Starting phenix.real_space_refine on Sun Feb 18 04:38:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vi0_21208/02_2024/6vi0_21208.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vi0_21208/02_2024/6vi0_21208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vi0_21208/02_2024/6vi0_21208.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vi0_21208/02_2024/6vi0_21208.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vi0_21208/02_2024/6vi0_21208.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vi0_21208/02_2024/6vi0_21208.pdb" } resolution = 3.43 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= 0.013 sd= 0.094 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 138 5.16 5 C 12987 2.51 5 N 3447 2.21 5 O 4251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 584": "OE1" <-> "OE2" Residue "B ARG 588": "NH1" <-> "NH2" Residue "B GLU 647": "OE1" <-> "OE2" Residue "G GLU 153": "OE1" <-> "OE2" Residue "G ARG 327": "NH1" <-> "NH2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 16": "OE1" <-> "OE2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "A GLU 584": "OE1" <-> "OE2" Residue "A ARG 588": "NH1" <-> "NH2" Residue "A GLU 647": "OE1" <-> "OE2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 16": "OE1" <-> "OE2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "F GLU 584": "OE1" <-> "OE2" Residue "F ARG 588": "NH1" <-> "NH2" Residue "F GLU 647": "OE1" <-> "OE2" Residue "I GLU 153": "OE1" <-> "OE2" Residue "I ARG 327": "NH1" <-> "NH2" Residue "J TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K ARG 71": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20823 Number of models: 1 Model: "" Number of chains: 45 Chain: "B" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1044 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "G" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 744 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 6, 'TRANS': 89} Chain: "H" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1039 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 9, 'TRANS': 119} Chain: "A" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1044 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "C" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 744 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 6, 'TRANS': 89} Chain: "E" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1039 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 9, 'TRANS': 119} Chain: "F" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1044 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 744 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 6, 'TRANS': 89} Chain: "K" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1039 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 9, 'TRANS': 119} 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "P" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "X" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "a" 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "f" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "i" 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: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: "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: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" 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: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.38, per 1000 atoms: 0.50 Number of scatterers: 20823 At special positions: 0 Unit cell: (148.109, 143.816, 123.424, 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 138 16.00 O 4251 8.00 N 3447 7.00 C 12987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.01 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.02 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 32 " - pdb=" SG CYS H 98 " distance=2.04 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.02 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 32 " - pdb=" SG CYS E 98 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS I 501 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.04 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.02 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.02 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.02 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.04 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.02 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.02 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 32 " - pdb=" SG CYS K 98 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN O 4 " - " MAN O 5 " " MAN P 4 " - " MAN P 5 " " MAN W 4 " - " MAN W 5 " " MAN X 4 " - " MAN X 5 " " MAN e 4 " - " MAN e 5 " " MAN f 4 " - " MAN f 5 " ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " MAN P 6 " - " MAN P 7 " " BMA R 3 " - " MAN R 6 " " MAN R 4 " - " MAN R 5 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " MAN X 6 " - " MAN X 7 " " BMA Z 3 " - " MAN Z 6 " " MAN Z 4 " - " MAN Z 5 " " BMA e 3 " - " MAN e 4 " " BMA f 3 " - " MAN f 4 " " MAN f 6 " - " MAN f 7 " " BMA h 3 " - " MAN h 6 " " MAN h 4 " - " MAN h 5 " ALPHA1-6 " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 6 " " BMA P 3 " - " MAN P 6 " " MAN P 6 " - " MAN P 8 " " BMA R 3 " - " MAN R 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 6 " " BMA X 3 " - " MAN X 6 " " MAN X 6 " - " MAN X 8 " " BMA Z 3 " - " MAN Z 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 6 " " BMA f 3 " - " MAN f 6 " " MAN f 6 " - " MAN f 8 " " BMA h 3 " - " MAN h 4 " 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 O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " 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 Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A1611 " - " ASN A 611 " " NAG A1637 " - " ASN A 637 " " NAG B1611 " - " ASN B 611 " " NAG B1637 " - " ASN B 637 " " NAG C1088 " - " ASN C 88 " " NAG C1133 " - " ASN C 133 " " NAG C1156 " - " ASN C 156 " " NAG C1234 " - " ASN C 234 " " NAG C1301 " - " ASN C 301 " " NAG C1332 " - " ASN C 332 " " NAG C1339 " - " ASN C 339 " " NAG C1355 " - " ASN C 355 " " NAG C1392 " - " ASN C 392 " " NAG D1072 " - " ASN D 72 " " NAG F1611 " - " ASN F 611 " " NAG F1637 " - " ASN F 637 " " NAG G1088 " - " ASN G 88 " " NAG G1133 " - " ASN G 133 " " NAG G1156 " - " ASN G 156 " " NAG G1234 " - " ASN G 234 " " NAG G1301 " - " ASN G 301 " " NAG G1332 " - " ASN G 332 " " NAG G1339 " - " ASN G 339 " " NAG G1355 " - " ASN G 355 " " NAG G1392 " - " ASN G 392 " " NAG I1088 " - " ASN I 88 " " NAG I1133 " - " ASN I 133 " " NAG I1156 " - " ASN I 156 " " NAG I1234 " - " ASN I 234 " " NAG I1301 " - " ASN I 301 " " NAG I1332 " - " ASN I 332 " " NAG I1339 " - " ASN I 339 " " NAG I1355 " - " ASN I 355 " " NAG I1392 " - " ASN I 392 " " NAG J1072 " - " ASN J 72 " " NAG L1072 " - " ASN L 72 " " NAG M 1 " - " ASN G 160 " " NAG N 1 " - " ASN G 197 " " NAG O 1 " - " ASN G 262 " " NAG P 1 " - " ASN G 276 " " NAG Q 1 " - " ASN G 295 " " NAG R 1 " - " ASN G 363 " " NAG S 1 " - " ASN G 386 " " NAG T 1 " - " ASN G 448 " " NAG U 1 " - " ASN C 160 " " NAG V 1 " - " ASN C 197 " " NAG W 1 " - " ASN C 262 " " NAG X 1 " - " ASN C 276 " " NAG Y 1 " - " ASN C 295 " " NAG Z 1 " - " ASN C 363 " " NAG a 1 " - " ASN C 386 " " NAG b 1 " - " ASN C 448 " " NAG c 1 " - " ASN I 160 " " NAG d 1 " - " ASN I 197 " " NAG e 1 " - " ASN I 262 " " NAG f 1 " - " ASN I 276 " " NAG g 1 " - " ASN I 295 " " NAG h 1 " - " ASN I 363 " " NAG i 1 " - " ASN I 386 " " NAG j 1 " - " ASN I 448 " Time building additional restraints: 9.93 Conformation dependent library (CDL) restraints added in 3.3 seconds 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4470 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 48 sheets defined 18.2% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.255A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 593 removed outlier: 3.684A pdb=" N TRP B 571 " --> pdb=" O LYS B 567 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 597 removed outlier: 4.032A pdb=" N GLY B 597 " --> pdb=" O GLY B 594 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 594 through 597' Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.597A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 639 removed outlier: 4.159A pdb=" N THR B 639 " --> pdb=" O SER B 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 636 through 639' Processing helix chain 'B' and resid 641 through 658 removed outlier: 4.293A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 63 Processing helix chain 'G' and resid 99 through 115 removed outlier: 3.597A pdb=" N THR G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.907A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 354 removed outlier: 3.701A pdb=" N GLU G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE G 353 " --> pdb=" O LEU G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 482 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.865A pdb=" N ASP L 82 " --> pdb=" O GLU L 79 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.733A pdb=" N GLN H 64 " --> pdb=" O ARG H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 543 removed outlier: 4.254A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 593 removed outlier: 3.682A pdb=" N TRP A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 597 removed outlier: 4.032A pdb=" N GLY A 597 " --> pdb=" O GLY A 594 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 594 through 597' Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.597A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 639 removed outlier: 4.159A pdb=" N THR A 639 " --> pdb=" O SER A 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 636 through 639' Processing helix chain 'A' and resid 641 through 664 removed outlier: 4.293A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 648 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 63 Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.597A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.907A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 354 removed outlier: 3.699A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 482 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.865A pdb=" N ASP D 82 " --> pdb=" O GLU D 79 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 79 through 83' Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.732A pdb=" N GLN E 64 " --> pdb=" O ARG E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.256A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 566 through 593 removed outlier: 3.683A pdb=" N TRP F 571 " --> pdb=" O LYS F 567 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU F 581 " --> pdb=" O GLN F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 597 removed outlier: 4.033A pdb=" N GLY F 597 " --> pdb=" O GLY F 594 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 594 through 597' Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.597A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 639 removed outlier: 4.159A pdb=" N THR F 639 " --> pdb=" O SER F 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 636 through 639' Processing helix chain 'F' and resid 641 through 658 removed outlier: 4.293A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 63 Processing helix chain 'I' and resid 99 through 115 removed outlier: 3.597A pdb=" N THR I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN I 114 " --> pdb=" O SER I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 removed outlier: 3.907A pdb=" N CYS I 126 " --> pdb=" O THR I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 354 removed outlier: 3.701A pdb=" N GLU I 340 " --> pdb=" O ALA I 336 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS I 347 " --> pdb=" O GLY I 343 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE I 353 " --> pdb=" O LEU I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 482 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.866A pdb=" N ASP J 82 " --> pdb=" O GLU J 79 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE J 83 " --> pdb=" O SER J 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 79 through 83' Processing helix chain 'K' and resid 61 through 64 removed outlier: 3.733A pdb=" N GLN K 64 " --> pdb=" O ARG K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 609 removed outlier: 7.347A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.693A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.713A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 129 through 130 Processing sheet with id=AA6, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AA7, first strand: chain 'G' and resid 158 through 162 Processing sheet with id=AA8, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.586A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 271 through 273 removed outlier: 7.119A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 11.256A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.795A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU G 466 " --> pdb=" O ILE G 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 302 through 308 removed outlier: 6.643A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 423 through 424 removed outlier: 4.271A pdb=" N ILE G 424 " --> pdb=" O MET G 434 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.635A pdb=" N TYR L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER L 65 " --> pdb=" O ASN L 72 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.811A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.572A pdb=" N GLN H 72 " --> pdb=" O THR H 77 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB7, first strand: chain 'H' and resid 49 through 52 removed outlier: 3.610A pdb=" N TRP H 50 " --> pdb=" O ASN H 58 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN H 58 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 603 through 609 removed outlier: 7.346A pdb=" N THR A 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL C 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL A 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.692A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC2, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.713A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AC4, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AC5, first strand: chain 'C' and resid 158 through 162 Processing sheet with id=AC6, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.587A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.120A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.254A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.260A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.795A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.840A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 466 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 302 through 308 removed outlier: 6.643A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 423 through 424 removed outlier: 4.168A pdb=" N ILE C 424 " --> pdb=" O MET C 434 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.635A pdb=" N TYR D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D 65 " --> pdb=" O ASN D 72 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.813A pdb=" N ILE D 48 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.571A pdb=" N GLN E 72 " --> pdb=" O THR E 77 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AD5, first strand: chain 'E' and resid 49 through 52 removed outlier: 3.610A pdb=" N TRP E 50 " --> pdb=" O ASN E 58 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN E 58 " --> pdb=" O TRP E 50 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 603 through 609 removed outlier: 7.347A pdb=" N THR F 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL I 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL F 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.692A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AD9, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.713A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 129 through 130 Processing sheet with id=AE2, first strand: chain 'I' and resid 154 through 155 Processing sheet with id=AE3, first strand: chain 'I' and resid 158 through 162 Processing sheet with id=AE4, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.585A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU I 381 " --> pdb=" O CYS I 378 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 271 through 273 removed outlier: 7.118A pdb=" N THR I 450 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 11.256A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.795A pdb=" N VAL I 292 " --> pdb=" O VAL I 446 " (cutoff:3.500A) removed outlier: 9.840A pdb=" N VAL I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N ILE I 294 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N ARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU I 466 " --> pdb=" O ILE I 358 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 302 through 308 removed outlier: 6.645A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 423 through 424 removed outlier: 4.089A pdb=" N ILE I 424 " --> pdb=" O MET I 434 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 5 through 6 removed outlier: 3.635A pdb=" N TYR J 71 " --> pdb=" O CYS J 23 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER J 65 " --> pdb=" O ASN J 72 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.812A pdb=" N ILE J 48 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.571A pdb=" N GLN K 72 " --> pdb=" O THR K 77 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=AF3, first strand: chain 'K' and resid 49 through 52 removed outlier: 3.610A pdb=" N TRP K 50 " --> pdb=" O ASN K 58 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN K 58 " --> pdb=" O TRP K 50 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1386 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: 7.03 Time building geometry restraints manager: 10.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3554 1.32 - 1.45: 5923 1.45 - 1.57: 11589 1.57 - 1.69: 0 1.69 - 1.82: 186 Bond restraints: 21252 Sorted by residual: bond pdb=" N CYS G 201 " pdb=" CA CYS G 201 " ideal model delta sigma weight residual 1.463 1.392 0.071 1.27e-02 6.20e+03 3.11e+01 bond pdb=" CA SER I 199 " pdb=" CB SER I 199 " ideal model delta sigma weight residual 1.532 1.450 0.081 1.56e-02 4.11e+03 2.71e+01 bond pdb=" N CYS I 201 " pdb=" CA CYS I 201 " ideal model delta sigma weight residual 1.460 1.402 0.058 1.20e-02 6.94e+03 2.35e+01 bond pdb=" CA SER C 199 " pdb=" CB SER C 199 " ideal model delta sigma weight residual 1.532 1.451 0.081 1.68e-02 3.54e+03 2.35e+01 bond pdb=" CA SER G 199 " pdb=" CB SER G 199 " ideal model delta sigma weight residual 1.530 1.454 0.076 1.69e-02 3.50e+03 2.05e+01 ... (remaining 21247 not shown) Histogram of bond angle deviations from ideal: 98.80 - 106.14: 570 106.14 - 113.47: 12629 113.47 - 120.81: 8590 120.81 - 128.14: 6825 128.14 - 135.48: 240 Bond angle restraints: 28854 Sorted by residual: angle pdb=" C ASN I 156 " pdb=" CA ASN I 156 " pdb=" CB ASN I 156 " ideal model delta sigma weight residual 111.68 100.79 10.89 1.67e+00 3.59e-01 4.25e+01 angle pdb=" C ASN C 156 " pdb=" CA ASN C 156 " pdb=" CB ASN C 156 " ideal model delta sigma weight residual 111.68 100.85 10.83 1.67e+00 3.59e-01 4.20e+01 angle pdb=" C ASN G 156 " pdb=" CA ASN G 156 " pdb=" CB ASN G 156 " ideal model delta sigma weight residual 111.68 100.86 10.82 1.67e+00 3.59e-01 4.19e+01 angle pdb=" CA ALA I 200 " pdb=" C ALA I 200 " pdb=" O ALA I 200 " ideal model delta sigma weight residual 121.11 115.25 5.86 1.13e+00 7.83e-01 2.69e+01 angle pdb=" N LEU A 663 " pdb=" CA LEU A 663 " pdb=" C LEU A 663 " ideal model delta sigma weight residual 111.28 105.83 5.45 1.09e+00 8.42e-01 2.50e+01 ... (remaining 28849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.87: 13242 21.87 - 43.74: 935 43.74 - 65.60: 142 65.60 - 87.47: 96 87.47 - 109.34: 60 Dihedral angle restraints: 14475 sinusoidal: 7533 harmonic: 6942 Sorted by residual: dihedral pdb=" CB CYS K 32 " pdb=" SG CYS K 32 " pdb=" SG CYS K 98 " pdb=" CB CYS K 98 " ideal model delta sinusoidal sigma weight residual -86.00 -13.56 -72.44 1 1.00e+01 1.00e-02 6.70e+01 dihedral pdb=" CB CYS H 32 " pdb=" SG CYS H 32 " pdb=" SG CYS H 98 " pdb=" CB CYS H 98 " ideal model delta sinusoidal sigma weight residual -86.00 -13.57 -72.43 1 1.00e+01 1.00e-02 6.70e+01 dihedral pdb=" CB CYS E 32 " pdb=" SG CYS E 32 " pdb=" SG CYS E 98 " pdb=" CB CYS E 98 " ideal model delta sinusoidal sigma weight residual -86.00 -13.60 -72.40 1 1.00e+01 1.00e-02 6.70e+01 ... (remaining 14472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.288: 3518 0.288 - 0.576: 55 0.576 - 0.864: 6 0.864 - 1.152: 3 1.152 - 1.441: 3 Chirality restraints: 3585 Sorted by residual: chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.96 -1.44 2.00e-02 2.50e+03 5.19e+03 chirality pdb=" C1 BMA V 3 " pdb=" O4 NAG V 2 " pdb=" C2 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.96 -1.44 2.00e-02 2.50e+03 5.16e+03 chirality pdb=" C1 BMA d 3 " pdb=" O4 NAG d 2 " pdb=" C2 BMA d 3 " pdb=" O5 BMA d 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.97 -1.43 2.00e-02 2.50e+03 5.13e+03 ... (remaining 3582 not shown) Planarity restraints: 3558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG h 2 " 0.308 2.00e-02 2.50e+03 2.59e-01 8.41e+02 pdb=" C7 NAG h 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG h 2 " 0.190 2.00e-02 2.50e+03 pdb=" N2 NAG h 2 " -0.445 2.00e-02 2.50e+03 pdb=" O7 NAG h 2 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " 0.308 2.00e-02 2.50e+03 2.59e-01 8.40e+02 pdb=" C7 NAG R 2 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " 0.190 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " -0.444 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 2 " 0.307 2.00e-02 2.50e+03 2.59e-01 8.39e+02 pdb=" C7 NAG Z 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG Z 2 " 0.190 2.00e-02 2.50e+03 pdb=" N2 NAG Z 2 " -0.443 2.00e-02 2.50e+03 pdb=" O7 NAG Z 2 " 0.030 2.00e-02 2.50e+03 ... (remaining 3555 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4427 2.77 - 3.30: 17738 3.30 - 3.84: 32644 3.84 - 4.37: 37378 4.37 - 4.90: 66247 Nonbonded interactions: 158434 Sorted by model distance: nonbonded pdb=" OG SER D 63 " pdb=" OG1 THR D 74 " model vdw 2.241 2.440 nonbonded pdb=" OG SER L 63 " pdb=" OG1 THR L 74 " model vdw 2.241 2.440 nonbonded pdb=" OG SER J 63 " pdb=" OG1 THR J 74 " model vdw 2.241 2.440 nonbonded pdb=" O ASP B 632 " pdb=" OG SER B 636 " model vdw 2.306 2.440 nonbonded pdb=" O ASP A 632 " pdb=" OG SER A 636 " model vdw 2.307 2.440 ... (remaining 158429 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'T' selection = chain 'U' selection = chain 'Y' selection = chain 'b' selection = chain 'c' selection = chain 'g' selection = chain 'j' } ncs_group { reference = chain 'N' selection = chain 'V' selection = chain 'd' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'W' selection = chain 'Z' selection = chain 'e' selection = chain 'h' } ncs_group { reference = chain 'P' selection = chain 'X' selection = chain 'f' } ncs_group { reference = chain 'S' selection = chain 'a' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.500 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 54.620 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.360 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.008 0.081 21252 Z= 0.532 Angle : 1.120 10.888 28854 Z= 0.568 Chirality : 0.103 1.441 3585 Planarity : 0.015 0.259 3498 Dihedral : 17.431 109.340 9870 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.79 % Favored : 92.05 % Rotamer: Outliers : 1.23 % Allowed : 8.13 % Favored : 90.64 % Cbeta Deviations : 0.13 % 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: -5.43 (0.13), residues: 2376 helix: -4.82 (0.08), residues: 390 sheet: -3.18 (0.16), residues: 720 loop : -3.48 (0.13), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 50 HIS 0.011 0.002 HIS I 249 PHE 0.018 0.002 PHE G 53 TYR 0.028 0.002 TYR G 435 ARG 0.004 0.001 ARG K 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 278 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 603 ILE cc_start: 0.8994 (mt) cc_final: 0.8700 (tt) REVERT: B 632 ASP cc_start: 0.8695 (t70) cc_final: 0.8336 (t0) REVERT: B 651 ASN cc_start: 0.8180 (t0) cc_final: 0.7492 (p0) REVERT: G 166 ARG cc_start: 0.7641 (mmm-85) cc_final: 0.7112 (ttp-170) REVERT: L 17 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7906 (mt-10) REVERT: L 54 ARG cc_start: 0.7985 (mtm110) cc_final: 0.7780 (ptp-110) REVERT: H 76 ASP cc_start: 0.7987 (p0) cc_final: 0.7764 (p0) REVERT: A 603 ILE cc_start: 0.8960 (mt) cc_final: 0.8661 (tt) REVERT: A 632 ASP cc_start: 0.8630 (t70) cc_final: 0.8316 (t0) REVERT: A 633 LYS cc_start: 0.9071 (mtpt) cc_final: 0.8850 (mtmm) REVERT: A 651 ASN cc_start: 0.8059 (t0) cc_final: 0.7439 (p0) REVERT: C 114 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7574 (tm-30) REVERT: C 166 ARG cc_start: 0.7607 (mmm-85) cc_final: 0.7159 (ttp-110) REVERT: C 426 MET cc_start: 0.8615 (tpp) cc_final: 0.8397 (tpt) REVERT: D 17 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7775 (mt-10) REVERT: D 42 GLN cc_start: 0.8356 (mt0) cc_final: 0.8062 (mt0) REVERT: D 75 ILE cc_start: 0.7683 (mt) cc_final: 0.7459 (tt) REVERT: F 603 ILE cc_start: 0.8980 (mt) cc_final: 0.8614 (tt) REVERT: F 632 ASP cc_start: 0.8873 (t70) cc_final: 0.8520 (t0) REVERT: F 651 ASN cc_start: 0.8177 (t0) cc_final: 0.7600 (p0) REVERT: I 100 MET cc_start: 0.9090 (mtp) cc_final: 0.8804 (mtt) REVERT: I 166 ARG cc_start: 0.7757 (mmm-85) cc_final: 0.7096 (ttp-110) REVERT: I 424 ILE cc_start: 0.8563 (pt) cc_final: 0.8299 (pt) REVERT: I 426 MET cc_start: 0.8697 (tpp) cc_final: 0.8477 (tpt) REVERT: J 17 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7709 (mt-10) REVERT: J 24 ARG cc_start: 0.7936 (tpt90) cc_final: 0.7622 (tpt170) REVERT: J 42 GLN cc_start: 0.8357 (mt0) cc_final: 0.7945 (mp10) REVERT: J 60 ASP cc_start: 0.8413 (m-30) cc_final: 0.8201 (m-30) REVERT: K 76 ASP cc_start: 0.8102 (p0) cc_final: 0.7857 (p0) REVERT: K 96 LYS cc_start: 0.9229 (tttm) cc_final: 0.8810 (tttm) outliers start: 26 outliers final: 10 residues processed: 302 average time/residue: 0.3972 time to fit residues: 177.4410 Evaluate side-chains 198 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 188 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 430 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 0.8980 chunk 179 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 95 optimal weight: 0.0370 chunk 185 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 112 optimal weight: 0.4980 chunk 138 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN G 114 GLN G 293 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN H 3 GLN A 591 GLN C 114 GLN C 293 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN E 3 GLN F 590 GLN F 591 GLN I 293 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21252 Z= 0.182 Angle : 0.695 11.747 28854 Z= 0.323 Chirality : 0.047 0.350 3585 Planarity : 0.004 0.044 3498 Dihedral : 13.083 74.114 5347 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.03 % Allowed : 11.54 % Favored : 86.43 % 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: -4.30 (0.14), residues: 2376 helix: -3.17 (0.17), residues: 390 sheet: -2.68 (0.18), residues: 681 loop : -2.88 (0.14), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 100B HIS 0.013 0.001 HIS K 102 PHE 0.012 0.001 PHE I 382 TYR 0.015 0.001 TYR A 638 ARG 0.009 0.000 ARG J 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 215 time to evaluate : 2.336 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: B 603 ILE cc_start: 0.9004 (mt) cc_final: 0.8723 (tt) REVERT: B 632 ASP cc_start: 0.8776 (t70) cc_final: 0.8433 (t0) REVERT: G 114 GLN cc_start: 0.8003 (tm130) cc_final: 0.7683 (tm-30) REVERT: G 166 ARG cc_start: 0.7646 (mmm-85) cc_final: 0.7037 (ttp-110) REVERT: L 75 ILE cc_start: 0.7224 (mt) cc_final: 0.6815 (tt) REVERT: L 97 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.6308 (pm20) REVERT: H 76 ASP cc_start: 0.7998 (p0) cc_final: 0.7683 (p0) REVERT: A 603 ILE cc_start: 0.9000 (mt) cc_final: 0.8757 (tt) REVERT: A 616 ASN cc_start: 0.8440 (p0) cc_final: 0.8180 (p0) REVERT: A 632 ASP cc_start: 0.8612 (t70) cc_final: 0.8279 (t0) REVERT: C 114 GLN cc_start: 0.8052 (tm130) cc_final: 0.7781 (tm-30) REVERT: C 166 ARG cc_start: 0.7556 (mmm-85) cc_final: 0.7121 (ttp-110) REVERT: D 97 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7136 (pt0) REVERT: E 72 GLN cc_start: 0.8121 (tt0) cc_final: 0.7826 (mt0) REVERT: E 75 GLN cc_start: 0.8845 (mt0) cc_final: 0.8616 (mt0) REVERT: E 87 THR cc_start: 0.8998 (m) cc_final: 0.8765 (p) REVERT: F 603 ILE cc_start: 0.8998 (mt) cc_final: 0.8660 (tt) REVERT: F 616 ASN cc_start: 0.8621 (p0) cc_final: 0.8375 (p0) REVERT: F 632 ASP cc_start: 0.8861 (t70) cc_final: 0.8500 (t0) REVERT: F 655 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7446 (mmmt) REVERT: I 95 MET cc_start: 0.8858 (ttp) cc_final: 0.8630 (ttp) REVERT: I 166 ARG cc_start: 0.7742 (mmm-85) cc_final: 0.7091 (ttp-110) REVERT: I 426 MET cc_start: 0.8593 (tpp) cc_final: 0.8348 (tpt) REVERT: J 97 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7094 (pt0) REVERT: K 76 ASP cc_start: 0.8028 (p0) cc_final: 0.7699 (p0) outliers start: 43 outliers final: 24 residues processed: 254 average time/residue: 0.3116 time to fit residues: 124.6138 Evaluate side-chains 216 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 188 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 70 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 119 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 232 optimal weight: 0.0470 chunk 192 optimal weight: 0.4980 chunk 213 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 172 optimal weight: 0.3980 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN H 3 GLN ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21252 Z= 0.203 Angle : 0.669 16.450 28854 Z= 0.309 Chirality : 0.048 0.374 3585 Planarity : 0.004 0.039 3498 Dihedral : 10.829 59.935 5340 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.12 % Allowed : 13.00 % Favored : 83.88 % 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: -3.45 (0.16), residues: 2376 helix: -1.75 (0.23), residues: 369 sheet: -2.06 (0.19), residues: 702 loop : -2.62 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 100B HIS 0.007 0.001 HIS E 102 PHE 0.009 0.001 PHE G 53 TYR 0.019 0.001 TYR A 638 ARG 0.011 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 202 time to evaluate : 2.421 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 530 MET cc_start: 0.8776 (mtp) cc_final: 0.8458 (mtp) REVERT: B 603 ILE cc_start: 0.9045 (mt) cc_final: 0.8787 (tt) REVERT: B 632 ASP cc_start: 0.8794 (t70) cc_final: 0.8455 (t0) REVERT: G 114 GLN cc_start: 0.8020 (tm130) cc_final: 0.7707 (tm-30) REVERT: G 166 ARG cc_start: 0.7644 (mmm-85) cc_final: 0.7069 (ttp-110) REVERT: L 54 ARG cc_start: 0.7768 (ptp-110) cc_final: 0.7534 (mtm110) REVERT: L 97 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7163 (pt0) REVERT: H 76 ASP cc_start: 0.7997 (p0) cc_final: 0.7682 (p0) REVERT: A 603 ILE cc_start: 0.9022 (mt) cc_final: 0.8779 (tt) REVERT: A 632 ASP cc_start: 0.8674 (t70) cc_final: 0.8371 (t0) REVERT: C 114 GLN cc_start: 0.8094 (tm130) cc_final: 0.7832 (tm-30) REVERT: C 166 ARG cc_start: 0.7585 (mmm-85) cc_final: 0.7131 (ttp-110) REVERT: C 320 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8528 (p) REVERT: D 97 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7283 (pt0) REVERT: E 72 GLN cc_start: 0.8132 (tt0) cc_final: 0.7809 (mt0) REVERT: E 87 THR cc_start: 0.8928 (m) cc_final: 0.8708 (p) REVERT: F 603 ILE cc_start: 0.9015 (mt) cc_final: 0.8703 (tt) REVERT: F 616 ASN cc_start: 0.8601 (p0) cc_final: 0.8281 (p0) REVERT: F 632 ASP cc_start: 0.8853 (t70) cc_final: 0.8483 (t0) REVERT: F 655 LYS cc_start: 0.8045 (pttt) cc_final: 0.7408 (mmmt) REVERT: I 95 MET cc_start: 0.8925 (ttp) cc_final: 0.8593 (ttp) REVERT: I 166 ARG cc_start: 0.7740 (mmm-85) cc_final: 0.7042 (ttp-170) REVERT: J 97 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7221 (pt0) REVERT: K 76 ASP cc_start: 0.8027 (p0) cc_final: 0.7706 (p0) REVERT: K 96 LYS cc_start: 0.9161 (tttm) cc_final: 0.8815 (tttm) outliers start: 66 outliers final: 33 residues processed: 261 average time/residue: 0.3107 time to fit residues: 127.6136 Evaluate side-chains 222 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 185 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 465 THR Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 70 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 3.9990 chunk 162 optimal weight: 0.1980 chunk 111 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 102 optimal weight: 0.3980 chunk 144 optimal weight: 9.9990 chunk 216 optimal weight: 0.0020 chunk 229 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 GLN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21252 Z= 0.212 Angle : 0.642 12.790 28854 Z= 0.297 Chirality : 0.047 0.382 3585 Planarity : 0.003 0.048 3498 Dihedral : 9.331 59.998 5340 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.26 % Allowed : 13.81 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.16), residues: 2376 helix: -1.13 (0.26), residues: 360 sheet: -1.79 (0.20), residues: 702 loop : -2.38 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 112 HIS 0.004 0.001 HIS K 102 PHE 0.010 0.001 PHE G 53 TYR 0.014 0.001 TYR A 638 ARG 0.010 0.000 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 191 time to evaluate : 2.311 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 603 ILE cc_start: 0.9019 (mt) cc_final: 0.8757 (tt) REVERT: B 632 ASP cc_start: 0.8778 (t70) cc_final: 0.8442 (t0) REVERT: B 648 GLU cc_start: 0.8438 (pm20) cc_final: 0.8147 (pm20) REVERT: B 659 ASP cc_start: 0.8324 (m-30) cc_final: 0.8102 (t0) REVERT: G 114 GLN cc_start: 0.7978 (tm130) cc_final: 0.7711 (tm-30) REVERT: G 166 ARG cc_start: 0.7649 (mmm-85) cc_final: 0.7081 (ttp-110) REVERT: G 377 ASN cc_start: 0.8827 (p0) cc_final: 0.8591 (p0) REVERT: L 54 ARG cc_start: 0.7789 (ptp-110) cc_final: 0.7240 (mtm110) REVERT: L 60 ASP cc_start: 0.8683 (m-30) cc_final: 0.8324 (m-30) REVERT: L 97 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7245 (pt0) REVERT: H 76 ASP cc_start: 0.7974 (p0) cc_final: 0.7656 (p0) REVERT: A 584 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7746 (pt0) REVERT: A 603 ILE cc_start: 0.9005 (mt) cc_final: 0.8773 (tt) REVERT: A 632 ASP cc_start: 0.8696 (t70) cc_final: 0.8401 (t0) REVERT: C 114 GLN cc_start: 0.8084 (tm130) cc_final: 0.7803 (tm-30) REVERT: C 478 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8344 (m-40) REVERT: D 97 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7265 (pt0) REVERT: E 87 THR cc_start: 0.8954 (m) cc_final: 0.8735 (p) REVERT: F 603 ILE cc_start: 0.9023 (mt) cc_final: 0.8729 (tt) REVERT: F 632 ASP cc_start: 0.8874 (t70) cc_final: 0.8546 (t0) REVERT: F 655 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7364 (mmmt) REVERT: I 95 MET cc_start: 0.8880 (ttp) cc_final: 0.8474 (ttp) REVERT: I 166 ARG cc_start: 0.7759 (mmm-85) cc_final: 0.7061 (ttp-110) REVERT: J 54 ARG cc_start: 0.7938 (mtm110) cc_final: 0.7660 (mtm110) REVERT: J 97 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7236 (pt0) REVERT: K 76 ASP cc_start: 0.8023 (p0) cc_final: 0.7682 (p0) REVERT: K 96 LYS cc_start: 0.9144 (tttm) cc_final: 0.8775 (tttm) outliers start: 69 outliers final: 40 residues processed: 251 average time/residue: 0.2990 time to fit residues: 119.8551 Evaluate side-chains 232 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 186 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 0.5980 chunk 130 optimal weight: 0.0030 chunk 3 optimal weight: 0.6980 chunk 170 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 195 optimal weight: 0.9990 chunk 158 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 205 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 ASN ** G 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21252 Z= 0.153 Angle : 0.601 10.267 28854 Z= 0.275 Chirality : 0.046 0.371 3585 Planarity : 0.003 0.058 3498 Dihedral : 8.678 59.977 5340 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.88 % Allowed : 15.04 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.17), residues: 2376 helix: -0.67 (0.27), residues: 357 sheet: -1.65 (0.20), residues: 714 loop : -2.20 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 112 HIS 0.004 0.001 HIS G 249 PHE 0.007 0.001 PHE G 53 TYR 0.011 0.001 TYR A 638 ARG 0.013 0.000 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 197 time to evaluate : 2.169 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 584 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7719 (pt0) REVERT: B 603 ILE cc_start: 0.8991 (mt) cc_final: 0.8724 (tt) REVERT: B 632 ASP cc_start: 0.8770 (t70) cc_final: 0.8465 (t0) REVERT: B 648 GLU cc_start: 0.8449 (pm20) cc_final: 0.7988 (pm20) REVERT: G 114 GLN cc_start: 0.7951 (tm130) cc_final: 0.7683 (tm-30) REVERT: G 166 ARG cc_start: 0.7662 (mmm-85) cc_final: 0.7053 (ttp-110) REVERT: G 269 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6356 (pm20) REVERT: G 377 ASN cc_start: 0.8789 (p0) cc_final: 0.8578 (p0) REVERT: L 54 ARG cc_start: 0.7756 (ptp-110) cc_final: 0.7302 (mtm110) REVERT: L 60 ASP cc_start: 0.8623 (m-30) cc_final: 0.8418 (m-30) REVERT: H 76 ASP cc_start: 0.7981 (p0) cc_final: 0.7680 (p0) REVERT: A 530 MET cc_start: 0.8520 (mtp) cc_final: 0.8289 (mtm) REVERT: A 584 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7772 (pt0) REVERT: A 603 ILE cc_start: 0.8973 (mt) cc_final: 0.8728 (tt) REVERT: A 616 ASN cc_start: 0.8482 (p0) cc_final: 0.8011 (p0) REVERT: A 632 ASP cc_start: 0.8671 (t70) cc_final: 0.8399 (t0) REVERT: C 114 GLN cc_start: 0.8082 (tm130) cc_final: 0.7812 (tm-30) REVERT: C 269 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6124 (pm20) REVERT: C 478 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8341 (m-40) REVERT: F 584 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7264 (pt0) REVERT: F 603 ILE cc_start: 0.8980 (mt) cc_final: 0.8667 (tt) REVERT: F 616 ASN cc_start: 0.8551 (p0) cc_final: 0.8302 (p0) REVERT: F 632 ASP cc_start: 0.8865 (t70) cc_final: 0.8534 (t0) REVERT: F 655 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7336 (mmmt) REVERT: I 95 MET cc_start: 0.8772 (ttp) cc_final: 0.8317 (ttp) REVERT: I 166 ARG cc_start: 0.7745 (mmm-85) cc_final: 0.7023 (ttp-170) REVERT: I 269 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6533 (pm20) REVERT: K 76 ASP cc_start: 0.7964 (p0) cc_final: 0.7664 (p0) REVERT: K 96 LYS cc_start: 0.9123 (tttm) cc_final: 0.8776 (tttm) outliers start: 61 outliers final: 35 residues processed: 250 average time/residue: 0.3030 time to fit residues: 120.5739 Evaluate side-chains 229 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 186 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 269 GLU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 269 GLU Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 465 THR Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 70 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 4.9990 chunk 206 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 190 optimal weight: 0.0670 chunk 106 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 ASN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21252 Z= 0.329 Angle : 0.676 10.850 28854 Z= 0.316 Chirality : 0.048 0.398 3585 Planarity : 0.004 0.099 3498 Dihedral : 8.735 59.985 5340 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 3.31 % Allowed : 15.46 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.17), residues: 2376 helix: -0.29 (0.28), residues: 339 sheet: -1.60 (0.20), residues: 702 loop : -2.30 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 112 HIS 0.004 0.001 HIS G 249 PHE 0.013 0.002 PHE G 53 TYR 0.016 0.001 TYR D 91 ARG 0.018 0.000 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 186 time to evaluate : 2.239 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 603 ILE cc_start: 0.9016 (mt) cc_final: 0.8747 (tt) REVERT: B 632 ASP cc_start: 0.8828 (t70) cc_final: 0.8496 (t0) REVERT: B 648 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8169 (pm20) REVERT: G 114 GLN cc_start: 0.7976 (tm130) cc_final: 0.7713 (tm-30) REVERT: G 166 ARG cc_start: 0.7675 (mmm-85) cc_final: 0.7116 (ttp-110) REVERT: L 54 ARG cc_start: 0.7820 (ptp-110) cc_final: 0.7542 (ptp-110) REVERT: L 97 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7307 (pt0) REVERT: H 76 ASP cc_start: 0.8021 (p0) cc_final: 0.7675 (p0) REVERT: A 584 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7766 (pt0) REVERT: A 603 ILE cc_start: 0.8995 (mt) cc_final: 0.8780 (tt) REVERT: A 616 ASN cc_start: 0.8523 (p0) cc_final: 0.8031 (p0) REVERT: A 632 ASP cc_start: 0.8739 (t70) cc_final: 0.8439 (t0) REVERT: C 114 GLN cc_start: 0.8082 (tm130) cc_final: 0.7810 (tm-30) REVERT: C 269 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6620 (pm20) REVERT: C 478 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8395 (m-40) REVERT: D 97 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7485 (pt0) REVERT: F 616 ASN cc_start: 0.8631 (p0) cc_final: 0.8338 (p0) REVERT: F 632 ASP cc_start: 0.8905 (t70) cc_final: 0.8561 (t0) REVERT: F 655 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7327 (mmmt) REVERT: I 95 MET cc_start: 0.8924 (ttp) cc_final: 0.8528 (ttp) REVERT: I 166 ARG cc_start: 0.7761 (mmm-85) cc_final: 0.7064 (ttp-110) REVERT: J 97 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7518 (pt0) REVERT: K 76 ASP cc_start: 0.8056 (p0) cc_final: 0.7710 (p0) REVERT: K 96 LYS cc_start: 0.9133 (tttm) cc_final: 0.8773 (tttm) outliers start: 70 outliers final: 46 residues processed: 248 average time/residue: 0.2849 time to fit residues: 113.9176 Evaluate side-chains 238 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 184 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 465 THR Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 0.0070 chunk 25 optimal weight: 2.9990 chunk 130 optimal weight: 0.0050 chunk 167 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 228 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.6014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 ASN ** G 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21252 Z= 0.154 Angle : 0.611 10.198 28854 Z= 0.280 Chirality : 0.046 0.366 3585 Planarity : 0.003 0.033 3498 Dihedral : 8.234 59.603 5337 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.31 % Allowed : 16.17 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.17), residues: 2376 helix: 0.17 (0.29), residues: 339 sheet: -1.44 (0.20), residues: 702 loop : -2.18 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 100B HIS 0.004 0.001 HIS G 249 PHE 0.008 0.001 PHE C 383 TYR 0.011 0.001 TYR A 638 ARG 0.006 0.000 ARG J 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 198 time to evaluate : 2.320 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 584 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7661 (pt0) REVERT: B 603 ILE cc_start: 0.8982 (mt) cc_final: 0.8720 (tt) REVERT: B 632 ASP cc_start: 0.8783 (t70) cc_final: 0.8486 (t0) REVERT: B 648 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8030 (pm20) REVERT: G 114 GLN cc_start: 0.7938 (tm130) cc_final: 0.7678 (tm-30) REVERT: G 166 ARG cc_start: 0.7673 (mmm-85) cc_final: 0.7074 (ttp-110) REVERT: L 54 ARG cc_start: 0.7789 (ptp-110) cc_final: 0.7411 (mtm110) REVERT: L 97 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7172 (pt0) REVERT: H 76 ASP cc_start: 0.7990 (p0) cc_final: 0.7691 (p0) REVERT: A 584 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7733 (pt0) REVERT: A 603 ILE cc_start: 0.8976 (mt) cc_final: 0.8741 (tt) REVERT: A 616 ASN cc_start: 0.8546 (p0) cc_final: 0.8095 (p0) REVERT: A 632 ASP cc_start: 0.8683 (t70) cc_final: 0.8420 (t0) REVERT: C 114 GLN cc_start: 0.8036 (tm130) cc_final: 0.7777 (tm-30) REVERT: C 269 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6397 (pm20) REVERT: D 97 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7261 (pt0) REVERT: F 584 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7267 (pt0) REVERT: F 616 ASN cc_start: 0.8598 (p0) cc_final: 0.8313 (p0) REVERT: F 632 ASP cc_start: 0.8881 (t70) cc_final: 0.8542 (t0) REVERT: F 655 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7373 (mmmt) REVERT: I 95 MET cc_start: 0.8833 (ttp) cc_final: 0.8425 (ttp) REVERT: I 166 ARG cc_start: 0.7779 (mmm-85) cc_final: 0.7047 (ttp-110) REVERT: I 269 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6586 (pm20) REVERT: J 97 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7213 (pt0) REVERT: K 76 ASP cc_start: 0.7939 (p0) cc_final: 0.7675 (p0) REVERT: K 96 LYS cc_start: 0.9090 (tttm) cc_final: 0.8737 (tttm) outliers start: 70 outliers final: 38 residues processed: 256 average time/residue: 0.2867 time to fit residues: 118.2793 Evaluate side-chains 232 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 184 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 269 GLU Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 465 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 48 MET Chi-restraints excluded: chain K residue 68 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 0.3980 chunk 91 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 68 optimal weight: 0.0980 chunk 44 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21252 Z= 0.230 Angle : 0.631 10.513 28854 Z= 0.291 Chirality : 0.047 0.383 3585 Planarity : 0.003 0.034 3498 Dihedral : 8.164 59.957 5336 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.88 % Allowed : 16.78 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.17), residues: 2376 helix: 0.28 (0.29), residues: 339 sheet: -1.41 (0.20), residues: 702 loop : -2.19 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 112 HIS 0.004 0.001 HIS G 249 PHE 0.010 0.001 PHE G 53 TYR 0.013 0.001 TYR D 91 ARG 0.003 0.000 ARG J 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 186 time to evaluate : 2.253 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 584 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7658 (pt0) REVERT: B 603 ILE cc_start: 0.9015 (mt) cc_final: 0.8767 (tt) REVERT: B 632 ASP cc_start: 0.8808 (t70) cc_final: 0.8499 (t0) REVERT: B 648 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7947 (pm20) REVERT: G 114 GLN cc_start: 0.7957 (tm130) cc_final: 0.7702 (tm-30) REVERT: G 166 ARG cc_start: 0.7679 (mmm-85) cc_final: 0.7105 (ttp-110) REVERT: L 97 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7434 (pt0) REVERT: H 76 ASP cc_start: 0.7994 (p0) cc_final: 0.7691 (p0) REVERT: A 584 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7710 (pt0) REVERT: A 603 ILE cc_start: 0.9013 (mt) cc_final: 0.8790 (tt) REVERT: A 616 ASN cc_start: 0.8542 (p0) cc_final: 0.8080 (p0) REVERT: A 632 ASP cc_start: 0.8718 (t70) cc_final: 0.8438 (t0) REVERT: C 114 GLN cc_start: 0.8049 (tm130) cc_final: 0.7792 (tm-30) REVERT: C 269 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6575 (pm20) REVERT: D 97 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7383 (pt0) REVERT: F 584 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7277 (pt0) REVERT: F 603 ILE cc_start: 0.8856 (mt) cc_final: 0.8589 (tt) REVERT: F 616 ASN cc_start: 0.8591 (p0) cc_final: 0.8302 (p0) REVERT: F 632 ASP cc_start: 0.8898 (t70) cc_final: 0.8551 (t0) REVERT: F 655 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7379 (mmmt) REVERT: I 95 MET cc_start: 0.8977 (ttp) cc_final: 0.8528 (ttp) REVERT: I 166 ARG cc_start: 0.7757 (mmm-85) cc_final: 0.7044 (ttp-110) REVERT: I 269 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6609 (pm20) REVERT: J 97 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7466 (pt0) REVERT: K 76 ASP cc_start: 0.7973 (p0) cc_final: 0.7670 (p0) REVERT: K 96 LYS cc_start: 0.9117 (tttm) cc_final: 0.8753 (tttm) outliers start: 61 outliers final: 46 residues processed: 236 average time/residue: 0.2903 time to fit residues: 110.3609 Evaluate side-chains 238 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 182 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 269 GLU Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 465 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 101 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 5.9990 chunk 199 optimal weight: 9.9990 chunk 212 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 65 optimal weight: 0.4980 chunk 192 optimal weight: 1.9990 chunk 201 optimal weight: 0.0010 chunk 139 optimal weight: 2.9990 chunk 225 optimal weight: 0.0370 overall best weight: 0.6666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 21252 Z= 0.161 Angle : 0.611 10.241 28854 Z= 0.281 Chirality : 0.046 0.368 3585 Planarity : 0.003 0.034 3498 Dihedral : 7.861 59.572 5336 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.55 % Allowed : 17.35 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.17), residues: 2376 helix: 0.23 (0.29), residues: 357 sheet: -1.46 (0.20), residues: 741 loop : -2.16 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 100B HIS 0.004 0.001 HIS G 249 PHE 0.007 0.001 PHE G 53 TYR 0.011 0.001 TYR J 91 ARG 0.016 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 188 time to evaluate : 2.322 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: B 584 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7657 (pt0) REVERT: B 603 ILE cc_start: 0.8988 (mt) cc_final: 0.8735 (tt) REVERT: B 632 ASP cc_start: 0.8779 (t70) cc_final: 0.8486 (t0) REVERT: B 648 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7924 (pm20) REVERT: G 114 GLN cc_start: 0.7947 (tm130) cc_final: 0.7697 (tm-30) REVERT: G 121 LYS cc_start: 0.9078 (mmmm) cc_final: 0.8870 (mptt) REVERT: G 166 ARG cc_start: 0.7657 (mmm-85) cc_final: 0.7089 (ttp-110) REVERT: L 97 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7312 (pt0) REVERT: H 76 ASP cc_start: 0.7988 (p0) cc_final: 0.7692 (p0) REVERT: A 584 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7653 (pt0) REVERT: A 603 ILE cc_start: 0.8980 (mt) cc_final: 0.8758 (tt) REVERT: A 616 ASN cc_start: 0.8516 (p0) cc_final: 0.8051 (p0) REVERT: A 632 ASP cc_start: 0.8692 (t70) cc_final: 0.8436 (t0) REVERT: C 114 GLN cc_start: 0.8041 (tm130) cc_final: 0.7790 (tm-30) REVERT: C 269 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6457 (pm20) REVERT: D 97 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7319 (pt0) REVERT: F 584 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7186 (pt0) REVERT: F 603 ILE cc_start: 0.8793 (mt) cc_final: 0.8496 (tt) REVERT: F 616 ASN cc_start: 0.8574 (p0) cc_final: 0.8288 (p0) REVERT: F 632 ASP cc_start: 0.8886 (t70) cc_final: 0.8550 (t0) REVERT: F 655 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7609 (mmmt) REVERT: I 95 MET cc_start: 0.8909 (ttp) cc_final: 0.8496 (ttp) REVERT: I 166 ARG cc_start: 0.7731 (mmm-85) cc_final: 0.7019 (ttp-110) REVERT: I 269 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6619 (pm20) REVERT: J 97 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7297 (pt0) REVERT: K 20 ILE cc_start: 0.8928 (pt) cc_final: 0.8636 (pt) REVERT: K 76 ASP cc_start: 0.7939 (p0) cc_final: 0.7675 (p0) REVERT: K 96 LYS cc_start: 0.9080 (tttm) cc_final: 0.8745 (tttm) outliers start: 54 outliers final: 42 residues processed: 233 average time/residue: 0.2987 time to fit residues: 112.0277 Evaluate side-chains 240 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 188 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 269 GLU Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 465 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 0.0670 chunk 106 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 217 optimal weight: 7.9990 chunk 188 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 200 optimal weight: 0.6980 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21252 Z= 0.182 Angle : 0.611 10.398 28854 Z= 0.281 Chirality : 0.046 0.377 3585 Planarity : 0.003 0.062 3498 Dihedral : 7.692 59.545 5336 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.51 % Allowed : 17.45 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.17), residues: 2376 helix: 0.25 (0.29), residues: 360 sheet: -1.41 (0.20), residues: 741 loop : -2.12 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 479 HIS 0.004 0.001 HIS I 249 PHE 0.008 0.001 PHE G 53 TYR 0.010 0.001 TYR D 91 ARG 0.014 0.000 ARG L 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 190 time to evaluate : 2.327 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: B 584 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7588 (pt0) REVERT: B 603 ILE cc_start: 0.9003 (mt) cc_final: 0.8753 (tt) REVERT: B 632 ASP cc_start: 0.8786 (t70) cc_final: 0.8495 (t0) REVERT: B 648 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7920 (pm20) REVERT: G 114 GLN cc_start: 0.7945 (tm130) cc_final: 0.7693 (tm-30) REVERT: G 166 ARG cc_start: 0.7663 (mmm-85) cc_final: 0.7095 (ttp-110) REVERT: G 271 MET cc_start: 0.7520 (tpt) cc_final: 0.6926 (tpt) REVERT: L 97 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7507 (pt0) REVERT: H 76 ASP cc_start: 0.7998 (p0) cc_final: 0.7697 (p0) REVERT: A 529 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8638 (m) REVERT: A 584 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7534 (pt0) REVERT: A 603 ILE cc_start: 0.8987 (mt) cc_final: 0.8767 (tt) REVERT: A 616 ASN cc_start: 0.8540 (p0) cc_final: 0.8076 (p0) REVERT: A 632 ASP cc_start: 0.8703 (t70) cc_final: 0.8448 (t0) REVERT: C 114 GLN cc_start: 0.8058 (tm130) cc_final: 0.7796 (tm-30) REVERT: C 269 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6533 (pm20) REVERT: D 97 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7221 (pt0) REVERT: F 584 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7206 (pt0) REVERT: F 603 ILE cc_start: 0.8790 (mt) cc_final: 0.8506 (tt) REVERT: F 616 ASN cc_start: 0.8576 (p0) cc_final: 0.8291 (p0) REVERT: F 632 ASP cc_start: 0.8902 (t70) cc_final: 0.8572 (t0) REVERT: F 655 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7610 (mmmt) REVERT: I 95 MET cc_start: 0.8918 (ttp) cc_final: 0.8508 (ttp) REVERT: I 166 ARG cc_start: 0.7741 (mmm-85) cc_final: 0.7030 (ttp-110) REVERT: I 269 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6655 (pm20) REVERT: J 97 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7413 (pt0) REVERT: K 76 ASP cc_start: 0.7949 (p0) cc_final: 0.7671 (p0) REVERT: K 96 LYS cc_start: 0.9077 (tttm) cc_final: 0.8728 (tttm) outliers start: 53 outliers final: 40 residues processed: 234 average time/residue: 0.3011 time to fit residues: 112.7613 Evaluate side-chains 239 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 188 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 269 GLU Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 465 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 0.7980 chunk 173 optimal weight: 0.1980 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 188 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 193 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.104771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.085498 restraints weight = 43560.329| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.80 r_work: 0.3279 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21252 Z= 0.157 Angle : 0.601 10.228 28854 Z= 0.277 Chirality : 0.046 0.370 3585 Planarity : 0.003 0.053 3498 Dihedral : 7.484 59.443 5336 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.46 % Allowed : 17.35 % Favored : 80.19 % 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: -2.09 (0.17), residues: 2376 helix: 0.58 (0.30), residues: 342 sheet: -1.33 (0.20), residues: 741 loop : -2.00 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 112 HIS 0.004 0.001 HIS G 249 PHE 0.007 0.001 PHE I 53 TYR 0.011 0.001 TYR J 91 ARG 0.014 0.000 ARG L 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3906.18 seconds wall clock time: 72 minutes 31.87 seconds (4351.87 seconds total)