Starting phenix.real_space_refine on Sat Feb 17 14:13:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x97_22103/02_2024/6x97_22103.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x97_22103/02_2024/6x97_22103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x97_22103/02_2024/6x97_22103.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x97_22103/02_2024/6x97_22103.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x97_22103/02_2024/6x97_22103.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x97_22103/02_2024/6x97_22103.pdb" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.070 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 11862 2.51 5 N 3171 2.21 5 O 3711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 87": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "G PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 95": "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: 18873 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3373 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 4 Chain: "B" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 938 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "H" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 804 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "C" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3373 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 4 Chain: "D" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 938 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "E" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "F" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 804 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "G" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3373 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 4 Chain: "I" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 938 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "J" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "K" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 804 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} 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: 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: "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: "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: 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: "S" 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: "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: "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: "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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "G" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 9.79, per 1000 atoms: 0.52 Number of scatterers: 18873 At special positions: 0 Unit cell: (145.41, 158.51, 115.28, 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 3711 8.00 N 3171 7.00 C 11862 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=2.12 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 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=2.04 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=2.05 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=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.06 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.10 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.07 Simple disulfide: pdb=" SG CYS H 35A" - pdb=" SG CYS H 50 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.12 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=2.04 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=2.05 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=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.06 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.10 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.07 Simple disulfide: pdb=" SG CYS E 35A" - pdb=" SG CYS E 50 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.12 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.05 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.02 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.06 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS I 605 " distance=2.10 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.07 Simple disulfide: pdb=" SG CYS J 35A" - pdb=" SG CYS J 50 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " 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-ASN " NAG A 608 " - " ASN A 332 " " NAG A 611 " - " ASN A 234 " " NAG A 612 " - " ASN A 386 " " NAG A 613 " - " ASN A 156 " " NAG A 614 " - " ASN A 160 " " NAG A 615 " - " ASN A 392 " " NAG A 616 " - " ASN A 197 " " NAG A 619 " - " ASN A 339 " " NAG A 620 " - " ASN A 133 " " NAG C 608 " - " ASN C 332 " " NAG C 611 " - " ASN C 234 " " NAG C 612 " - " ASN C 386 " " NAG C 613 " - " ASN C 156 " " NAG C 614 " - " ASN C 160 " " NAG C 615 " - " ASN C 392 " " NAG C 616 " - " ASN C 197 " " NAG C 619 " - " ASN C 339 " " NAG C 620 " - " ASN C 133 " " NAG G 608 " - " ASN G 332 " " NAG G 611 " - " ASN G 234 " " NAG G 612 " - " ASN G 386 " " NAG G 613 " - " ASN G 156 " " NAG G 614 " - " ASN G 160 " " NAG G 615 " - " ASN G 392 " " NAG G 616 " - " ASN G 197 " " NAG G 619 " - " ASN G 339 " " NAG G 620 " - " ASN G 133 " " NAG M 1 " - " ASN A 448 " " NAG N 1 " - " ASN A 262 " " NAG O 1 " - " ASN A 295 " " NAG P 1 " - " ASN A 88 " " NAG Q 1 " - " ASN A 363 " " NAG R 1 " - " ASN C 448 " " NAG S 1 " - " ASN C 262 " " NAG T 1 " - " ASN C 295 " " NAG U 1 " - " ASN C 88 " " NAG V 1 " - " ASN C 363 " " NAG W 1 " - " ASN G 448 " " NAG X 1 " - " ASN G 262 " " NAG Y 1 " - " ASN G 295 " " NAG Z 1 " - " ASN G 88 " " NAG a 1 " - " ASN G 363 " Time building additional restraints: 7.77 Conformation dependent library (CDL) restraints added in 3.2 seconds 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4260 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 48 sheets defined 19.3% alpha, 42.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.079A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 335 through 351 removed outlier: 4.008A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 541 removed outlier: 3.655A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 4.016A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 626 removed outlier: 4.613A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 652 removed outlier: 3.542A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.079A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 351 removed outlier: 4.008A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 480 Processing helix chain 'C' and resid 481 through 483 No H-bonds generated for 'chain 'C' and resid 481 through 483' Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 541 removed outlier: 3.655A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 596 removed outlier: 4.016A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'D' and resid 618 through 626 removed outlier: 4.613A pdb=" N ASP D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 652 removed outlier: 3.542A pdb=" N GLN D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'G' and resid 98 through 117 removed outlier: 4.079A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 139 through 151 Processing helix chain 'G' and resid 335 through 351 removed outlier: 4.007A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 475 through 480 Processing helix chain 'G' and resid 481 through 483 No H-bonds generated for 'chain 'G' and resid 481 through 483' Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 541 removed outlier: 3.654A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 569 through 596 removed outlier: 4.016A pdb=" N LYS I 574 " --> pdb=" O VAL I 570 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLN I 575 " --> pdb=" O TRP I 571 " (cutoff:3.500A) Processing helix chain 'I' and resid 611 through 615 Processing helix chain 'I' and resid 618 through 626 removed outlier: 4.613A pdb=" N ASP I 624 " --> pdb=" O SER I 620 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 652 removed outlier: 3.542A pdb=" N GLN I 650 " --> pdb=" O LEU I 646 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.314A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.887A 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 200 through 203 removed outlier: 6.072A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 256 through 257 removed outlier: 3.617A pdb=" N SER A 375 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.509A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.542A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.078A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 274 Processing sheet with id=AB1, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.921A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP A 322 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.518A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG H 56 " --> pdb=" O PHE H 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.603A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N SER H 96 " --> pdb=" O GLY H 100E" (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLY H 100E" --> pdb=" O SER H 96 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR H 98 " --> pdb=" O GLY H 100C" (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLY H 100C" --> pdb=" O THR H 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.553A pdb=" N VAL L 11 " --> pdb=" O VAL L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.541A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.314A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.886A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC4, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.072A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 256 through 257 removed outlier: 3.618A pdb=" N SER C 375 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.508A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.542A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 259 through 261 Processing sheet with id=AC7, first strand: chain 'C' and resid 271 through 274 Processing sheet with id=AC8, first strand: chain 'C' and resid 315 through 323A removed outlier: 6.921A pdb=" N ALA C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE C 309 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP C 322 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.517A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG E 56 " --> pdb=" O PHE E 52 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.604A pdb=" N LEU E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N SER E 96 " --> pdb=" O GLY E 100E" (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLY E 100E" --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR E 98 " --> pdb=" O GLY E 100C" (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLY E 100C" --> pdb=" O THR E 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AD4, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.553A pdb=" N VAL F 11 " --> pdb=" O VAL F 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.540A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 494 through 499 removed outlier: 5.314A pdb=" N VAL I 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL G 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR I 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N TYR G 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N CYS I 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AD8, first strand: chain 'G' and resid 75 through 76 removed outlier: 6.887A pdb=" N CYS G 54 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AE1, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AE2, first strand: chain 'G' and resid 200 through 203 removed outlier: 6.072A pdb=" N ALA G 200 " --> pdb=" O ALA G 433 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYR G 435 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 256 through 257 removed outlier: 3.618A pdb=" N SER G 375 " --> pdb=" O THR G 257 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.508A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.542A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 259 through 261 Processing sheet with id=AE5, first strand: chain 'G' and resid 271 through 274 Processing sheet with id=AE6, first strand: chain 'G' and resid 315 through 323A removed outlier: 6.921A pdb=" N ALA G 316 " --> pdb=" O ILE G 309 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE G 309 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N TYR G 318 " --> pdb=" O ILE G 307 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE G 307 " --> pdb=" O TYR G 318 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N THR G 320 " --> pdb=" O LYS G 305 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS G 305 " --> pdb=" O THR G 320 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP G 322 " --> pdb=" O THR G 303 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.518A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG J 56 " --> pdb=" O PHE J 52 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.603A pdb=" N LEU J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N SER J 96 " --> pdb=" O GLY J 100E" (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLY J 100E" --> pdb=" O SER J 96 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR J 98 " --> pdb=" O GLY J 100C" (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLY J 100C" --> pdb=" O THR J 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AF2, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.553A pdb=" N VAL K 11 " --> pdb=" O VAL K 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.540A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 690 hydrogen bonds defined for protein. 1800 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: 7.43 Time building geometry restraints manager: 8.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3809 1.32 - 1.46: 6249 1.46 - 1.59: 8957 1.59 - 1.73: 80 1.73 - 1.87: 162 Bond restraints: 19257 Sorted by residual: bond pdb=" CB ILE L 2 " pdb=" CG1 ILE L 2 " ideal model delta sigma weight residual 1.530 1.669 -0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" CB ILE F 2 " pdb=" CG1 ILE F 2 " ideal model delta sigma weight residual 1.530 1.669 -0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" CB ILE K 2 " pdb=" CG1 ILE K 2 " ideal model delta sigma weight residual 1.530 1.669 -0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" CB HIS C 85 " pdb=" CG HIS C 85 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.06e+01 bond pdb=" CB HIS A 85 " pdb=" CG HIS A 85 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.06e+01 ... (remaining 19252 not shown) Histogram of bond angle deviations from ideal: 100.23 - 107.08: 1003 107.08 - 113.93: 10372 113.93 - 120.78: 8510 120.78 - 127.63: 6049 127.63 - 134.48: 223 Bond angle restraints: 26157 Sorted by residual: angle pdb=" N VAL L 3 " pdb=" CA VAL L 3 " pdb=" C VAL L 3 " ideal model delta sigma weight residual 111.62 118.48 -6.86 7.90e-01 1.60e+00 7.55e+01 angle pdb=" N VAL F 3 " pdb=" CA VAL F 3 " pdb=" C VAL F 3 " ideal model delta sigma weight residual 111.62 118.47 -6.85 7.90e-01 1.60e+00 7.52e+01 angle pdb=" N VAL K 3 " pdb=" CA VAL K 3 " pdb=" C VAL K 3 " ideal model delta sigma weight residual 111.62 118.47 -6.85 7.90e-01 1.60e+00 7.52e+01 angle pdb=" C ARG G 298 " pdb=" N PRO G 299 " pdb=" CA PRO G 299 " ideal model delta sigma weight residual 119.56 127.63 -8.07 1.01e+00 9.80e-01 6.38e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.62 -8.06 1.01e+00 9.80e-01 6.37e+01 ... (remaining 26152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.18: 11865 21.18 - 42.36: 234 42.36 - 63.54: 90 63.54 - 84.72: 51 84.72 - 105.90: 15 Dihedral angle restraints: 12255 sinusoidal: 5622 harmonic: 6633 Sorted by residual: dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 173.70 -80.70 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CB CYS G 228 " pdb=" SG CYS G 228 " pdb=" SG CYS G 239 " pdb=" CB CYS G 239 " ideal model delta sinusoidal sigma weight residual 93.00 173.70 -80.70 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CB CYS C 228 " pdb=" SG CYS C 228 " pdb=" SG CYS C 239 " pdb=" CB CYS C 239 " ideal model delta sinusoidal sigma weight residual 93.00 173.69 -80.69 1 1.00e+01 1.00e-02 8.05e+01 ... (remaining 12252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2091 0.105 - 0.210: 694 0.210 - 0.315: 187 0.315 - 0.420: 107 0.420 - 0.525: 47 Chirality restraints: 3126 Sorted by residual: chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.17e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 BMA X 3 " pdb=" O4 NAG X 2 " pdb=" C2 BMA X 3 " pdb=" O5 BMA X 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.14e+02 ... (remaining 3123 not shown) Planarity restraints: 3285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 339 " 0.086 2.00e-02 2.50e+03 8.83e-02 9.76e+01 pdb=" CG ASN A 339 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN A 339 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN A 339 " -0.135 2.00e-02 2.50e+03 pdb=" C1 NAG A 619 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 339 " -0.086 2.00e-02 2.50e+03 8.83e-02 9.75e+01 pdb=" CG ASN C 339 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN C 339 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN C 339 " 0.135 2.00e-02 2.50e+03 pdb=" C1 NAG C 619 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 339 " 0.085 2.00e-02 2.50e+03 8.81e-02 9.70e+01 pdb=" CG ASN G 339 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN G 339 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN G 339 " -0.135 2.00e-02 2.50e+03 pdb=" C1 NAG G 619 " 0.107 2.00e-02 2.50e+03 ... (remaining 3282 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 9760 2.98 - 3.46: 16783 3.46 - 3.94: 31799 3.94 - 4.42: 36193 4.42 - 4.90: 56800 Nonbonded interactions: 151335 Sorted by model distance: nonbonded pdb=" N THR C 50 " pdb=" O THR C 50 " model vdw 2.496 2.496 nonbonded pdb=" N THR A 50 " pdb=" O THR A 50 " model vdw 2.496 2.496 nonbonded pdb=" N THR G 50 " pdb=" O THR G 50 " model vdw 2.496 2.496 nonbonded pdb=" N THR C 303 " pdb=" O THR C 303 " model vdw 2.508 2.496 nonbonded pdb=" N THR A 303 " pdb=" O THR A 303 " model vdw 2.508 2.496 ... (remaining 151330 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 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'S' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 0.010 Extract box with map and model: 8.550 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 51.800 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 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 : 0.022 0.139 19257 Z= 1.411 Angle : 1.768 15.917 26157 Z= 1.161 Chirality : 0.138 0.525 3126 Planarity : 0.009 0.044 3243 Dihedral : 11.601 105.896 7869 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 0.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.30 % Allowed : 0.30 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.36 (0.17), residues: 2265 helix: -0.76 (0.25), residues: 342 sheet: 0.52 (0.19), residues: 672 loop : 0.54 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.011 TRP I 628 HIS 0.010 0.003 HIS G 72 PHE 0.031 0.007 PHE C 383 TYR 0.078 0.010 TYR I 638 ARG 0.007 0.001 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 534 time to evaluate : 2.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7774 (m-40) REVERT: A 427 TRP cc_start: 0.7051 (m-10) cc_final: 0.6623 (m-10) REVERT: B 586 TYR cc_start: 0.8766 (t80) cc_final: 0.8546 (t80) REVERT: B 627 THR cc_start: 0.8108 (m) cc_final: 0.7764 (p) REVERT: B 628 TRP cc_start: 0.8452 (t-100) cc_final: 0.8007 (t-100) REVERT: B 657 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7777 (mt-10) REVERT: H 45 LEU cc_start: 0.7735 (mt) cc_final: 0.7394 (mt) REVERT: C 133 ASN cc_start: 0.7742 (OUTLIER) cc_final: 0.7537 (m-40) REVERT: D 607 ASN cc_start: 0.8216 (m-40) cc_final: 0.7968 (m110) REVERT: D 627 THR cc_start: 0.7876 (m) cc_final: 0.7375 (p) REVERT: D 628 TRP cc_start: 0.8389 (t-100) cc_final: 0.8140 (t-100) REVERT: D 657 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7523 (mt-10) REVERT: E 45 LEU cc_start: 0.7359 (mt) cc_final: 0.6854 (mt) REVERT: E 84 VAL cc_start: 0.8679 (m) cc_final: 0.8463 (t) REVERT: G 150 MET cc_start: 0.7754 (mmm) cc_final: 0.7322 (mmm) REVERT: G 173 TYR cc_start: 0.8079 (p90) cc_final: 0.7798 (p90) REVERT: G 271 MET cc_start: 0.7796 (mmm) cc_final: 0.7571 (mmm) REVERT: G 427 TRP cc_start: 0.7025 (m-10) cc_final: 0.6654 (m-10) outliers start: 6 outliers final: 1 residues processed: 540 average time/residue: 0.3283 time to fit residues: 260.9786 Evaluate side-chains 298 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 295 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain G residue 133 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 189 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 204 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 HIS ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN B 577 GLN L 6 GLN C 130 GLN C 195 ASN C 249 HIS ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN D 630 GLN F 6 GLN G 130 GLN G 195 ASN G 249 HIS G 425 ASN ** I 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 607 ASN K 6 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19257 Z= 0.266 Angle : 0.714 8.444 26157 Z= 0.386 Chirality : 0.048 0.154 3126 Planarity : 0.004 0.035 3243 Dihedral : 8.213 70.154 3729 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.65 % Allowed : 8.86 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.29 (0.17), residues: 2265 helix: 0.59 (0.28), residues: 348 sheet: 0.34 (0.18), residues: 765 loop : 0.09 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 596 HIS 0.004 0.001 HIS G 72 PHE 0.025 0.002 PHE J 52 TYR 0.020 0.002 TYR D 643 ARG 0.005 0.001 ARG K 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 376 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 568 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7863 (tt) REVERT: H 97 ASP cc_start: 0.7847 (t0) cc_final: 0.7627 (t0) REVERT: C 39 TYR cc_start: 0.8505 (m-80) cc_final: 0.8241 (m-10) REVERT: C 271 MET cc_start: 0.7403 (mmm) cc_final: 0.7181 (mmp) REVERT: C 318 TYR cc_start: 0.7928 (m-80) cc_final: 0.7725 (m-80) REVERT: D 588 ARG cc_start: 0.8635 (tpt-90) cc_final: 0.8395 (tpp80) REVERT: D 617 ARG cc_start: 0.7494 (mtp-110) cc_final: 0.7077 (mtp-110) REVERT: D 630 GLN cc_start: 0.8281 (mt0) cc_final: 0.8051 (mt0) REVERT: D 648 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8343 (pt0) REVERT: D 651 ASN cc_start: 0.6610 (p0) cc_final: 0.6355 (p0) REVERT: E 45 LEU cc_start: 0.7535 (mt) cc_final: 0.7057 (mt) REVERT: G 150 MET cc_start: 0.7371 (mmm) cc_final: 0.7142 (mmm) REVERT: G 161 MET cc_start: 0.7037 (OUTLIER) cc_final: 0.6402 (ttm) REVERT: I 607 ASN cc_start: 0.8298 (m-40) cc_final: 0.7820 (m110) REVERT: I 610 TRP cc_start: 0.8218 (t-100) cc_final: 0.7843 (t-100) REVERT: I 617 ARG cc_start: 0.7816 (mtp-110) cc_final: 0.7464 (mtp-110) REVERT: I 625 ASN cc_start: 0.8791 (m-40) cc_final: 0.8071 (t0) REVERT: I 648 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8654 (mm-30) REVERT: I 649 SER cc_start: 0.8955 (m) cc_final: 0.8666 (t) REVERT: I 650 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8070 (tt0) outliers start: 53 outliers final: 34 residues processed: 404 average time/residue: 0.3213 time to fit residues: 193.3264 Evaluate side-chains 337 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 300 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 626 MET Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain I residue 618 ASN Chi-restraints excluded: chain I residue 627 THR Chi-restraints excluded: chain I residue 641 ILE Chi-restraints excluded: chain I residue 650 GLN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 204 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 182 optimal weight: 0.8980 chunk 202 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN L 38 GLN C 195 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN E 39 GLN F 38 GLN G 195 ASN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN K 38 GLN K 70 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19257 Z= 0.265 Angle : 0.651 9.757 26157 Z= 0.344 Chirality : 0.046 0.173 3126 Planarity : 0.004 0.040 3243 Dihedral : 6.741 46.066 3729 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.50 % Allowed : 10.01 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.18), residues: 2265 helix: 0.40 (0.28), residues: 363 sheet: 0.45 (0.19), residues: 720 loop : -0.02 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 479 HIS 0.004 0.001 HIS G 105 PHE 0.017 0.002 PHE C 376 TYR 0.019 0.002 TYR F 92 ARG 0.006 0.001 ARG G 500 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 348 time to evaluate : 2.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 ARG cc_start: 0.8312 (ttp-170) cc_final: 0.8066 (tpp80) REVERT: B 648 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8191 (pt0) REVERT: B 649 SER cc_start: 0.9317 (m) cc_final: 0.8964 (t) REVERT: B 650 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8333 (tt0) REVERT: C 39 TYR cc_start: 0.8620 (m-80) cc_final: 0.8156 (m-10) REVERT: D 542 ARG cc_start: 0.8649 (ttp-170) cc_final: 0.8261 (tpp80) REVERT: D 579 ARG cc_start: 0.7998 (mtm-85) cc_final: 0.7704 (mtm-85) REVERT: D 593 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7510 (mp) REVERT: D 617 ARG cc_start: 0.7459 (mtp-110) cc_final: 0.7076 (mtp-110) REVERT: D 630 GLN cc_start: 0.8173 (mt0) cc_final: 0.7902 (mt0) REVERT: D 634 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8642 (mm-30) REVERT: D 648 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8388 (pt0) REVERT: D 650 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8274 (tt0) REVERT: G 161 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6685 (ttm) REVERT: I 579 ARG cc_start: 0.7887 (mtm180) cc_final: 0.7657 (mtp180) REVERT: I 610 TRP cc_start: 0.8315 (t-100) cc_final: 0.7787 (t-100) REVERT: I 617 ARG cc_start: 0.7860 (mtp-110) cc_final: 0.7519 (mtp-110) REVERT: I 648 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8142 (pt0) REVERT: I 650 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.7378 (tm-30) REVERT: I 651 ASN cc_start: 0.6222 (p0) cc_final: 0.5740 (p0) REVERT: K 69 THR cc_start: 0.8774 (p) cc_final: 0.8469 (p) outliers start: 70 outliers final: 43 residues processed: 390 average time/residue: 0.3256 time to fit residues: 188.8064 Evaluate side-chains 345 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 297 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 618 ASN Chi-restraints excluded: chain I residue 650 GLN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 202 optimal weight: 0.9980 chunk 153 optimal weight: 9.9990 chunk 106 optimal weight: 0.0030 chunk 22 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 205 optimal weight: 7.9990 chunk 217 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN F 27 GLN G 195 ASN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 591 GLN ** I 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19257 Z= 0.251 Angle : 0.614 8.110 26157 Z= 0.321 Chirality : 0.045 0.195 3126 Planarity : 0.004 0.035 3243 Dihedral : 5.835 44.115 3729 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.06 % Favored : 95.81 % Rotamer: Outliers : 3.05 % Allowed : 13.16 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.14 (0.18), residues: 2265 helix: 0.42 (0.29), residues: 369 sheet: 0.51 (0.19), residues: 723 loop : -0.19 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 628 HIS 0.004 0.001 HIS G 105 PHE 0.017 0.002 PHE C 376 TYR 0.028 0.002 TYR I 586 ARG 0.002 0.000 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 316 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.6456 (mpp) cc_final: 0.6113 (mpp) REVERT: B 545 LEU cc_start: 0.8640 (tp) cc_final: 0.8403 (mt) REVERT: B 634 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8576 (mm-30) REVERT: B 648 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8132 (pt0) REVERT: B 649 SER cc_start: 0.9348 (m) cc_final: 0.8962 (t) REVERT: B 650 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: C 39 TYR cc_start: 0.8760 (m-80) cc_final: 0.8167 (m-10) REVERT: D 617 ARG cc_start: 0.7487 (mtp-110) cc_final: 0.7191 (mtp-110) REVERT: D 634 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8786 (mm-30) REVERT: D 648 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8210 (pt0) REVERT: D 650 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: G 125 LEU cc_start: 0.8662 (mt) cc_final: 0.8405 (mt) REVERT: G 161 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6559 (ttt) REVERT: I 545 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8258 (tt) REVERT: I 607 ASN cc_start: 0.8213 (m-40) cc_final: 0.7807 (m-40) REVERT: I 610 TRP cc_start: 0.8401 (t-100) cc_final: 0.7740 (t-100) REVERT: I 617 ARG cc_start: 0.7830 (mtp-110) cc_final: 0.7564 (mtp-110) REVERT: I 648 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8091 (pt0) REVERT: I 650 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: I 651 ASN cc_start: 0.5872 (p0) cc_final: 0.5646 (p0) REVERT: K 69 THR cc_start: 0.8716 (p) cc_final: 0.8407 (p) outliers start: 61 outliers final: 44 residues processed: 356 average time/residue: 0.3346 time to fit residues: 175.9083 Evaluate side-chains 332 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 283 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 618 ASN Chi-restraints excluded: chain I residue 619 LEU Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain I residue 650 GLN Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 181 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 185 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 195 optimal weight: 0.9990 chunk 54 optimal weight: 0.0870 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 70 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19257 Z= 0.198 Angle : 0.580 7.805 26157 Z= 0.301 Chirality : 0.044 0.173 3126 Planarity : 0.003 0.033 3243 Dihedral : 5.460 42.073 3729 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.89 % Favored : 95.98 % Rotamer: Outliers : 3.30 % Allowed : 13.51 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.18), residues: 2265 helix: 0.49 (0.29), residues: 363 sheet: 0.45 (0.19), residues: 756 loop : -0.21 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 628 HIS 0.003 0.001 HIS G 105 PHE 0.013 0.001 PHE A 53 TYR 0.020 0.002 TYR B 586 ARG 0.004 0.000 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 296 time to evaluate : 2.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 545 LEU cc_start: 0.8651 (tp) cc_final: 0.8374 (mt) REVERT: B 627 THR cc_start: 0.7325 (t) cc_final: 0.7051 (t) REVERT: B 648 GLU cc_start: 0.8563 (mm-30) cc_final: 0.7993 (pt0) REVERT: B 649 SER cc_start: 0.9225 (m) cc_final: 0.8900 (t) REVERT: B 650 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: C 39 TYR cc_start: 0.8678 (m-80) cc_final: 0.8123 (m-10) REVERT: D 593 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7743 (mp) REVERT: D 648 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8226 (pt0) REVERT: D 650 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: F 91 THR cc_start: 0.8451 (p) cc_final: 0.8066 (p) REVERT: G 150 MET cc_start: 0.6832 (mmm) cc_final: 0.6628 (mmm) REVERT: G 161 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6541 (ttt) REVERT: I 607 ASN cc_start: 0.8245 (m-40) cc_final: 0.7801 (m110) REVERT: I 610 TRP cc_start: 0.8387 (t-100) cc_final: 0.7711 (t-100) REVERT: I 617 ARG cc_start: 0.7805 (mtp-110) cc_final: 0.7580 (mtp-110) REVERT: I 648 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8162 (pt0) REVERT: I 650 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.7782 (tm-30) REVERT: I 656 ASN cc_start: 0.7593 (t0) cc_final: 0.7252 (t0) REVERT: J 110 THR cc_start: 0.7665 (m) cc_final: 0.7465 (m) REVERT: K 69 THR cc_start: 0.8603 (p) cc_final: 0.8289 (p) outliers start: 66 outliers final: 47 residues processed: 338 average time/residue: 0.3345 time to fit residues: 166.7988 Evaluate side-chains 316 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 264 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 628 TRP Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 618 ASN Chi-restraints excluded: chain I residue 619 LEU Chi-restraints excluded: chain I residue 641 ILE Chi-restraints excluded: chain I residue 650 GLN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 73 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 217 optimal weight: 0.3980 chunk 180 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN L 32 HIS C 183 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN D 630 GLN D 656 ASN F 32 HIS G 183 GLN ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 19257 Z= 0.553 Angle : 0.806 8.550 26157 Z= 0.419 Chirality : 0.050 0.166 3126 Planarity : 0.005 0.040 3243 Dihedral : 6.351 31.868 3727 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.70 % Favored : 94.17 % Rotamer: Outliers : 3.90 % Allowed : 14.61 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.18), residues: 2265 helix: -0.07 (0.28), residues: 375 sheet: 0.17 (0.19), residues: 765 loop : -0.78 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 479 HIS 0.009 0.002 HIS A 374 PHE 0.037 0.003 PHE A 376 TYR 0.021 0.003 TYR E 33 ARG 0.005 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 271 time to evaluate : 2.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 634 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8623 (mm-30) REVERT: B 648 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8037 (pt0) REVERT: B 649 SER cc_start: 0.9146 (m) cc_final: 0.8455 (t) REVERT: B 650 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7628 (tm-30) REVERT: H 23 LYS cc_start: 0.8871 (pttt) cc_final: 0.8661 (ptmt) REVERT: C 39 TYR cc_start: 0.8845 (m-80) cc_final: 0.8327 (m-10) REVERT: C 150 MET cc_start: 0.6576 (mmt) cc_final: 0.6153 (mmt) REVERT: D 593 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8086 (mp) REVERT: D 617 ARG cc_start: 0.7542 (mtp-110) cc_final: 0.7170 (mtp-110) REVERT: D 634 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8709 (mm-30) REVERT: D 648 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8136 (pt0) REVERT: D 650 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8192 (tt0) REVERT: D 651 ASN cc_start: 0.6069 (p0) cc_final: 0.5779 (p0) REVERT: D 656 ASN cc_start: 0.7760 (OUTLIER) cc_final: 0.7367 (m-40) REVERT: G 161 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.7008 (ttm) REVERT: I 535 MET cc_start: 0.8202 (mmm) cc_final: 0.7855 (mmm) REVERT: I 545 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8525 (tt) REVERT: I 607 ASN cc_start: 0.8461 (m-40) cc_final: 0.8031 (m110) REVERT: I 617 ARG cc_start: 0.7805 (mtp-110) cc_final: 0.7571 (mtp-110) REVERT: J 23 LYS cc_start: 0.8492 (pttm) cc_final: 0.8261 (ptmm) REVERT: J 81 MET cc_start: 0.7664 (mtt) cc_final: 0.7455 (mtt) REVERT: J 110 THR cc_start: 0.7970 (m) cc_final: 0.7754 (m) outliers start: 78 outliers final: 62 residues processed: 325 average time/residue: 0.3322 time to fit residues: 160.1017 Evaluate side-chains 321 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 253 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 628 TRP Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain D residue 656 ASN Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 618 ASN Chi-restraints excluded: chain I residue 619 LEU Chi-restraints excluded: chain I residue 641 ILE Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 77 ASP Chi-restraints excluded: chain K residue 98 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 209 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 chunk 124 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 216 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN ** D 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN F 70 GLN G 195 ASN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 ASN J 61 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19257 Z= 0.191 Angle : 0.618 10.796 26157 Z= 0.320 Chirality : 0.045 0.168 3126 Planarity : 0.004 0.041 3243 Dihedral : 5.753 34.375 3727 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.75 % Favored : 96.11 % Rotamer: Outliers : 3.20 % Allowed : 16.67 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.32 (0.18), residues: 2265 helix: 0.11 (0.28), residues: 378 sheet: 0.38 (0.19), residues: 738 loop : -0.66 (0.19), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 628 HIS 0.003 0.001 HIS C 249 PHE 0.020 0.001 PHE F 98 TYR 0.015 0.001 TYR A 486 ARG 0.003 0.000 ARG G 151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 273 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 634 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8610 (tt0) REVERT: B 650 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7663 (tm-30) REVERT: L 46 LEU cc_start: 0.7954 (tt) cc_final: 0.7694 (tt) REVERT: C 39 TYR cc_start: 0.8681 (m-80) cc_final: 0.8340 (m-80) REVERT: C 150 MET cc_start: 0.6466 (mmt) cc_final: 0.6199 (mmt) REVERT: D 593 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7933 (mp) REVERT: D 634 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8741 (mm-30) REVERT: D 647 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7742 (mm-30) REVERT: D 648 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8186 (pt0) REVERT: D 650 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: D 656 ASN cc_start: 0.8290 (t0) cc_final: 0.7665 (m110) REVERT: F 91 THR cc_start: 0.8500 (p) cc_final: 0.8131 (p) REVERT: G 427 TRP cc_start: 0.7582 (m-10) cc_final: 0.7311 (m-10) REVERT: I 607 ASN cc_start: 0.8439 (m-40) cc_final: 0.8033 (m110) REVERT: I 617 ARG cc_start: 0.7727 (mtp-110) cc_final: 0.7473 (mtp-110) REVERT: I 656 ASN cc_start: 0.7616 (t0) cc_final: 0.6953 (t0) REVERT: J 81 MET cc_start: 0.7625 (mtt) cc_final: 0.7420 (mtt) REVERT: J 110 THR cc_start: 0.7775 (m) cc_final: 0.7569 (m) outliers start: 64 outliers final: 52 residues processed: 315 average time/residue: 0.3351 time to fit residues: 157.5549 Evaluate side-chains 306 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 251 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 77 ASP Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 368 ASP Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 618 ASN Chi-restraints excluded: chain I residue 619 LEU Chi-restraints excluded: chain I residue 628 TRP Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 98 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 134 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 20 optimal weight: 0.2980 chunk 170 optimal weight: 0.1980 chunk 197 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 ASN G 195 ASN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19257 Z= 0.168 Angle : 0.589 11.083 26157 Z= 0.301 Chirality : 0.044 0.161 3126 Planarity : 0.004 0.036 3243 Dihedral : 5.280 36.583 3727 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.50 % Favored : 95.36 % Rotamer: Outliers : 3.00 % Allowed : 17.02 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.05 % 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: -0.13 (0.18), residues: 2265 helix: 0.27 (0.29), residues: 363 sheet: 0.33 (0.19), residues: 807 loop : -0.44 (0.20), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 628 HIS 0.003 0.001 HIS C 249 PHE 0.018 0.001 PHE L 98 TYR 0.020 0.001 TYR C 40 ARG 0.007 0.000 ARG C 151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 269 time to evaluate : 2.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 VAL cc_start: 0.9197 (t) cc_final: 0.8985 (m) REVERT: B 649 SER cc_start: 0.9144 (m) cc_final: 0.8929 (t) REVERT: B 650 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.7784 (tm-30) REVERT: L 46 LEU cc_start: 0.8035 (tt) cc_final: 0.7760 (tt) REVERT: C 39 TYR cc_start: 0.8688 (m-80) cc_final: 0.8364 (m-80) REVERT: D 530 MET cc_start: 0.6845 (mmm) cc_final: 0.6639 (mmm) REVERT: D 579 ARG cc_start: 0.7886 (mtm-85) cc_final: 0.7628 (mtp180) REVERT: D 593 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7832 (mp) REVERT: D 650 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: D 656 ASN cc_start: 0.7743 (OUTLIER) cc_final: 0.7485 (m110) REVERT: F 91 THR cc_start: 0.8508 (p) cc_final: 0.8120 (p) REVERT: I 607 ASN cc_start: 0.8450 (m-40) cc_final: 0.8051 (m-40) REVERT: I 656 ASN cc_start: 0.7564 (t0) cc_final: 0.6761 (t0) REVERT: J 23 LYS cc_start: 0.8361 (pttm) cc_final: 0.8038 (ptmt) REVERT: J 81 MET cc_start: 0.7534 (mtt) cc_final: 0.7328 (mtt) REVERT: J 110 THR cc_start: 0.7880 (m) cc_final: 0.7661 (m) REVERT: K 69 THR cc_start: 0.8633 (p) cc_final: 0.8283 (p) outliers start: 60 outliers final: 42 residues processed: 311 average time/residue: 0.3259 time to fit residues: 152.6852 Evaluate side-chains 298 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 252 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain D residue 656 ASN Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 368 ASP Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 618 ASN Chi-restraints excluded: chain I residue 619 LEU Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 207 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 191 optimal weight: 0.4980 chunk 201 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN C 425 ASN D 656 ASN ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 19257 Z= 0.330 Angle : 0.656 13.011 26157 Z= 0.337 Chirality : 0.045 0.184 3126 Planarity : 0.004 0.034 3243 Dihedral : 5.460 39.335 3727 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.12 % Favored : 94.75 % Rotamer: Outliers : 2.75 % Allowed : 17.32 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.25 (0.18), residues: 2265 helix: 0.03 (0.28), residues: 384 sheet: 0.37 (0.20), residues: 762 loop : -0.54 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I 628 HIS 0.005 0.001 HIS A 374 PHE 0.021 0.002 PHE C 376 TYR 0.024 0.002 TYR D 643 ARG 0.006 0.001 ARG C 151 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 259 time to evaluate : 2.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 545 LEU cc_start: 0.8717 (mt) cc_final: 0.8433 (mt) REVERT: B 601 LYS cc_start: 0.9022 (mtpt) cc_final: 0.8794 (mtpp) REVERT: B 647 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7441 (mm-30) REVERT: B 649 SER cc_start: 0.9177 (m) cc_final: 0.8965 (t) REVERT: B 650 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7742 (tm-30) REVERT: H 23 LYS cc_start: 0.8778 (pttt) cc_final: 0.8576 (ptmt) REVERT: H 110 THR cc_start: 0.7776 (m) cc_final: 0.7556 (m) REVERT: C 39 TYR cc_start: 0.8703 (m-80) cc_final: 0.8101 (m-10) REVERT: D 579 ARG cc_start: 0.8083 (mtm-85) cc_final: 0.7810 (mtp180) REVERT: D 593 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8022 (mp) REVERT: D 650 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: D 656 ASN cc_start: 0.7769 (OUTLIER) cc_final: 0.7566 (m110) REVERT: F 91 THR cc_start: 0.8437 (p) cc_final: 0.8069 (p) REVERT: I 542 ARG cc_start: 0.8665 (ttm170) cc_final: 0.8009 (ttm170) REVERT: I 607 ASN cc_start: 0.8468 (m-40) cc_final: 0.8079 (m-40) REVERT: J 81 MET cc_start: 0.7635 (mtt) cc_final: 0.7412 (mtt) REVERT: J 110 THR cc_start: 0.7884 (m) cc_final: 0.7669 (m) REVERT: K 69 THR cc_start: 0.8694 (p) cc_final: 0.8289 (p) outliers start: 55 outliers final: 45 residues processed: 296 average time/residue: 0.3239 time to fit residues: 143.6358 Evaluate side-chains 293 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 244 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 77 ASP Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain D residue 656 ASN Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 368 ASP Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 618 ASN Chi-restraints excluded: chain I residue 619 LEU Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 77 ASP Chi-restraints excluded: chain K residue 98 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 213 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 101 optimal weight: 0.0060 chunk 148 optimal weight: 0.3980 chunk 224 optimal weight: 7.9990 chunk 206 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 656 ASN ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19257 Z= 0.265 Angle : 0.631 10.817 26157 Z= 0.324 Chirality : 0.045 0.151 3126 Planarity : 0.004 0.041 3243 Dihedral : 5.524 38.088 3727 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.17 % Favored : 94.70 % Rotamer: Outliers : 2.50 % Allowed : 17.32 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.28 (0.18), residues: 2265 helix: 0.04 (0.28), residues: 384 sheet: 0.36 (0.20), residues: 762 loop : -0.57 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 628 HIS 0.003 0.001 HIS C 216 PHE 0.016 0.002 PHE F 98 TYR 0.023 0.002 TYR C 40 ARG 0.006 0.000 ARG C 151 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 256 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 545 LEU cc_start: 0.8737 (mt) cc_final: 0.8489 (mt) REVERT: B 601 LYS cc_start: 0.9041 (mtpt) cc_final: 0.8769 (mtpp) REVERT: B 650 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.7724 (tm-30) REVERT: C 39 TYR cc_start: 0.8689 (m-80) cc_final: 0.8125 (m-10) REVERT: D 579 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7791 (mtp180) REVERT: D 593 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8035 (mp) REVERT: D 650 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: D 656 ASN cc_start: 0.7911 (OUTLIER) cc_final: 0.7608 (m110) REVERT: F 91 THR cc_start: 0.8537 (p) cc_final: 0.8157 (p) REVERT: G 325 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7872 (p0) REVERT: I 607 ASN cc_start: 0.8467 (m-40) cc_final: 0.8088 (m-40) REVERT: I 617 ARG cc_start: 0.7377 (mtp-110) cc_final: 0.7116 (mtp-110) REVERT: J 81 MET cc_start: 0.7611 (mtt) cc_final: 0.7387 (mtt) REVERT: J 110 THR cc_start: 0.7853 (m) cc_final: 0.7637 (m) REVERT: K 69 THR cc_start: 0.8700 (p) cc_final: 0.8300 (p) outliers start: 50 outliers final: 45 residues processed: 291 average time/residue: 0.3259 time to fit residues: 141.7208 Evaluate side-chains 295 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 245 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 77 ASP Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain D residue 656 ASN Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 368 ASP Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 618 ASN Chi-restraints excluded: chain I residue 619 LEU Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 77 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 190 optimal weight: 0.3980 chunk 54 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 178 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 156 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 ASN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.135051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.114178 restraints weight = 31705.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.117007 restraints weight = 19161.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.118942 restraints weight = 13591.579| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19257 Z= 0.193 Angle : 0.605 10.600 26157 Z= 0.310 Chirality : 0.044 0.165 3126 Planarity : 0.004 0.044 3243 Dihedral : 5.342 34.967 3725 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.81 % Favored : 95.06 % Rotamer: Outliers : 2.40 % Allowed : 17.67 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.19 (0.18), residues: 2265 helix: 0.06 (0.28), residues: 384 sheet: 0.45 (0.20), residues: 759 loop : -0.52 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 628 HIS 0.003 0.001 HIS C 249 PHE 0.015 0.001 PHE F 98 TYR 0.023 0.001 TYR C 40 ARG 0.006 0.000 ARG C 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3859.49 seconds wall clock time: 71 minutes 37.85 seconds (4297.85 seconds total)