Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 17:43:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vi0_21208/04_2023/6vi0_21208.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vi0_21208/04_2023/6vi0_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_21208/04_2023/6vi0_21208.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vi0_21208/04_2023/6vi0_21208.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vi0_21208/04_2023/6vi0_21208.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vi0_21208/04_2023/6vi0_21208.pdb" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 10.83, per 1000 atoms: 0.52 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: 10.28 Conformation dependent library (CDL) restraints added in 2.9 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: 1.21 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: 6.59 Time building geometry restraints manager: 10.97 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 - 16.49: 10269 16.49 - 32.98: 1202 32.98 - 49.48: 208 49.48 - 65.97: 48 65.97 - 82.46: 15 Dihedral angle restraints: 11742 sinusoidal: 4800 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 11739 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: 1.280 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: 8.210 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 53.690 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.350 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: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.140 ------------------------------------------------------------------------------- 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 : 13.991 82.459 7137 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 % 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 *********************** 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 : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 302 average time/residue: 0.3909 time to fit residues: 174.3396 Evaluate side-chains 188 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 178 time to evaluate : 2.340 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1787 time to fit residues: 6.5001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 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: 0.9990 chunk 71 optimal weight: 0.0570 chunk 112 optimal weight: 0.4980 chunk 138 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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 293 GLN 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 21252 Z= 0.173 Angle : 0.694 11.038 28854 Z= 0.326 Chirality : 0.046 0.302 3585 Planarity : 0.004 0.044 3498 Dihedral : 5.458 32.874 2601 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer Outliers : 1.84 % 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: -4.30 (0.14), residues: 2376 helix: -3.23 (0.17), residues: 390 sheet: -2.67 (0.18), residues: 681 loop : -2.86 (0.14), residues: 1305 *********************** 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 249 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 210 time to evaluate : 2.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 17 residues processed: 244 average time/residue: 0.3092 time to fit residues: 119.9058 Evaluate side-chains 189 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 2.294 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1860 time to fit residues: 9.0606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 179 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 232 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 213 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 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** ** K 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.057 21252 Z= 0.376 Angle : 0.738 16.594 28854 Z= 0.350 Chirality : 0.048 0.325 3585 Planarity : 0.004 0.051 3498 Dihedral : 5.434 30.415 2601 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer Outliers : 2.27 % 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: -3.79 (0.15), residues: 2376 helix: -2.05 (0.23), residues: 372 sheet: -2.26 (0.19), residues: 708 loop : -2.85 (0.15), residues: 1296 *********************** 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 230 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 182 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 24 residues processed: 220 average time/residue: 0.3054 time to fit residues: 108.5952 Evaluate side-chains 187 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 2.381 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2041 time to fit residues: 12.2072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/iotbx/cli_parser.py", line 870, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.1174 > 50: distance: 22 - 25: 16.934 distance: 25 - 26: 25.209 distance: 25 - 138: 19.891 distance: 26 - 27: 11.933 distance: 26 - 29: 9.148 distance: 27 - 28: 30.102 distance: 27 - 39: 16.435 distance: 29 - 30: 3.018 distance: 30 - 31: 3.821 distance: 30 - 32: 3.955 distance: 31 - 33: 6.321 distance: 32 - 34: 5.430 distance: 32 - 35: 4.202 distance: 33 - 34: 5.417 distance: 34 - 36: 3.443 distance: 37 - 38: 3.329 distance: 39 - 40: 17.716 distance: 39 - 195: 17.508 distance: 40 - 41: 27.542 distance: 40 - 43: 20.554 distance: 41 - 42: 32.508 distance: 41 - 51: 27.692 distance: 42 - 192: 17.275 distance: 43 - 44: 9.521 distance: 44 - 45: 7.513 distance: 44 - 46: 11.799 distance: 45 - 47: 7.956 distance: 46 - 48: 23.329 distance: 48 - 49: 12.417 distance: 49 - 50: 12.785 distance: 51 - 52: 37.938 distance: 52 - 53: 25.547 distance: 52 - 55: 40.679 distance: 53 - 54: 24.550 distance: 53 - 60: 14.285 distance: 55 - 56: 43.686 distance: 56 - 57: 20.746 distance: 57 - 58: 11.206 distance: 57 - 59: 21.407 distance: 60 - 61: 25.880 distance: 60 - 177: 18.233 distance: 61 - 62: 6.294 distance: 61 - 64: 21.442 distance: 62 - 63: 9.066 distance: 62 - 69: 29.504 distance: 63 - 174: 24.976 distance: 64 - 65: 31.424 distance: 65 - 66: 6.664 distance: 66 - 67: 24.627 distance: 66 - 68: 33.736 distance: 69 - 70: 18.439 distance: 70 - 71: 20.057 distance: 70 - 73: 22.846 distance: 71 - 72: 7.916 distance: 71 - 80: 23.102 distance: 73 - 74: 16.195 distance: 74 - 75: 26.921 distance: 75 - 76: 18.887 distance: 77 - 78: 7.804 distance: 77 - 79: 4.220 distance: 80 - 81: 19.377 distance: 80 - 86: 20.588 distance: 81 - 82: 20.759 distance: 81 - 84: 7.604 distance: 82 - 83: 15.349 distance: 82 - 87: 18.019 distance: 84 - 85: 12.453 distance: 85 - 86: 12.219 distance: 87 - 88: 17.599 distance: 88 - 89: 36.796 distance: 89 - 90: 48.184 distance: 89 - 91: 6.742 distance: 91 - 92: 25.619 distance: 92 - 93: 44.210 distance: 92 - 95: 20.579 distance: 93 - 94: 46.822 distance: 93 - 100: 27.471 distance: 95 - 96: 43.060 distance: 96 - 97: 21.545 distance: 97 - 98: 9.695 distance: 97 - 99: 15.020 distance: 100 - 101: 15.943 distance: 101 - 102: 33.996 distance: 101 - 104: 24.175 distance: 102 - 103: 25.899 distance: 102 - 105: 23.123 distance: 105 - 106: 23.114 distance: 105 - 111: 30.920 distance: 106 - 107: 21.273 distance: 106 - 109: 10.783 distance: 107 - 108: 22.911 distance: 107 - 112: 19.664 distance: 109 - 110: 28.913 distance: 110 - 111: 5.679