0.8275 (ttt-90) cc_final: 0.8046 (ttt-90) REVERT: A 502 LYS cc_start: 0.7373 (ttpt) cc_final: 0.7033 (tttt) REVERT: B 542 ARG cc_start: 0.8590 (mtp-110) cc_final: 0.7682 (mtt90) REVERT: B 655 LYS cc_start: 0.7221 (mtmt) cc_final: 0.5622 (pttt) REVERT: C 103 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: C 327 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7750 (ptt-90) REVERT: C 412 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7528 (p0) REVERT: D 632 ASP cc_start: 0.8357 (t70) cc_final: 0.8075 (t0) REVERT: D 658 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6627 (tt0) REVERT: E 95 MET cc_start: 0.9068 (ptm) cc_final: 0.8722 (ptm) REVERT: E 97 LYS cc_start: 0.8503 (mmpt) cc_final: 0.8108 (mptt) REVERT: E 103 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: E 141 ASP cc_start: 0.7828 (p0) cc_final: 0.7606 (p0) REVERT: E 178 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7904 (tpt170) REVERT: E 246 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7230 (tm-30) REVERT: E 327 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7899 (ptt-90) REVERT: H 79 GLN cc_start: 0.5319 (OUTLIER) cc_final: 0.4788 (tp40) REVERT: J 1 ASP cc_start: 0.5495 (OUTLIER) cc_final: 0.4512 (OUTLIER) REVERT: J 20 THR cc_start: 0.7299 (m) cc_final: 0.6740 (p) REVERT: L 79 GLN cc_start: 0.5438 (OUTLIER) cc_final: 0.5182 (tp40) outliers start: 62 outliers final: 34 residues processed: 295 average time/residue: 1.3545 time to fit residues: 451.0823 Evaluate side-chains 294 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 248 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain J residue 1 ASP Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 228 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 105 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 137 ASN B 658 GLN C 136 ASN C 137 ASN E 136 ASN E 137 ASN E 315 GLN F 651 ASN G 76 ASN I 76 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 20337 Z= 0.317 Angle : 0.631 12.045 27603 Z= 0.322 Chirality : 0.047 0.297 3351 Planarity : 0.004 0.050 3402 Dihedral : 6.926 58.518 4361 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.36 % Allowed : 13.57 % Favored : 83.07 % 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: 0.62 (0.17), residues: 2352 helix: 0.84 (0.26), residues: 408 sheet: 0.78 (0.18), residues: 771 loop : 0.11 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 427 HIS 0.006 0.001 HIS H 90 PHE 0.016 0.002 PHE A 383 TYR 0.016 0.002 TYR A 318 ARG 0.004 0.000 ARG A 178 *********************** 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 321 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 251 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8912 (t) REVERT: A 103 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: A 444 ARG cc_start: 0.8325 (ttt-90) cc_final: 0.8115 (ttt-90) REVERT: A 501 CYS cc_start: 0.7523 (OUTLIER) cc_final: 0.6881 (p) REVERT: A 502 LYS cc_start: 0.7682 (ttpt) cc_final: 0.7288 (tttt) REVERT: B 542 ARG cc_start: 0.8586 (mtp-110) cc_final: 0.7684 (mtt90) REVERT: B 655 LYS cc_start: 0.7259 (mtmt) cc_final: 0.5685 (pttt) REVERT: C 103 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: C 327 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7793 (ptt-90) REVERT: D 632 ASP cc_start: 0.8351 (t70) cc_final: 0.8101 (t70) REVERT: D 658 GLN cc_start: 0.7180 (OUTLIER) cc_final: 0.6646 (tt0) REVERT: E 95 MET cc_start: 0.9090 (ptm) cc_final: 0.8742 (ptm) REVERT: E 97 LYS cc_start: 0.8510 (mmpt) cc_final: 0.8104 (mptt) REVERT: E 103 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7712 (tt0) REVERT: E 141 ASP cc_start: 0.7859 (p0) cc_final: 0.7654 (p0) REVERT: E 178 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7935 (tpt170) REVERT: E 246 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7271 (tm-30) REVERT: E 327 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7940 (ptt-90) REVERT: H 79 GLN cc_start: 0.5350 (OUTLIER) cc_final: 0.4800 (tp40) REVERT: J 20 THR cc_start: 0.7310 (m) cc_final: 0.6795 (p) REVERT: L 79 GLN cc_start: 0.5412 (OUTLIER) cc_final: 0.5114 (tp40) outliers start: 70 outliers final: 43 residues processed: 295 average time/residue: 1.2983 time to fit residues: 434.4902 Evaluate side-chains 304 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 249 time to evaluate : 2.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP 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 501 CYS Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 179 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 137 ASN B 658 GLN C 136 ASN C 137 ASN E 136 ASN E 137 ASN E 315 GLN G 76 ASN H 3 GLN I 76 ASN J 45 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20337 Z= 0.206 Angle : 0.560 11.050 27603 Z= 0.288 Chirality : 0.044 0.287 3351 Planarity : 0.004 0.049 3402 Dihedral : 6.408 58.960 4361 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.12 % Allowed : 14.05 % Favored : 82.83 % 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: 1.06 (0.26), residues: 408 sheet: 0.85 (0.18), residues: 789 loop : 0.18 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 427 HIS 0.006 0.001 HIS H 90 PHE 0.013 0.001 PHE A 383 TYR 0.012 0.001 TYR A 318 ARG 0.003 0.000 ARG F 585 *********************** 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 326 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 261 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8931 (t) REVERT: A 103 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7752 (tt0) REVERT: B 542 ARG cc_start: 0.8564 (mtp-110) cc_final: 0.7676 (mtt90) REVERT: B 655 LYS cc_start: 0.7213 (mtmt) cc_final: 0.5546 (pttm) REVERT: C 103 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7727 (tt0) REVERT: C 327 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7776 (ptt-90) REVERT: D 542 ARG cc_start: 0.8216 (mtm-85) cc_final: 0.7977 (mtt90) REVERT: D 632 ASP cc_start: 0.8344 (t70) cc_final: 0.8066 (t0) REVERT: D 658 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.6599 (tt0) REVERT: E 95 MET cc_start: 0.9073 (ptm) cc_final: 0.8751 (ptm) REVERT: E 97 LYS cc_start: 0.8493 (mmpt) cc_final: 0.8109 (mptt) REVERT: E 178 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7893 (tpt170) REVERT: E 246 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7231 (tm-30) REVERT: E 327 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7896 (ptt-90) REVERT: H 79 GLN cc_start: 0.5342 (OUTLIER) cc_final: 0.4778 (tp40) REVERT: L 20 THR cc_start: 0.7387 (m) cc_final: 0.6994 (p) REVERT: L 79 GLN cc_start: 0.5410 (OUTLIER) cc_final: 0.5111 (tp40) outliers start: 65 outliers final: 44 residues processed: 301 average time/residue: 1.2960 time to fit residues: 442.3147 Evaluate side-chains 310 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 256 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 325 ASP 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 501 CYS Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 6.9990 chunk 199 optimal weight: 0.7980 chunk 212 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 65 optimal weight: 0.0770 chunk 192 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 137 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 137 ASN E 136 ASN E 137 ASN E 315 GLN F 651 ASN G 76 ASN I 76 ASN L 70 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 20337 Z= 0.323 Angle : 0.637 12.410 27603 Z= 0.324 Chirality : 0.047 0.293 3351 Planarity : 0.004 0.049 3402 Dihedral : 6.675 58.859 4361 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.93 % Allowed : 14.39 % Favored : 82.69 % 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: 0.61 (0.17), residues: 2352 helix: 0.84 (0.26), residues: 408 sheet: 0.77 (0.18), residues: 771 loop : 0.11 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 50 HIS 0.006 0.001 HIS H 90 PHE 0.016 0.002 PHE A 383 TYR 0.016 0.002 TYR E 384 ARG 0.004 0.000 ARG A 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 308 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 247 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8912 (t) REVERT: A 103 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: B 542 ARG cc_start: 0.8577 (mtp-110) cc_final: 0.7677 (mtt90) REVERT: B 655 LYS cc_start: 0.7271 (mtmt) cc_final: 0.5672 (pttt) REVERT: C 103 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: C 327 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7769 (ptt-90) REVERT: D 542 ARG cc_start: 0.8240 (mtm-85) cc_final: 0.7963 (mtt90) REVERT: D 632 ASP cc_start: 0.8356 (t70) cc_final: 0.8096 (t0) REVERT: D 658 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6626 (tt0) REVERT: E 95 MET cc_start: 0.9093 (ptm) cc_final: 0.8729 (ptm) REVERT: E 97 LYS cc_start: 0.8511 (mmpt) cc_final: 0.8108 (mptt) REVERT: E 103 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: E 178 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7939 (tpt170) REVERT: E 246 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7253 (tm-30) REVERT: E 327 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7925 (ptt-90) REVERT: H 79 GLN cc_start: 0.5372 (OUTLIER) cc_final: 0.4832 (tp40) REVERT: H 90 HIS cc_start: 0.6711 (OUTLIER) cc_final: 0.5264 (p-80) REVERT: L 79 GLN cc_start: 0.5353 (OUTLIER) cc_final: 0.5058 (tp40) outliers start: 61 outliers final: 44 residues processed: 285 average time/residue: 1.2639 time to fit residues: 408.2153 Evaluate side-chains 302 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 246 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 90 HIS Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 156 optimal weight: 0.5980 chunk 236 optimal weight: 0.5980 chunk 217 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 137 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 137 ASN E 136 ASN E 137 ASN E 315 GLN F 658 GLN G 76 ASN H 3 GLN I 76 ASN J 45 ASN L 3 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20337 Z= 0.193 Angle : 0.555 10.464 27603 Z= 0.285 Chirality : 0.044 0.283 3351 Planarity : 0.004 0.048 3402 Dihedral : 6.088 55.108 4361 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.78 % Allowed : 14.72 % Favored : 82.49 % 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: 0.73 (0.18), residues: 2352 helix: 1.06 (0.26), residues: 408 sheet: 0.87 (0.18), residues: 756 loop : 0.12 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 50 HIS 0.006 0.001 HIS H 90 PHE 0.013 0.001 PHE A 383 TYR 0.011 0.001 TYR A 40 ARG 0.005 0.000 ARG A 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 304 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 246 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: B 542 ARG cc_start: 0.8648 (mtp-110) cc_final: 0.7677 (mtt90) REVERT: B 655 LYS cc_start: 0.7188 (mtmt) cc_final: 0.5545 (pttm) REVERT: C 103 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7711 (tt0) REVERT: C 327 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7744 (ptt-90) REVERT: D 542 ARG cc_start: 0.8220 (mtm-85) cc_final: 0.7955 (mtt90) REVERT: D 632 ASP cc_start: 0.8361 (t70) cc_final: 0.8082 (t0) REVERT: D 658 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6574 (tt0) REVERT: E 95 MET cc_start: 0.9075 (ptm) cc_final: 0.8716 (ptm) REVERT: E 97 LYS cc_start: 0.8481 (mmpt) cc_final: 0.8096 (mptt) REVERT: E 246 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7210 (tm-30) REVERT: E 327 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7868 (ptt-90) REVERT: H 79 GLN cc_start: 0.5395 (OUTLIER) cc_final: 0.4855 (tp40) REVERT: H 90 HIS cc_start: 0.6583 (OUTLIER) cc_final: 0.5103 (p-80) REVERT: L 79 GLN cc_start: 0.5335 (OUTLIER) cc_final: 0.5034 (tp40) outliers start: 58 outliers final: 37 residues processed: 285 average time/residue: 1.2850 time to fit residues: 417.2639 Evaluate side-chains 286 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 240 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 90 HIS Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 0.0070 chunk 173 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 137 ASN D 651 ASN E 136 ASN E 137 ASN I 76 ASN J 3 GLN K 76 ASN L 3 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.174890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.127519 restraints weight = 21413.836| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.97 r_work: 0.3328 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20337 Z= 0.290 Angle : 0.618 11.905 27603 Z= 0.315 Chirality : 0.046 0.285 3351 Planarity : 0.004 0.048 3402 Dihedral : 6.264 57.424 4361 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.54 % Allowed : 15.01 % Favored : 82.45 % 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: 0.71 (0.18), residues: 2352 helix: 0.89 (0.26), residues: 408 sheet: 0.82 (0.18), residues: 795 loop : 0.19 (0.19), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 50 HIS 0.006 0.001 HIS H 90 PHE 0.017 0.002 PHE A 383 TYR 0.015 0.002 TYR A 318 ARG 0.005 0.000 ARG A 444 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7450.73 seconds wall clock time: 133 minutes 51.31 seconds (8031.31 seconds total)